# Omicron news



## weltweit (Nov 27, 2021)

Might be worth having a dedicated thread to keep track of this. 

At the moment UK has two confirmed cases, as does Germany.


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## cupid_stunt (Nov 27, 2021)

Cases seem to be popping up across the world.


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## Steel Icarus (Nov 27, 2021)

Respectfully suggest it just goes in the Mutations thread, given we don't know yet how serious it is or whether it'll be superseded by a deadlier still one later


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## Pickman's model (Nov 27, 2021)

So the government's action on flights from southern Africa to buy time for scientists to find out more about the variant, as grant shapps said on the toady programme, bought them enough time to read the andromeda strain


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## Pickman's model (Nov 27, 2021)

S☼I said:


> Respectfully suggest it just goes in the Mutations thread, given we don't know yet how serious it is or whether it'll be superseded by a deadlier still one later


Yeh but at least by then we'll know the Greek alphabet


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## cupid_stunt (Nov 27, 2021)

S☼I said:


> Respectfully suggest it just goes in the Mutations thread, given we don't know yet how serious it is or whether it'll be superseded by a deadlier still one later



Yeah, it's already being discussed there -









						Covid Mutations
					

Its got a mutation of the spike protein-thing that means the spike is not a perfect match to exisiting antibody-thing, does this equal partial vaccine evasion?  There are huge numbers of variants tweaking the spike all the time. Many of those changes don't amount to any evasion of immunity (some...




					www.urban75.net


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## weltweit (Nov 27, 2021)

Omicron: How worried should we be?
					

Scientists are closely watching a new variant - but there are few clear answers.



					www.bbc.co.uk


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## Yossarian (Nov 27, 2021)

The world response, even from Boris Johnson's pro-COVID government, has been a lot speedier than I expected, though since omicron cases have been found going back to at least Nov. 9, I'm not sure how much travel restrictions are going to help.


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## elbows (Nov 27, 2021)

S☼I said:


> Respectfully suggest it just goes in the Mutations thread, given we don't know yet how serious it is or whether it'll be superseded by a deadlier still one later


Its a rather technical thread, I suggest preserving that one for the more nerdy aspects and this one can be a more general discussion, chat and news sharing exercise.


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## weltweit (Nov 27, 2021)

Yossarian said:


> The world response, even from Boris Johnson's pro-COVID government, has been a lot speedier than I expected, though since omicron cases have been found going back to at least Nov. 9, I'm not sure how much travel restrictions are going to help.


Nov 9th? where were they found then?


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## elbows (Nov 27, 2021)

Yossarian said:


> The world response, even from Boris Johnson's pro-COVID government, has been a lot speedier than I expected, though since omicron cases have been found going back to at least Nov. 9, I'm not sure how much travel restrictions are going to help.


They buy a little time, some of which can be used for good things and some of which will just be used by our government to drag its heels in other areas.


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## elbows (Nov 27, 2021)

As I've mentioned in another thread, people should wonder what the test specimen dates were for the 2 cases confirmed in the UK so far.

Not that the UK authorities are even going through with the full pretence that the announced measures are a genuine act of containment this time around, unlike previous occasions where there was plenty of extra bullshit on that front.


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## Yossarian (Nov 27, 2021)

weltweit said:


> Nov 9th? where were they found then?



South Africa - don't know when the first known case outside SA was.



> IThe B.1.1.529 variant was first reported to WHO from South Africa on 24 November 2021 ... In recent weeks, infections have increased steeply, coinciding with the detection of B.1.1.529 variant. The first known confirmed B.1.1.529 infection was from a specimen collected on 9 November 2021.








						Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern
					

The Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE) is an independent group of experts that periodically monitors and evaluates the evolution of SARS-CoV-2 and assesses if specific mutations and combinations of mutations alter the behaviour of the virus. The TAG-VE was convened...




					www.who.int


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## weltweit (Nov 27, 2021)

Prime Minister sets out new measures as Omicron variant identified in UK: 27 November 2021
					

The Prime Minister has today confirmed new temporary and precautionary measures following the emergence of the Omicron variant in the UK.




					www.gov.uk


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## MrSki (Nov 27, 2021)

They have given it its own Greek letter so surely worth its own thread?


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## Ax^ (Nov 27, 2021)

why is everyone woried about a transformer








*gets coat


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## magneze (Nov 27, 2021)

Orson Welles final gig☝️


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## Supine (Nov 27, 2021)

Next few weeks will be interesting. Vax companies already running experiments to determine efficiency of existing vaccines. 

Cases so far appear to be mild but lots to learn asap.


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## weltweit (Nov 27, 2021)

Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern
					

The Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE) is an independent group of experts that periodically monitors and evaluates the evolution of SARS-CoV-2 and assesses if specific mutations and combinations of mutations alter the behaviour of the virus. The TAG-VE was convened...




					www.who.int
				






> The B.1.1.529 variant was first reported to WHO from South Africa on 24 November 2021. The epidemiological situation in South Africa has been characterized by three distinct peaks in reported cases, the latest of which was predominantly the Delta variant. In recent weeks, infections have increased steeply, coinciding with the detection of B.1.1.529 variant. The first known confirmed B.1.1.529 infection was from a specimen collected on 9 November 2021.





> This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant. Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.
> There are a number of studies underway and the TAG-VE will continue to evaluate this variant. WHO will communicate new findings with Member States and to the public as needed.
> 
> Based on the evidence presented indicative of a detrimental change in COVID-19 epidemiology, the TAG-VE has advised WHO that this variant should be designated as a VOC, and the WHO has designated B.1.1.529 as a VOC, named Omicron.





> As such, countries are asked to do the following:
> 
> 
> enhance surveillance and sequencing efforts to better understand circulating SARS-CoV-2 variants.
> ...


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## weltweit (Nov 27, 2021)

South African scientists brace for wave propelled by omicron
					

JOHANNESBURG (AP) — Worried scientists in South Africa are scrambling to combat the lightning spread across the country of the new and highly transmissible omicron COVID-19 variant as the world grapples with its emergence.




					apnews.com
				






> JOHANNESBURG (AP) — Worried scientists in South Africa are scrambling to combat the lightning spread across the country of the new and highly transmissible omicron COVID-19 variant as the world grapples with its emergence.
> 
> In the space of two weeks, the omicron variant has sent South Africa from a period of low transmission to rapid growth of new confirmed cases. The country’s numbers are still relatively low, with 2,828 new confirmed cases recorded Friday, but omicron’s speed in infecting young South Africans has alarmed health professionals.





> “Young people, in their 20s to just over their late 30s, are coming in with moderate to severe disease, some needing intensive care. About 65% are not vaccinated and most of the rest are only half-vaccinated,” said Mathivha. “I’m worried that as the numbers go up, the public health care facilities will become overwhelmed.”





> What looked like a cluster infection among some university students in Pretoria ballooned into hundreds of new cases and then thousands, first in the capital city and then to nearby Johannesburg, South Africa’s largest city.
> 
> Studying the surge, scientists identified the new variant that diagnostic tests indicate is likely responsible for as many as 90% of the new cases, according to South Africa’s health officials. Early studies show that it has a reproduction rate of 2 — meaning that every person infected by it is likely to spread it to two other people.





> A key factor is vaccination. The new variant appears to be spreading most quickly among those who are unvaccinated. Currently, only about 40% of adult South Africans are vaccinated, and the number is much lower among those in the 20 to 40-year-old age group.


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## Riklet (Nov 27, 2021)

South Africa is boo hooing about how theyre being treated unfairly.. it's clearly really shitty for them this new variant but their vaccination roll out is a shambles... they have way too much stock and not enough people getting jabbed. its almost December and they're still way behind with vaccine roll out despite being the most "developed" country in Africa.

It's really shit because these southern african countries are likely to be more badly affected than Western Europe. I completely support the travel bans though and PCR testing all international arrivals, contact tracing, imposing quarantine if necessary etc.


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## mx wcfc (Nov 27, 2021)

Riklet said:


> South Africa is boo hooing about how theyre being treated unfairly.. it's clearly really shitty for them this new variant but their vaccination roll out is a shambles... they have way too much stock and not enough people getting jabbed. its almost December and they're still way behind with vaccine roll out despite being the most "developed" country in Africa.
> 
> It's really shit because these southern african countries are likely to be more badly affected than Western Europe. I completely support the travel bans though and PCR testing all international arrivals, contact tracing, imposing quarantine if necessary etc.


I'm firmly of the opinion that we should have closed our borders to all but essential food and medicine back in March 2020, of not earlier.  We are an island, which gives certain advantages.

Even these restrictions - self isolate, test within a couple of days are rubbish. 

Get off a plane at Heathrow, mingle with other people from all over the world in arrivals, get the tube to Kings Cross, get home to wherever, then self isolate?  How many people have caught it off you in the meantime? 

New variants are all over the world before we know about them.  

The lessons form Omicron are

1) Vaccinate the world
2) stop international flights till this is under control.

Sorry, pissed and ranting, but I'm sick of this shit and government's hopeless approach.


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## Ax^ (Nov 27, 2021)

i'm quite surprised ZA had not put restricted on the united kingdom before Friday


South africa has a hell of a lot more immune surpressed members of the population than the united kingdom
and even with the vaccine the UK had higher rates of daily infections

they are pissed because of tourist and business visitor numbers


daily passager flights only really started up again recently


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## mx wcfc (Nov 27, 2021)

Ax^ said:


> i'm quite surprised ZA had not put restricted on the united kingdom before Friday
> 
> 
> South africa has a help of a lot more immune surpressed members of the population that the united kingdom
> ...


Frankly, I'm surprised the whole world hasn't banned UK travellers, given our government's record.


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## TopCat (Nov 27, 2021)

Do I need to get another jab?


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## 8ball (Nov 27, 2021)

mx wcfc said:


> Frankly, I'm surprised the whole world hasn't banned UK travellers, given our government's record.



Well, given our country’s record generally, historically speaking.


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## Ax^ (Nov 27, 2021)

not right now


you had your booster right?


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## 8ball (Nov 27, 2021)

TopCat said:


> Do I need to get another jab?



Had a booster?


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## TopCat (Nov 27, 2021)

8ball said:


> Had a booster?


Yeah but no moderna or sputnik


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## Ax^ (Nov 27, 2021)

well atm they trying to figure out if this varriant avoid the immunisation you have with your booster

so until thats worked out you have the best coverage avalable

stick with the mask mind


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## 8ball (Nov 27, 2021)

TopCat said:


> Yeah but no moderna or sputnik



I think your next one is likely to be the Omicron Plus one, then.
Apparently this one will have the 5G working properly.


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## Ax^ (Nov 27, 2021)

hear the Omicron Plus one will give you power of lighting

will be able to take birds out of the sky with your mind

and wilt trees with a wave of your hand


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## Supine (Nov 28, 2021)

TopCat said:


> Do I need to get another jab?



How about someone in Africa having a first one instead.


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## kenny g (Nov 28, 2021)

Visiting Nottingham and found out about one of the two UK cases being here from the compere in a packed comedy night.


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## elbows (Nov 28, 2021)




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## Yossarian (Nov 28, 2021)

Supine said:


> How about someone in Africa having a first one instead.



If somebody advised to have a COVID shot declines it, they don't put it back in the bottle and send it to Africa.


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## elbows (Nov 28, 2021)

Although the amount of genomic surveillance is ratehr different than the UKs, these translated tweets may still provide people with a useful sense of the sort of lag between detecting a few cases and the likely real picture.


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## Epona (Nov 28, 2021)

Covid: South Africa 'punished' for detecting new Omicron variant
					

South Africa should be praised for discovering Omicron, not hit with travel bans, its officials say.



					www.bbc.co.uk


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## cupid_stunt (Nov 28, 2021)

Ax^ said:


> hear the Omicron Plus one will give you power of lighting
> 
> will be able to take birds out of the sky with your mind


Excellent, I could finally deal with the seagulls.


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## MrCurry (Nov 28, 2021)

Deffo a good idea to have a thread dedicated to this one variant, IMHO.

I’m worried now about my 80+ parents, who after weathering the early part of the pandemic by shielding and allowing others to do shopping for them have, post vaccination, returned to going to the supermarket once a week, plus other shops.

The sooner we have confirmed info on how much Omicron defeats the current vaccine, the better, as even if I start lobbying them to isolate I know they‘re going to resist.  Nothing was helped by the Daily Mail (their favourite source of propagandist disinformation) having the headline “Experts say jabs WILL work on variant” on the front page yesterday.  Simultaneously technically correct and massively misleading, in the truest DM tradition.


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## platinumsage (Nov 28, 2021)

MrCurry said:


> The sooner we have confirmed info on how much Omicron defeats the current vaccine, the better



Not really. It’ll start with antibody studies done in a petri dish showing how well it evades the vaccine, and some people will panic, this will be followed months later by real-world studies showing how very well-protected boosted people are against serious disease and death. That’s my prediction anyway, basically don’t jump on the first “confirmed info”.


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## nagapie (Nov 28, 2021)

Riklet said:


> South Africa is boo hooing about how theyre being treated unfairly.. it's clearly really shitty for them this new variant but their vaccination roll out is a shambles... they have way too much stock and not enough people getting jabbed. its almost December and they're still way behind with vaccine roll out despite being the most "developed" country in Africa.
> 
> It's really shit because these southern african countries are likely to be more badly affected than Western Europe. I completely support the travel bans though and PCR testing all international arrivals, contact tracing, imposing quarantine if necessary etc.


Actually the new variant was discovered in Botswana, who are struggling to get vaccines. 
This mutation is a direct result of the. West's hoarding of vaccinations not the developing world's failure to deliver them.
With detections all over the world, the African countries are asking why not a shut down of all travel rather than just southern Africa.


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## platinumsage (Nov 28, 2021)

nagapie said:


> Actually the new variant was discovered in Botswana, who are struggling to get vaccines.
> This mutation is a direct result of the. West's hoarding of vaccinations not the developing world's failure to deliver them.
> With detections all over the world, the African countries are asking why not a shut down of all travel rather than just southern Africa.



It likely has nothing to do with vaccination rates, especially as vaccine-resistant strains are unlikely to evolve in the absence of vaccinated individuals. Since we don't know which country patient zero was in, or whether or not they were vaccinated and/or immunocompromised, it's a bit pointless using this specific variant as a developing-world vaccination failure hammer.


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## nagapie (Nov 28, 2021)

platinumsage said:


> It likely has nothing to do with vaccination rates, especially as vaccine-resistant strains are unlikely to evolve in the absence of vaccinated individuals. Since we don't know which country patient zero was in, or whether or not they were vaccinated and/or immunocompromised, it's a bit pointless using this specific variant as a developing-world vaccination failure hammer.


I was responding to a post that cited failure of African countries to vaccinate timely as the issue.
If we're going down that road, then vaccine inequality is very much relevant.
And we also know failure to fairly vaccinate the developing world is another reason we will see mutations.


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## lefteri (Nov 28, 2021)

waiting for the omega variant that wipes out the entire human race except one


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## Supine (Nov 28, 2021)

Interesting interview on Marr with the SA doctor who first detected the new variant. 

The patients all had unusually mild symptoms. Not the classic symptoms we all know about.


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## Mation (Nov 28, 2021)

Supine said:


> Interesting interview on Marr with the SA doctor who first detected the new variant.
> 
> The patients all had unusually mild symptoms. Not the classic symptoms we all know about.


What were their symptoms?


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## Pickman's model (Nov 28, 2021)

lefteri said:


> waiting for the omega variant that wipes out the entire human race except one


Yes the cockroach Johnson will survive


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## lefteri (Nov 28, 2021)

Pickman's model said:


> Yes the cockroach Johnson will survive


him and heston did have a lot in common politically


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## Badgers (Nov 28, 2021)

🤔🤔


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## StoneRoad (Nov 28, 2021)

That is, Apart from ramming everybody together, before the tests ?

Pretty sure the two cases already found are just the tip of the iceberg ...
[not that I'm really cynical, just basing it on prior [non-]activity of our dear leader]


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## Badgers (Nov 28, 2021)

StoneRoad said:


> That is, Apart from ramming everybody together, before the tests ?
> 
> Pretty sure the two cases already found are just the tip of the iceberg ...
> [not that I'm really cynical, just basing it on prior [non-]activity of our dear leader]


I think that cynism is no longer happening. We are not even seeing the worst failings and incompetence of this beshitted government and disgraced Prime Minister de Pfeffel Johnson.


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## IC3D (Nov 28, 2021)

Its being mooted an HIV patient could be the starting point of this coronavirus as was the case here Woman with HIV had Covid-19 for 216 days, virus mutated 32 times inside her

This isn't the first time an immunosuppressed patient may have been a vector for virus mutation and merging. It was widely published around the time the Kent varient may have come from a long term intubated  patient 





> A 36-year-old woman with advanced HIV carried the novel coronavirus for 216 days, during which the virus accumulated more than 30 mutations, a new study has found.
> The case report, which has not been peer-reviewed, was published as a preprint on _medRxiv_ on Thursday. The woman, who has not been named, was identified as a 36-year-old living in South Africa.
> The coronaviruses gathered 13 mutations to the spike protein, which is known to help the virus escape the immune response, and 19 other mutations that could change the behaviour of the virus.


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## elbows (Nov 28, 2021)

Supine said:


> Interesting interview on Marr with the SA doctor who first detected the new variant.
> 
> The patients all had unusually mild symptoms. Not the classic symptoms we all know about.


This one I presume:









						Omicron symptoms mild so far - South African doctor
					

The South African doctor who found the new variant says patients are showing very mild symptoms so far.



					www.bbc.co.uk
				




If we are very lucky then the most spreadable, immune-evading variant will also turn out to be milder for most people. Some rather oversimplified traditional views on how pandemics play out include such a prospect. I dont rule that out, especially as mild symptoms can be one reason why a version of the virus is able to spread better, eg people dont realise theyve got it and carry on with their lives. However I place very little weight in her comments at this stage for reasons including:

There have always been plenty of mild cases with every version of the virus.  Indeed there have always been a fair proportion of cases that show no symptoms at all.

We were less likely to formally identify such cases earlier in the pandemic, due to more limited testing regimes.

The age groups where initial spread was most prevalent can have an impact on the average severity of cases initially seen.

I need proper hospital data, and I havent gone looking for any for that region of South Africa yet.

Vaccinations potential role in moderating symptom severity, even where some forms of immune escape are involved.


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## elbows (Nov 28, 2021)

IC3D said:


> Its being mooted an HIV patient could be the starting point of this coronavirus as was the case here Woman with HIV had Covid-19 for 216 days, virus mutated 32 times inside her
> 
> This isn't the first time an immunosuppressed patient may have been a vector for virus mutation and merging. It was widely published around the time the Kent varient may have come from a long term intubated  patient


Its a plausible hypothesis but I think a lack of certainty puts a lot of people off from dwelling on it so much, which is probably a mistake.Not that I have a lot of ideas about how to reduce this risk, aside from the obvious of trying to keep the number of people who catch the virus in the first place down to a minimum. I could start ranting about all the stories with obvious agendas that were desperate to sneer at and shit all over countries that were still pursuing a 'zero covid' approach this year.


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## elbows (Nov 28, 2021)

> *Israel is to ban foreigners from entering the country for 14 days and use surveillance to halt the spread of the new Covid variant, local media report.*
> 
> The ban is expected to come into effect at midnight on Sunday, following full cabinet approval.





> In addition to the entry ban for non-Israelis, a three-day mandatory quarantine would be required for all vaccinated Israeli nationals, and a seven-day quarantine for those who have not been vaccinated.
> 
> The cabinet also authorised surveillance of confirmed coronavirus patients by the Israel's Shin Bet security agency.
> 
> In a statement, Prime Minister Naftali Bennett said phone-tracking technology would be used.











						Covid: Israel to impose travel ban for foreigners over new variant
					

Travellers from all countries will be banned from entering Israel for 14 days, local media report.



					www.bbc.co.uk


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## elbows (Nov 28, 2021)

13 out of the 61 positive cases on that flight to the Netherlands that was in the news yesterday have the Omicron variant:









						Covid: 13 test positive for Omicron after S Africa-Netherlands flights
					

Thirteen people who travelled from South Africa to the Netherlands have tested positive for Omicron.



					www.bbc.co.uk


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## elbows (Nov 28, 2021)

Ferguson still comes out with some useful info from time to time, including today, but I cannot say I'm impressed with his overall stance these days.



> The expert whose modelling helped instigate the first lockdown welcomed the new measures to slow the spread of the Omicron variant of coronavirus but said all options should be kept on the table in case it spreads very rapidly.
> 
> Professor Neil Ferguson, a member of the Scientific Advisory Group for Emergencies (Sage), said he expects to see “substantially larger numbers” of the Omicron variant in the coming days in the UK.





> He told BBC Radio 4’s The World This Weekend programme: “We together with the Netherlands ... we’re the two European countries with the largest number of passenger flights to and from South Africa, so it’s likely we’ll detect quite a lot more cases in the coming days.”
> 
> He said he backs the new measures announced by the Government as “proportionate” to slow the spread of the new variant during the “waiting game” over the next two weeks as scientists analyse its properties.



                           26m ago    13:37


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## MrCurry (Nov 28, 2021)

elbows said:


> 13 out of the 61 positive cases on that flight to the Netherlands that was in the news yesterday have the Omicron variant:
> 
> 
> 
> ...


This genie is really out of the bottle already, isn’t it?


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## elbows (Nov 28, 2021)

MrCurry said:


> This genie is really out of the bottle already, isn’t it?


That bit was one of the few certainties regarding this new variant at this stage. Its everything else about it that has big question marks at the moment.


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## StoneRoad (Nov 28, 2021)

MrCurry said:


> This genie is really out of the bottle already, isn’t it?


unfortunately, I would say that it is.

the question is, how well will the UK re-act ?

my pov is that, as usual, it will be too little, too late.
although the speed of imposing the travel ban, pcr tests & isolation [not quarantine] was better than previously.


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## Aladdin (Nov 28, 2021)

SA dr on this morning. 
Saying its a  mild cold. 

But they said that about c19 at first and then people started dying.


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## 2hats (Nov 28, 2021)

MrCurry said:


> elbows said:
> 
> 
> > 13 out of the 61 positive cases on that flight to the Netherlands that was in the news yesterday have the Omicron variant
> ...


One has to be a little cautious because that tells you little of the dynamics that led up to that brief snapshot (it's not likely a representative sample of the SA population, could be skewed by super spreader events, could be skewed if omicron proves to have an accelerated infection cycle => in-flight infection). How many of the other positives will eventually turn out to be omicron and how many are delta-lineage, or other, could prove interesting.


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## weltweit (Nov 28, 2021)

Sugar Kane said:


> SA dr on this morning.
> Saying its a  mild cold.
> 
> But they said that about c19 at first and then people started dying.


Yes, I am seeing some news reports that it is very contagious (in that it infects easily) but that it isn't very deadly. And that if it overtakes the delta variant this could be a good thing. I don't know how much data they are based on however.


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## 8ball (Nov 28, 2021)

kenny g said:


> Visiting Nottingham and found out about one of the two UK cases being here from the compere in a packed comedy night.



Oh, that’s nice.
Will maybe work from home tomorrow…

Was it glee club?


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## platinumsage (Nov 28, 2021)

Sugar Kane said:


> SA dr on this morning.
> Saying its a  mild cold.
> 
> But they said that about c19 at first and then people started dying.



TBF it wasn't Chinese doctors who were saying that. This SA doctor (Dr Angelique Coetzee) is well-placed to be informed about such matters, as she regularly sees COVID patients and is chair of the South African Medical Association and a member of the national advisory committee on vaccines, and discusses the subject every day with colleagues who are also on the ground seeing COVID patients. She's reporting lots of mild cases with no loss of smell but with where fatigue and increased heart rate are more common symptoms.


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## elbows (Nov 28, 2021)

And what age are her patients?


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## platinumsage (Nov 28, 2021)

elbows said:


> And what age are her patients?



I'd imagine reflective of the community as she's not a pediatrician or geriatrician. She's obviously comparing current symptoms in her patient population to the previous symptom profile in that same population.


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## elbows (Nov 28, 2021)

Well I dont place much weight on those sorts of early remarks anyway. Same approach as with the early stories about the hospitalisations and deaths from Delta variant in India, there are many potential factors that I cannot separate to get a clear picture of the disease severity profile of new variants. It takes time.

Meanwhile the president of South Africa will address the nation in a few hours time, not sure if there will be anything especially noteworthy from that but I suppose we'll hear about it if there is.


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## Aladdin (Nov 28, 2021)

platinumsage said:


> TBF it wasn't Chinese doctors who were saying that.



Yes I know that. I wasn't referring to the Chinese.  
There were plenty in Europe and the UK telling us it was not a serious disease at first


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## Pickman's model (Nov 28, 2021)

elbows said:


> Well I dont place much weight on those sorts of early remarks anyway. Same approach as with the early stories about the hospitalisations and deaths from Delta variant in India, there are many potential factors that I cannot separate to get a clear picture of the disease severity profile of new variants. It takes time.
> 
> Meanwhile the president of South Africa will address the nation in a few hours time, not sure if there will be anything especially noteworthy from that but I suppose we'll hear about it if there is.


You have more confidence in the media to relay such things than I'd expect


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## Pickman's model (Nov 28, 2021)

8ball said:


> Oh, that’s nice.
> Will maybe work from home tomorrow…
> 
> Was it glee club?


The first rule of glee club is...


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## Pickman's model (Nov 28, 2021)

weltweit said:


> Yes, I am seeing some news reports that it is very contagious (in that it infects easily) but that it isn't very deadly. And that if it overtakes the delta variant this could be a good thing. I don't know how much data they are based on however.


As I understand it scientists are concerned that it might gain some of delta's potency while retaining or developing its transmissibility and ability to get past vaccines


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## elbows (Nov 28, 2021)

Pickman's model said:


> You have more confidence in the media to relay such things than I'd expect


Well they are more likely the pay attention due to the current position of Omicron on the news agenda. Plus I can always resort to media from South Africa, or the youtube channel of the office of the presidency.


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## Storm Fox (Nov 28, 2021)

Third case of Omicron Covid variant detected in UK
					

Sajid Javid, the health secretary, says country ‘nowhere near’ imposing social distancing rules despite concerns




					www.theguardian.com
				




So they are going to ignore this almost totally, instead of being more careful now, such as having more distancing, until the scientists can work out Omicron's potency. Then if it is potent then we'll end up with another lockdown and being in a lot worse situation.

It's just depressing.


----------



## Pickman's model (Nov 28, 2021)

Storm Fox said:


> Third case of Omicron Covid variant detected in UK
> 
> 
> Sajid Javid, the health secretary, says country ‘nowhere near’ imposing social distancing rules despite concerns
> ...


It's sadly typical


----------



## Storm Fox (Nov 28, 2021)

Pickman's model said:


> It's sadly typical


Yeah every fucking time. 
1) Bring in restrictions too late
2) Undermine the restrictions
3) End restrictions too soon
4) Go to 1

I really hope Omicron is very mild. I don't give a shit about any crowing of I told you so from the twat brigade.


----------



## 2hats (Nov 28, 2021)

IC3D said:


> Its being mooted an HIV patient could be the starting point of this coronavirus as was the case here Woman with HIV had Covid-19 for 216 days, virus mutated 32 times inside her


The interesting phylogenetics of omicron open up a small number of (not necessarily exclusive) possibilities.


----------



## Pickman's model (Nov 28, 2021)

Storm Fox said:


> Yeah every fucking time.
> 1) Bring in restrictions too late
> 2) Undermine the restrictions
> 3) End restrictions too soon
> ...


After so many I told you so moments there's scant attraction in another one


----------



## elbows (Nov 28, 2021)

Third detected case in the UK visited the Westminster area.

And some details about the Essex case offers clues about how long ago it was, timing I had expressed a keen interest in:









						Covid: Third case of Omicron variant detected in the UK
					

It comes as England prepares to adopt tighter rules on masks and international travel from Tuesday.



					www.bbc.co.uk
				






> Essex County Council is now asking people who were at a church and a KFC outlet in the town to get a PCR test. The appeal is for members of the congregation who were at Trinity Church in the Pilgrims Hatch area on 21 November and staff, customers and delivery workers who were at KFC in Brentwood High Street on 19 November between 13:00 and 17:00.


----------



## Raheem (Nov 28, 2021)

elbows said:


> Third detected case in the UK visited the Westminster area.


Exactly what I would do.


----------



## elbows (Nov 28, 2021)

I watched the speech by the president of South Africa. He went on about vaccines a lot and said they would have a consultation about whether to make them mandatory. Went on about masks and ventilation and avoiding very large gatherings and raves, but they decided not to impose new measures at this time and to review things again in a week. Also complained about the travel bans others have imposed, and made points about vaccine inequality.


----------



## weltweit (Nov 28, 2021)

elbows said:


> I watched the speech by the president of South Africa. He went on about vaccines a lot and said they would have a consultation about whether to make them mandatory. Went on about masks and ventilation and avoiding very large gatherings and raves, but they decided not to impose new measures at this time and to review things again in a week. Also complained about the travel bans others have imposed, and made points about vaccine inequality.


Considering the steps other governments are taking in response to this specific variant I am surprised he isn't doing more. As to making vaccines compulsory my understanding is SA don't have enough to go round.


----------



## elbows (Nov 28, 2021)

They've got a hesitancy problem which is why he spent so long going on about vaccines.

They till have some measures in place that they didnt get rid of before these latest developments, eg masks are mandatory and legally required in various settings. There are size limits on certain gatherings. There is.a midnight-4am curfew. But they are into the 'live with covid' and 'vaccines are the best tool' approach so some rhetoric in common with UK etc.


----------



## Yossarian (Nov 28, 2021)

elbows said:


> And what age are her patients?



The coordinator of clinical and epidemiological data for the South African Covid Variant Research Consortium has sounded a note of caution about the "mild symptoms" headlines - he reckons we should know more about the possibility of severe illness caused by omicron in a week or two.

_Most of South Africa’s cases were initially found in the Gauteng province, mostly among younger people at universities and higher education institutions, said Dr. Lessells, who is also an infectious disease physician at the University of KwaZulu-Natal.

“We would of course expect the vast majority of those to be mild cases anyway, regardless of vaccination status,” he said.

In addition, cases overall have also been rising only in the last two weeks, Dr. Lessells noted: “There’s even barely enough time for infections to have had time to progress to severe disease and hospitalization.”

Should Omicron cause severe illness, that will become apparent if there is a significant rise in hospitalizations over the next week or two, he added._



			https://www.nytimes.com/live/2021/11/28/world/covid-omicron-variant-news#omicron-variant-severe-symptoms-mild


----------



## weltweit (Nov 28, 2021)

Dutch find 13 Omicron cases among S.Africa travellers
					

Dutch health authorities said on Sunday that 13 cases of the new Omicron coronavirus variant have been found in the Netherlands among passengers that were on two flights from South Africa that arrived on Friday.




					www.reuters.com
				






> ROTTERDAM, Nov 28 (Reuters) - Dutch health authorities said on Sunday that 13 cases of the new Omicron coronavirus variant have been found in the Netherlands among passengers that were on two flights from South Africa that arrived on Friday.
> 
> They were among 61 passengers who tested positive for COVID-19 on the two flights, which carried about 600 people. Those who tested positive are being kept in isolation at a hotel near the airport.


----------



## kenny g (Nov 28, 2021)

8ball said:


> Oh, that’s nice.
> Will maybe work from home tomorrow…
> 
> Was it glee club?


Saturday tonic club


----------



## kenny g (Nov 28, 2021)

New Concerning Variant: B.1.1.529
					

I hope everyone in the States had a fantastic Thanksgiving (even if you’re a Dallas Cowboys football fan). I hate to ruin the holiday, but… We have a new variant. I’ve not seen this much anxiety ridden chatter among scientists about a COVID19 variant before. Even among the calm, cool, and...




					yourlocalepidemiologist.substack.com
				




Is a good summary.


----------



## weltweit (Nov 28, 2021)

‘Absolute chaos’ in South Africa as flights grounded over Omicron
					

New Omicron variant of the coronavirus leaves South Africans isolated as countries ban travellers from the region.




					www.aljazeera.com
				






> *Johannesburg, South Africa –* Disbelief and confusion washed over South Africa as the announcement of the discovery of the Omicron COVID-19 variant grounded flights and raised fears of a hard lockdown in Africa’s most developed economy.


----------



## 2hats (Nov 28, 2021)

elbows said:


> And what age are her patients?


Predominately younger (<40) so more likely to be mild. Speculation: university super spreader events could have made a significant contribution; apparently a significant number of the cases identified thus far have come from university studies.


It will take around two weeks to begin to get a handle on transmissibility and around four weeks to get an idea of severity of disease - in her original interview Coetzee did caution that in "two weeks from now on we might say something different". Latest WHO report unsurprisingly sheds little more light.


----------



## elbows (Nov 28, 2021)

Cheers, any thoughts on this? I'll be coming up to 4 months since my 2nd dose in a week or so.



> Prof Paul Morgan, an immunologist at Cardiff University, said there was room for manoeuvre on the six-month gap, already cut to five months for some people.
> 
> “If boosters are given too soon, then they’re not as effective,” he said. “But I think six months was more about pragmatism and availability than about immunity. From three to four months on, the immune response should be virtually as good as at six months.”



(from Covid boosters may be expanded as soon as Monday to tackle Omincron spread )


----------



## StoneRoad (Nov 28, 2021)

elbows said:


> Cheers, any thoughts on this? I'll be coming up to 4 months since my 2nd dose in a week or so.
> 
> 
> 
> (from Covid boosters may be expanded as soon as Monday to tackle Omincron spread )


IIRC it's the drop in immunity in the AstraZenica version that has them worried.
There's isn't such a big drop with the Pfizer.


----------



## 8ball (Nov 28, 2021)

StoneRoad said:


> IIRC it's the drop in immunity in the AstraZenica version that has them worried.
> There's isn't such a big drop with the Pfizer.



Is this based on an observed drop in antibody levels or something else?


----------



## StoneRoad (Nov 28, 2021)

Something picked up by the ZOE study ...




cvd - ZOE pfizer vs az jabs par StoneRoad2013, on ipernity


----------



## donkyboy (Nov 28, 2021)

Should have named it Unicron. Missed opportunity


----------



## xenon (Nov 28, 2021)

So what happened to all the other variants of concern between Delta and omnicron? I remember reading about Lamder, months ago.


----------



## 8ball (Nov 28, 2021)

StoneRoad said:


> Something picked up by the ZOE study ...
> 
> 
> 
> ...



The term “survey suggests” made me a bit


----------



## StoneRoad (Nov 28, 2021)

8ball said:


> The term “survey suggests” made me a bit


and I had the same reaction - but that was the first graphic that came up [it's from October].
I'll have a look for another one ...


----------



## Raheem (Nov 28, 2021)

donkyboy said:


> Should have named it Unicron. Missed opportunity


Or E. Macron


----------



## Yossarian (Nov 28, 2021)

xenon said:


> So what happened to all the other variants of concern between Delta and omnicron? I remember reading about Lamder, months ago.



The most recent variant given a Greek letter was Mu, back in August - that variant, found in Colombia, was largely eclipsed by Delta, as were Lambda, Iota etc.


----------



## elbows (Nov 28, 2021)

Yeah we hear about those other variants because they have grown in some locations and/or have interesting mutations, but unless they show signs of outcompeting other strains they tend to fall off the radar.


----------



## Cloo (Nov 28, 2021)

Storm Fox said:


> Third case of Omicron Covid variant detected in UK
> 
> 
> Sajid Javid, the health secretary, says country ‘nowhere near’ imposing social distancing rules despite concerns
> ...


If only omicron had waited until after Christmas, then they might have actually done something about it. But 'cancelling Christmas' would actually cost the Tories more votes than 1000s extra deaths, because people are trash, and the Tories know that.


----------



## Yossarian (Nov 28, 2021)

Shit, two cases now reported in Canada -both with recent travel to Nigeria but apparently not southern Africa.

According to Our World in Data, 1.7% of Nigeria's 211 million people are fully vaccinated.


----------



## donkyboy (Nov 28, 2021)

WOW thats like only 3 million?


----------



## 2hats (Nov 29, 2021)

elbows said:


> Cheers, any thoughts on this? I'll be coming up to 4 months since my 2nd dose in a week or so.


Obviously you have to balance the intra-dose interval timing with your own personal risk of infection and circumstances (medical history including previous exposure to antigen, factor in vaccine types, clinical vulnerability, scope/practicalities for enacting NPIs). You could perhaps shorten it to as little as four months but then you could be trading degrees of potency/avidity/durability/breadth, in particular to antigenically diverse VOCs as yet unseen, for shorter term 'immediate'* protection. Indeed, some studies (DOI: 10.1101/2021.11.19.21266555, DOI: 10.1016/S0140-6736(21)01699-8) have found a significantly better overall immune response with intervals of around 8, up to 12 months (though perhaps an even longer interval might eventually be found to be immunologically optimal) and doubtless a fair few instances of hybrid immunity have 'fortuitously' benefited from this effect to degrees too (original first wave convalescents not receiving an initial vaccine dose for up to a year or more).


			Bloomberg - Are you a robot?
		


*e2a: 'immediate' here as in 'within a couple of weeks'.


----------



## MrSki (Nov 29, 2021)

Six cases just announced in Scotland bringing total in UK to nine so far.


----------



## donkyboy (Nov 29, 2021)

As I read this unfolding, I am reminded of the Hindu scripture, the Bhagavad-Gita:

"I am Omicron, destroyer of worlds..."


----------



## Steel Icarus (Nov 29, 2021)

Tbh - and unusually for me - I find myself unbothered by new Om cases, they were always inevitable. I'm waiting with curiosity to see _what_ it is, not _where_.


----------



## magneze (Nov 29, 2021)

Exactly - it'll already be everywhere once we start looking.


----------



## platinumsage (Nov 29, 2021)

The great news about it already being everywhere is that we will find out how it behaves in terms of vaccines and hospitalisations much sooner than we otherwise would.


----------



## magneze (Nov 29, 2021)

One for the "good news thread"? 🤔 Perhaps not ...


----------



## elbows (Nov 29, 2021)

MrSki said:


> Six cases just announced in Scotland bringing total in UK to nine so far.


Some important detail on that one. Stuff that sometimes surprised people during the early days of past variants but is to be expected and will probably surprise people less this time:



> The Scottish government announced on Monday morning that six cases of the variant had been identified in Scotland, with four in Lanarkshire and two in the Greater Glasgow and Clyde area.
> 
> Some of the cases identified in Scotland have had no travel history and *caught the virus variant in the community*, Deputy First Minister John Swinney told BBC's Good Morning Scotland.


Quote is from:








						Covid: JCVI scientists to announce decision on booster rollout
					

A reduction in time between doses and extending the scheme to younger age groups could be approved.



					www.bbc.co.uk


----------



## elbows (Nov 29, 2021)

2hats said:


> Obviously you have to balance the intra-dose interval timing with your own personal risk of infection and circumstances (medical history including previous exposure to antigen, factor in vaccine types, clinical vulnerability, scope/practicalities for enacting NPIs). You could perhaps shorten it to as little as four months but then you could be trading degrees of potency/avidity/durability/breadth, in particular to antigenically diverse VOCs as yet unseen, for shorter term 'immediate'* protection. Indeed, some studies (DOI: 10.1101/2021.11.19.21266555, DOI: 10.1016/S0140-6736(21)01699-8) have found a significantly better overall immune response with intervals of around 8, up to 12 months (though perhaps an even longer interval might eventually be found to be immunologically optimal) and doubtless a fair few instances of hybrid immunity have 'fortuitously' benefited from this effect to degrees too (original first wave convalescents not receiving an initial vaccine dose for up to a year or more).
> 
> 
> Bloomberg - Are you a robot?
> ...


Thaks very much for your thoughts on this. As with the initial roll-out, I will have quite a lot of wiggle room and personal decisions to make, because my circumstances mean that my risk of infection is almost zero, with leaving the house to get vaccinated being one of the exceptions to my near-zero risk.


----------



## LDC (Nov 29, 2021)

platinumsage said:


> The great news about it already being everywhere is that we will find out how it behaves in terms of vaccines and hospitalisations much sooner than we otherwise would.



I admire your optimism! Same as the good thing about cancer is that it's so common we have loads of experience dealing with it and impetus to develop treatments and cures.


----------



## elbows (Nov 29, 2021)

2hats said:


> Obviously you have to balance the intra-dose interval timing with your own personal risk of infection and circumstances (medical history including previous exposure to antigen, factor in vaccine types, clinical vulnerability, scope/practicalities for enacting NPIs). You could perhaps shorten it to as little as four months but then you could be trading degrees of potency/avidity/durability/breadth, in particular to antigenically diverse VOCs as yet unseen, for shorter term 'immediate'* protection. Indeed, some studies (DOI: 10.1101/2021.11.19.21266555, DOI: 10.1016/S0140-6736(21)01699-8) have found a significantly better overall immune response with intervals of around 8, up to 12 months (though perhaps an even longer interval might eventually be found to be immunologically optimal) and doubtless a fair few instances of hybrid immunity have 'fortuitously' benefited from this effect to degrees too (original first wave convalescents not receiving an initial vaccine dose for up to a year or more).
> 
> 
> Bloomberg - Are you a robot?
> ...


I was somewhat impressed that they acknowledged this sort of thing in todays press conference, and justified bringing the gap down to a minimum of three months on the basis of balancing the benefits of a longer gap with trying to get the timing right in relation to a new wave arriving. They mentioned a study that used a three months gap to justify using that as the lower limit.


----------



## girasol (Nov 29, 2021)

More virulent, less lethal?  That's what happens in vírus evolution, right? Hopefully it's the good news the world has been waiting for. We should know in a couple of weeks. Fingers crossed!


----------



## cupid_stunt (Nov 29, 2021)

girasol said:


> More virulent, less lethal?  That's what happens in vírus evolution, right? Hopefully it's the good news the world has been waiting for. We should know in a couple of weeks. Fingers crossed!



We don't know yet.



> “We’re seeing a marked change in the demographic profile of patients with COVID-19,” Rudo Mathivha, head of the intensive care unit at Soweto’s Baragwanath Hospital, told an online press briefing.
> 
> “Young people, in their 20s to just over their late 30s, are coming in with moderate to severe disease, some needing intensive care. About 65% are not vaccinated and most of the rest are only half-vaccinated,” said Mathivha. “I’m worried that as the numbers go up, the public health care facilities will become overwhelmed.”











						South African scientists brace for wave propelled by omicron
					

JOHANNESBURG (AP) — Worried scientists in South Africa are scrambling to combat the lightning spread across the country of the new and highly transmissible omicron COVID-19 variant as the world grapples with its emergence.




					apnews.com


----------



## elbows (Nov 29, 2021)

girasol said:


> More virulent, less lethal?  That's what happens in vírus evolution, right?


Its a cliche and tends to be a grotesque oversimplification.


----------



## StoneRoad (Nov 29, 2021)

StoneRoad said:


> and I had the same reaction - but that was the first graphic that came up [it's from October].
> I'll have a look for another one ...



This is the other graphic I was looking for, about effectiveness ...


----------



## girasol (Nov 29, 2021)

cupid_stunt said:


> We don't know yet.


That's literally what I said 😂😂


----------



## elbows (Nov 29, 2021)

> Nottinghamshire County Council said investigations into the spread of the variant locally were being carried out at a school in West Bridgford.
> 
> Jonathan Gribbin, director of public health for Nottinghamshire, did not name the school but said the parents of students had been informed.











						Omicron: Targeted testing in Nottinghamshire school
					

Parents are being asked to consent to testing after a case of Omicron was confirmed in Nottingham.



					www.bbc.co.uk


----------



## elbows (Nov 29, 2021)

> The UK Health Security Agency (UKHSA) has identified 2 further cases of COVID-19 with mutations consistent with B.1.1.529 in England, in addition to the previous 3 confirmed cases of the SARS-CoV-2 variant known as B.1.1.529 on 27 and 28 November. The total number of confirmed cases in England is now 5.
> 
> The individuals that have tested positive are not connected to each other and are not linked to the previously confirmed cases. Both have links to travel to Southern Africa. One case is located in Camden, London, and one case is located in Wandsworth, London. The individuals and their households have been told to self-isolate. UKHSA is carrying out targeted testing at locations where the positive cases were likely to be infectious.











						COVID-19 variants identified in the UK – latest updates
					

Latest updates on SARS-CoV-2 variants detected in the UK.




					www.gov.uk


----------



## _Russ_ (Nov 29, 2021)

girasol said:


> That's literally what I said 😂😂


No, you made a heavy inference and put a question mark after it.


----------



## xenon (Nov 29, 2021)

Depressingly virus' don't always evolve to become less lethal. See Ebola and MERS.

The idea is a virus that kills a large percentage of it's hosts has an evolutionary disadvantage. But there are viruses in the wild, like the above that have a 30% (roughly IIRC) lethality rate.

Granted they're unlikely to spread as far as something like coronavirus cos people die or stay out of the way. But I don't think it's a given that all virus's tend towards less lethality.


----------



## Magnus McGinty (Nov 29, 2021)

Well wiping out its host will wipe out itself. Although I suppose it could return to the bat reservoir happy that it dealt with climate change.


----------



## The39thStep (Nov 29, 2021)

Portugal acted fast over omicron and just got their bottom slapped by the EU



> The European Commission implicitly criticized one of the latest measures taken by Portugal. The government announced that tests will be mandatory for all travelers arriving in the country, even those who are double vaccinated.
> Brussels reiterated the principle that Member States should refrain from erecting undue barriers to Covid-19 vaccinated and recovered passengers.


----------



## mx wcfc (Nov 29, 2021)

The39thStep said:


> Portugal acted fast over omicron and just got their bottom slapped by the EU


Whilst I voted remain, the EU can be fucking dicks sometimes.


----------



## NoXion (Nov 29, 2021)

xenon said:


> Depressingly virus' don't always evolve to become less lethal. See Ebola and MERS.
> 
> The idea is a virus that kills a large percentage of it's hosts has an evolutionary disadvantage. But there are viruses in the wild, like the above that have a 30% (roughly IIRC) lethality rate.
> 
> Granted they're unlikely to spread as far as something like coronavirus cos people die or stay out of the way. But I don't think it's a given that all virus's tend towards less lethality.



I thought MERS was a bacterial infection? Or am I confusing that with MRSA?


----------



## StoneRoad (Nov 29, 2021)

NoXion said:


> I thought MERS was a bacterial infection? Or am I confusing that with MRSA?


confused as I think MERS is the viral & MRSA is bacterial.


----------



## NoXion (Nov 29, 2021)

The39thStep said:


> Portugal acted fast over omicron and just got their bottom slapped by the EU



I don't know why they wouldn't want to test everyone anyway, regardless of vaccination status. Why leave great big gaps in biosecurity measures? Especially since vaccinated people can still be carriers.



StoneRoad said:


> confused as I think MERS is the viral & MRSA is bacterial.



Yeah looked it up, MERS is viral.


----------



## Magnus McGinty (Nov 29, 2021)

NoXion said:


> I thought MERS was a bacterial infection? Or am I confusing that with MRSA?



One is a highly infectious but dangerous threat whilst the other came second on the X-Factor.


----------



## Numbers (Nov 29, 2021)

Magnus McGinty said:


> One is a highly infectious but dangerous threat whilst the other came second on the X-Factor.


2nd on X-Factor usually mean more success


----------



## Combustible (Nov 30, 2021)

xenon said:


> Depressingly virus' don't always evolve to become less lethal. See Ebola and MERS.


Considering the fact that deaths from Covid usually happen a considerable time after infection, it doesn't seem likely that becoming less lethal would necessarily give it an evolutionary advantage.


----------



## Aladdin (Nov 30, 2021)

Is there a chance that if this new variant is just like a simple mild cold and it becomes the dominant world wide, that it will wipe out the worse variants and be the end of this?


----------



## mystic pyjamas (Nov 30, 2021)

Sugar Kane said:


> Is there a chance that if this new variant is just like a simple mild cold and it becomes the dominant world wide, that it will wipe out the worse variants and be the end of this?


 No.


----------



## cupid_stunt (Nov 30, 2021)

7.40am post on the Telegraph's live update.  



> Stephane Bancel, chief of pharma giant Moderna, poured cold water over hopes that current vaccines will be able to handle the omicron variant. He told the FT: "There is no world, I think, where [the effectiveness] is the same level . . . we had with [the] Delta [variant].
> 
> “I think it’s going to be a material drop. I just don’t know how much because we need to wait for the data. But all the scientists I’ve talked to . . . are like, ‘This is not going to be good’.”
> 
> Mr Bancel said scientists were worried because 32 of the 50 mutations in the new strain were on the spike protein, which current vaccines focus on to boost the human body’s immune system to combat Covid.


----------



## prunus (Nov 30, 2021)

Sugar Kane said:


> Is there a chance that if this new variant is just like a simple mild cold and it becomes the dominant world wide, that it will wipe out the worse variants and be the end of this?



There is a chance, but it’s pretty remote and not really worth spending a second thinking about (yet - it would be a spectacular piece of luck though).

I suspect that this particular virus is still in the optimising for new host phase - ie it will be getting better at transmission and infectivity (omicron seems it may be a jump in that direction, though that may be escape mutation increasing its available pool of hosts).  Many of the ways it can improve infectivity are likely to increase virulence too - basically it becomes better at invading our cells, both on first contact and when replicating inside a new host.

Lethality is complex as it is an interaction of the severity of the actual infection (the damage done by the virus itself) and the immune response (the damage done by extreme immune reaction - cytokine storms and the like).  It’s not impossible that a more infectious version actually provokes a less over-the-top immune response, which will lead to fewer deaths. But it’s by no means certain, or even particularly likely.

The virus itself doesn’t ‘care’ if it kills all its hosts and die out. It just randomly changes and some of the resultant versions outcompete others and become dominant. If those versions also happen to be less lethal, jolly good. But they may also be more lethal.

In the long run there aren’t any pandemic (ie common and widespread) viruses with very high lethality not because they all become milder over time, but because the lethal ones (and the ones that became more lethal over time) have died out, taking most of their host population with them.


----------



## elbows (Nov 30, 2021)

prunus said:


> In the long run there aren’t any pandemic (ie common and widespread) viruses with very high lethality not because they all become milder over time, but because the lethal ones (and the ones that became more lethal over time) have died out, taking most of their host population with them.


Plus if there are some specific genetic traits that make some hosts much more susceptible to death from the virus in general, a lot of them may be wiped out, causing the overall population risk of death to change. Not sure how big a factor that actually is though, and there are all the hosts who are vulnerable due to other health conditions.

Some virologists end up perpetuating some of the myths too, since there is not universal agreement on all of the details and expectations, especially when people including authorities and journalists are seeking simplistic, reassuring stories and pictures of a positive future.

There are positive concepts to be found, or at least concepts with more positive end-games. For example even if the virus doesnt change, we do. In that people will have many opportunities to catch various versions of the virus when they are young and less vulnerable to the worst consequences, or even inherit some degree of protection by design or by luck. But I expect my own description of these things is also a bit sloppy and error-prone. Main point is that some of the viral evolution cliches are not grounded in fact.


----------



## elbows (Nov 30, 2021)

cupid_stunt said:


> 7.40am post on the Telegraph's live update.


The stock markets noticed.









						Global markets fall after Moderna Omicron warning
					

Stock markets slide after Moderna boss casts doubt on vaccine effectiveness against new variant.



					www.bbc.co.uk


----------



## DotCommunist (Nov 30, 2021)

I'm getting a booster on the 8th, hope this Omnicron doesn't fuck things up. Name reminds me of Unicron from the 1984 Transformers film (voiced by Orson Welles)


----------



## elbows (Nov 30, 2021)

I hate this sort of sloppy framing:



> The Omicron variant was in Europe days earlier than first believed, it emerges, with cases found in samples taken between 19 and 23 November - before it was identified in South Africa



When a case is first detected is not the same as when that variant was first believed to be here. And at this stage of the pandemic far more people were aware of that due to previous experiences with bullshit rhetoric about 'containing' recently detected variants. Rhetoric that even the UK authorities havent bothered with this time, instead going for something closer to reality by talking about slowing the spread instead.

Anyway that quote is from the BBC live updates page https://www.bbc.co.uk/news/live/59473695 and is sponsored by the Netherlands:



> Health officials in the Netherlands will carry out further studies to determine when the new Omicron variant first emerged in the country.
> 
> Newly sequenced tests from two people between 19 and 23 November found the variant was present in the country before it was first identified in South Africa.


----------



## elbows (Nov 30, 2021)

DotCommunist said:


> I'm getting a booster on the 8th, hope this Omnicron doesn't fuck things up. Name reminds me of Unicron from the 1984 Transformers film (voiced by Orson Welles)


UK authorities are using expansion and acceleration of the booster campaign as the main thrust of their initial Omicron response because:

Its viewed a bit like a tug of war - Omicron assumed to reduce vaccine efficacy but boosters can at least bump up the starting level of protection that is then eroded by the variants properties. We'll have to wait for much better data to see what the balance of these two competing factors will actually end up like.

They much prefer vaccine-based stuff to other measures, but dont be surprised if they are forced to do more of the other stuff in future too.


----------



## elbows (Nov 30, 2021)

Even Harries has cast doubt on the comments about it being 'mild' from the South African doctor that peope unwisely tried to make too much of the other day.



> *She said early reports about Omicron having only a mild impact in South Africa should be treated with caution because its population was so different.* She said the average age of the population in South Africa is 27. In the UK it is 41. And she said Omicron, like other coronavirus variants, is thought to be much worse for older people not younger younger.



                                   5h ago                            10:08


----------



## weepiper (Nov 30, 2021)

Scottish Omicron cases all linked to one ‘private event’, says Sturgeon
					

First minister says none of the nine people found to have been infected with new variant required hospital care




					www.theguardian.com


----------



## elbows (Nov 30, 2021)




----------



## skyscraper101 (Nov 30, 2021)

Perhaps it’s not as bad as first thought?









						Sigh of relief in South Africa as Omicron variant appears to be ‘super mild‘ mutation with Covid death rate not jumping
					

The WHO and Coronavirus experts are increasingly convinced the new Omicron variant is 'super mild' and has, so far, not led to a jump in Covid death rates




					www.cityam.com


----------



## 8ball (Nov 30, 2021)

skyscraper101 said:


> Perhaps it’s not as bad as first thought?
> 
> 
> 
> ...



Would love this to be true.  A mutation set for increased infectivity and milder disease out-competing the other variants would be a godsend.


----------



## Raheem (Nov 30, 2021)

Wouldn't not leading to an increase in deaths mean it's approximately as deadly as the other strains, rather than "super mild"?


----------



## 8ball (Nov 30, 2021)

Raheem said:


> Wouldn't not leading to an increase in deaths mean it's approximately as deadly as the other strains, rather than "super mild"?


Would depend on the rate of cases.


----------



## IC3D (Nov 30, 2021)

Perhaps let this one rip then.


----------



## cupid_stunt (Nov 30, 2021)

IC3D said:


> Perhaps let this one rip then.



You mean like with delta?


----------



## 8ball (Nov 30, 2021)

IC3D said:


> Perhaps let this one rip then.


----------



## Yossarian (Nov 30, 2021)

skyscraper101 said:


> Perhaps it’s not as bad as first thought?
> 
> 
> 
> ...



It'll be good news indeed if the optimistic take on the situation from CityAM's digital editor is correct - but I'm not going to put too much faith in someone who describes the reaction to omicron as "mass hysteria."


----------



## IC3D (Nov 30, 2021)

cupid_stunt said:


> You mean like with delta?


I have more faith in the virus to act like a virus  at this point than anything else


----------



## rubbershoes (Nov 30, 2021)

IC3D said:


> I have more faith in the virus to act like a virus  at this point than anything else



Which is to occasionally mutate. 
 That's what they do


----------



## 8ball (Nov 30, 2021)

Yossarian said:


> It'll be good news indeed if the optimistic take on the situation from CityAM's digital editor is correct - but I'm not going to put too much faith in someone who describes the reaction to omicron as "mass hysteria."



Until we have some decent data, best not to loosen any behaviour at all.


----------



## Yossarian (Nov 30, 2021)

This epidemiologist seems a lot more cautious - he also notes that a lot of the reporting about this variant being "mild" stems from a single out-of-context quote from a South African doctor.


----------



## cupid_stunt (Nov 30, 2021)

IC3D said:


> I have more faith in the virus to act like a virus  at this point than anything else



WTF does this mean?


----------



## cupid_stunt (Nov 30, 2021)

Yossarian said:


> This epidemiologist seems a lot more cautious - he also notes that a lot of the reporting about this variant being "mild" stems from a single out-of-context quote from a South African doctor.
> 
> 
> View attachment 298806



Yep, it's not making much sense, how can there be a 330% increase in hospitalisations, in just 2 weeks, if it's so mild?



> Hospitalisations have risen by 330% in the past two weeks in the South African province where the Omicron Covid variant was first detected.
> 
> Gauteng has had 580 hospitalisations caused by Covid which is a 330% rise from the 120 people that needed hospital treatment two weeks earlier.
> 
> ...



Basically, it's far too early to actually know how much of a problem it's going to be.









						Hospitalisations soar by 330% in South African area where Omicron first detected
					

The South African province of Gauteng where Omicron was first discovered has seen a 330% rise in hospitalisations over the past two weeks despite officials claiming the Covid variant has been mild




					www.mirror.co.uk


----------



## weltweit (Nov 30, 2021)

cupid_stunt said:


> ..
> Basically, it's far too early to actually know how much of a problem it's going to be.
> ..


I agree with this, we need sober scientific analysis and I don't think we have had that yet.


----------



## Supine (Nov 30, 2021)




----------



## 8ball (Nov 30, 2021)

Supine said:


>




... for seemingly handwavy values of '~'...


----------



## cupid_stunt (Nov 30, 2021)

weltweit said:


> I agree with this, we need sober scientific analysis and I don't think we have had that yet.



Indeed, all the experts are saying it will be another couple of weeks before they know enough to make a call on this.

Yet, IC3D suggests we should perhaps let it rip, without that data, and after posting just over a week ago "we all hope it will become a common cold like the other coronaviruses but I believe it could get worse too."


----------



## Magnus McGinty (Nov 30, 2021)

I’m grateful for optimism given the bleakness of the last two years. But the data hasn’t had enough time to be of any use really, and comes from South Africa which has a younger population than Western Europe.


----------



## 8ball (Nov 30, 2021)

cupid_stunt said:


> Indeed, all the experts are saying it will be another couple of weeks before they know enough to make a call on this.
> 
> Yet, IC3D suggests we should perhaps let it rip, without that data, and after posting just over a week ago "we all hope it will become a common cold like the other coronaviruses but I believe it could get worse too."



I thought IC3D was being sarcastic and was suggesting someone else on the thread (possibly me), was saying we should "let it rip".


----------



## LDC (Nov 30, 2021)

IC3D said:


> Perhaps let this one rip then.



Don't you work in medicine/the NHS? (Unless it's a very weird joke we've missed?)


----------



## elbows (Nov 30, 2021)

skyscraper101 said:


> Perhaps it’s not as bad as first thought?
> 
> 
> 
> ...


Thats based on the same stuff from a doctor that we've been discussing in recent days and that I put no weight in at all at this stage. Even if her comments are accurate they are more likely to be a sign of the age of the patients she saw, and even Harries has been pointing out the different demographics of South Africa compared to the UK. And others have highlighted some hospital admissions data, and not just on this thread, eg        #423      and        #427


----------



## elbows (Nov 30, 2021)

Plus even if a new variant were considered to be 'milder' by some direct measurements, it can still end up killing more people than previous strains if it (a) is more transmissible and (b) has some additional degree of escape from vaccines, especially if it explodes onto the scene at a time when people are in contact with more people than before and are doing less of the other things to reduce transmission than before. Thats why authorities like the UKs are unnerved by this variant.


----------



## platinumsage (Nov 30, 2021)

The main thing to take from her comments isn’t the supposed mildness, but the different symptom profile. Loss of smell for example first came to light through anecdata, so it does pay to listen to clinicians on the ground (albeit keeping the bigger picture in mind when they’re talking about wards full of children or lots of mild cases or whatever).


----------



## LDC (Nov 30, 2021)

elbows said:


> Plus even if a new variant were considered to be 'milder' by some direct measurements, it can still end up killing more people than previous strains if it (a) is more transmissible and (b) has some additional degree of escape from vaccines, especially if it explodes onto the scene at a time when people are in contact with more people than before and are doing less of the other things to reduce transmission than before. Thats why authorities like the UKs are unnerved by this variant.



Yeah, I've had the conversation with a couple of people, it is something that doesn't seem easy to grasp for some at first, 'common sense' makes people think milder=better irrespective of other factors.


----------



## 2hats (Nov 30, 2021)

Two Israeli doctors test positive for Omicron COVID variant


> One of the doctors, in his 50s, brought the variant into Israel on return from a medical conference in London. He tested negative when he boarded the airplane from the United Kingdom to Israel and on arrival, but a few days later began experiencing symptoms.
> 
> Once he tested positive, his results were sequenced and he was confirmed positive for the variant on Tuesday.
> 
> ...


----------



## wemakeyousoundb (Nov 30, 2021)

2hats said:


> Two Israeli doctors test positive for Omicron COVID variant


In the Air Tonight - union carbide productions
Not so helpful but summarising how I feel  about the whole show in a way


----------



## Combustible (Dec 1, 2021)

elbows said:


> Plus even if a new variant were considered to be 'milder' by some direct measurements, it can still end up killing more people than previous strains if it (a) is more transmissible


It's also worth pointing out that based on 'educated speculation', Omicron may well be intrinsically less transmissible than Delta, but that could be outweighed by it's ability to evade existing antibodies from previous infections/vaccines.


----------



## Cloo (Dec 1, 2021)

It seems like now really we're waiting to see what hospitalisations/ deaths do in the next 4 weeks.  Fucking shame the government will do nothing because Christmas.


----------



## Pickman's model (Dec 1, 2021)

Cloo said:


> It seems like now really we're waiting to see what hospitalisations/ deaths do in the next 4 weeks.  Fucking shame the government will do nothing because Christmas.


The government know what they should do. But Boris Johnson blames a shortage of revolvers and whisky shot glasses as he weasels his way out of it


----------



## brogdale (Dec 1, 2021)

This has a darkly familiar ring to it.


----------



## Pickman's model (Dec 1, 2021)

brogdale said:


> This has a darkly familiar ring to it.
> 
> View attachment 298891


Another Johnson moment


----------



## Cloo (Dec 1, 2021)

Pickman's model said:


> The government know what they should do. But Boris Johnson blames a shortage of revolvers and whisky shot glasses as he weasels his way out of it


As I've mentioned elsewhere,  sadly the Tories know that a 'cancelled Christmas' would cost them more than any excess deaths,  because people are tossers.


----------



## StoneRoad (Dec 1, 2021)

Javid was whittering on about asking people to use their "common sense" over the festive season.

But that's the problem - yer average "mr&mrs & 2.4  chliders" style family ... well, they don't have as much common sense as the term implies.
It should be "rare sense" not "common sense" as it is in such short supply.

I was out on a 'site visit' yesterday. Looking about whilst getting there & back, I could see very few masks. During the personal needs break on the way home, as a mask-wearer I was in a tiny minority. More smokers were in evidence ! ...


----------



## elbows (Dec 1, 2021)

Cloo said:


> It seems like now really we're waiting to see what hospitalisations/ deaths do in the next 4 weeks.  Fucking shame the government will do nothing because Christmas.


In the UK? First we need to see how Omicron takes hold in terms of cases. The hospitalisations and deaths picture will be driven by what happens with Delta infections unless/until Omicron really takes off.

edit - also see the leaked SAGE minutes which I just mentioned on the main UK thread:        #43,430


----------



## elbows (Dec 1, 2021)

NERVTAG minutes November 25th (published on the 29th):





__





						Box
					






					app.box.com
				




Some quotes:



> SA estimates an R-value of 1.9 for B.1.1.529 in Gauteng.





> The  R-value  estimate  of  1.9  is  occurring against  a  background  of  high  levels  of  immunity  following  the  recent  wave  (wave  number  3)  of  Delta  variant  infections  in  SA  and  an  active  immunisation programme.





> Although there is not yet any direct experimental evidence of immune escape, the genotype and  the  epidemiology  in  SA  are  highly  suggestive  that  B.1.1.529  is  an antigenically divergent variant that is able to successfully infect previously infected or vaccinated individuals.





> There are  currently  insufficient  data  to  make  any  comments  on  disease  severity  associated with B.1.1.529.





> Conclusion: the subgroup concludes that if introduced into the UK, B.1.1.529 would likely be capable of initiating a new wave of infections. We cannot exclude that this wave would be of a magnitude similar, or even larger, than previous waves.
> 
> Conclusion: Although  data  on  disease  severity  associated  with  B.1.1.529  are  not  yet available, a large wave of infections will be accompanied by a wave of severe cases and the subgroup cannot rule out that this may be sufficient to overwhelm NHS capacity





> Although  computational  analyses  are  ongoing,  the  multiple  mutations  observed  in  theB.1.1.529  spike  glycoprotein  are  likely  to  render  many  of  the  currently  available  monoclonal antibodies ineffective.





> Acceleration of the vaccine boosting campaign should be considered, which might provide some  residual  or  significant  VE  against  B1.1.529,  and  at  a  minimum  would  help control concurrent Delta impact.


----------



## Riklet (Dec 1, 2021)

brogdale said:


> This has a darkly familiar ring to it.
> 
> View attachment 298891



For alll we know it may well have originated in Nigeria.

Huge population
Plenty of immuno suppressed people
Very low vaccination rate (2%? all that oil money being spent well)
Hard hit already in some areas by Covid but not that much overall
Unlikely to have the testing or sequencing going on that South Africa does


----------



## brogdale (Dec 1, 2021)

Riklet said:


> For alll we know it may well have originated in Nigeria.
> 
> Huge population
> Plenty of immuno suppressed people
> ...


Indeed; just like when we were told that Covid emerged/arrived in Jan/Feb 2020 and then it emerged that it had been circulating in France since November 2019.


----------



## platinumsage (Dec 1, 2021)

brogdale said:


> Indeed; just like when we were told that Covid emerged/arrived in Jan/Feb 2020 and then it emerged that it had been circulating in France since November 2019.



We were also told it was circulating in Italy and the US in September 2019. I'd treat such claims with some degree of skepticism.


----------



## elbows (Dec 1, 2021)

platinumsage said:


> We were also told it was circulating in Italy and the US in September 2019. I'd treat such claims with some degree of skepticism.


An added possible factor in those claims about the first origins of SARS-Cov-2 in humans in terms of timing and location was that deliberate disinformation campaigns by China could have been involved in seeding and spreading such details, deliberately muddying the waters.


----------



## brogdale (Dec 1, 2021)

platinumsage said:


> We were also told it was circulating in Italy and the US in September 2019. I'd treat such claims with some degree of skepticism.


I understood that the epidemiological research stood this up?


----------



## elbows (Dec 1, 2021)

November 2019 is not September 2019.

Due to lack of surveillance it does make sense to leave a bit of wiggle room in our understanding of the exact timing of the emergence of the original virus. We were only setup to notice once notable impact on hospital admission numbers was noticed, once there had been an explosion of cases somewhere. November 2019 is plausible, especially when we are probably talking about low numbers at that time. Patchy and limited data, even when looking hard retrospectively, makes location even harder to determine than timing. I havent gone looking for any UK-specific studies on that but there was reasonably good anecdotal evidence that there were some sporadic cases in December 2019 that nobody noticed until hindsight was available. Fergus Walsh of the BBC did some articles about that, and was especially interested in the subject since it turns out he may have been an early case himself.


----------



## brogdale (Dec 1, 2021)

elbows said:


> November 2019 is not September 2019.
> 
> Due to lack of surveillance it does make sense to leave a bit of wiggle room in our understanding of the exact timing of the emergence of the original virus. We were only setup to notice once notable impact on hospital admission numbers was noticed, once there had been an explosion of cases somewhere. November 2019 is plausible, especially when we are probably talking about low numbers at that time. Patchy and limited data, even when looking hard retrospectively, makes location even harder to determine than timing. I havent gone looking for any UK-specific studies on that but there was reasonably good anecdotal evidence that there were some sporadic cases in December 2019 that nobody noticed until hindsight was available. Fergus Walsh of the BBC did some articles about that, and was especially interested in the subject since it turns out he may have been an early case himself.


Yes, to clarify, I was referring to the November in France evidence, not anything about September; hence my link.


----------



## elbows (Dec 1, 2021)

This article that involves an interview with the Israeli doctor who caught Omicron and thinks he got it at a conference in London, contains the usual bad framing bullshit that drives me mad. "one of the first people in the world to become infected with the Omicron variant" - NO! Just one of the first people to be confirmed to have this variant, in a country the media pay attention to, at a time when we've actually noticed that this variant exists and when there is much attention being paid towards this variant.









						Israeli doctor believes he caught Omicron variant of Covid in London
					

Exclusive: Cardiologist Elad Maor suspects he caught virus at conference attended by more than 1,200 people




					www.theguardian.com


----------



## PursuedByBears (Dec 1, 2021)

Just messaged my team to say that I won't be in the office for our team day tomorrow because "I think that we need to pause and gather more data before blithely assuming that the Omicron variant is mostly harmless".  Let's see how that goes down...  I'll wait a couple of days before I tell them I'm not coming to the Christmas meal on Fri 10th as well.


----------



## 8ball (Dec 1, 2021)

PursuedByBears said:


> Just messaged my team to say that I won't be in the office for our team day tomorrow because "I think that we need to pause and gather more data before blithely assuming that the Omicron variant is mostly harmless".  Let's see how that goes down...  I'll wait a couple of days before I tell them I'm not coming to the Christmas meal on Fri 10th as well.



I think "mostly harmless" is a long way from most current estimations.


----------



## Yossarian (Dec 1, 2021)

Cases doubling day-on-day in South Africa seems like an ominous - omicronous? - sign.









						South Africa's new COVID cases double in 1 day amid omicron | AP News
					

JOHANNESBURG (AP) — South Africa's new cases of COVID-19 nearly doubled in a day, authorities reported Wednesday, signaling a dramatic surge in the country where scientists detected the omicron variant last week.




					apnews.com


----------



## 2hats (Dec 2, 2021)

Positivity rate also rocketing (=> climb in case numbers is not an artefact of testing).






Perhaps take the following with a large pinch of salt (certainly unconfirmed/preliminary)...

Separately some Israeli journalists are reporting on a report*, providing numbers that indicate that omicron is around twice as likely to infect (mRNA) vaccinees (two-dose within six months or triple-dosed) as delta has been, whilst the unvaccinated are 2.4 times as likely to get infected by omicron as they were previously by delta. They also claim a similar level of protection to delta for those vaccinees against severe disease, whilst omicron's R is put at around 1.3x that of delta.

* Note: a report of a report, that the Israeli Ministry of Health say they don't have.


----------



## 2hats (Dec 2, 2021)

Possible indication of growing omicron community transmission in England - PCR SGTF rising in recent days.


----------



## skyscraper101 (Dec 2, 2021)

Japan has now reversed its travel ban owing to 'mild' variant









						Coronavirus U-turn: Japan partly reverses Covid travel ban as Omicron variant increasingly appears to be ‘mild‘ mutation
					

A ban on new incoming flight bookings in Japan has been dropped, the country's government said this morning. The policy, aimed at halting the new Omicron




					www.cityam.com


----------



## Yossarian (Dec 2, 2021)

skyscraper101 said:


> Japan has now reversed its travel ban owing to 'mild' variant
> 
> 
> 
> ...



Not sure if there's a connection between Japan changing the travel policy and reports of omicron symptom being mild - they reversed the ban on new incoming international bookings after they were accused of abandoning Japanese nationals overseas, the ban on non-Japanese citizens announced Monday is still in place.


----------



## gentlegreen (Dec 2, 2021)




----------



## skyscraper101 (Dec 2, 2021)

Yossarian said:


> Not sure if there's a connection between Japan changing the travel policy and reports of omicron symptom being mild - they reversed the ban on new incoming international bookings after they were accused of abandoning Japanese nationals overseas, the ban on non-Japanese citizens announced Monday is still in place.



Fair enough. I skim read it and didn't realize it was only a partial reversal.


----------



## elbows (Dec 2, 2021)

Yossarian said:


> Not sure if there's a connection between Japan changing the travel policy and reports of omicron symptom being mild - they reversed the ban on new incoming international bookings after they were accused of abandoning Japanese nationals overseas, the ban on non-Japanese citizens announced Monday is still in place.


And excessive emphasis on stories about it being 'mild' continue for pretty obvious reasons, people clinging to hope or justifying not taking much action, or trying to defuse some of the more extreme concerns people leap to when fears over a new variant are high.

Indicators from South Africa continue to follow a pretty typical path so far:



> *Health officials say the new coronavirus variant Omicron has now become dominant in South Africa and is driving a sharp increase in new infections.*
> 
> Some 8,500 new Covid infections were registered in the latest daily figures.
> 
> ...





> The rate of new infections is expected to increase in what is now the beginning of the fourth wave in South Africa, and the national health department says there has also been a slight increase in hospital admissions.





> As with previous variants Beta and Delta, the full picture in South Africa will not become clear until "people get so sick that they need to go to hospital" which is generally "three, four weeks later," says Prof Salim Abdool Karim of the Africa Task Force for Coronavirus.
> 
> "But the feedback we're getting from the ground is that there's really no red flags - we're not seeing anything dramatically different, what we're seeing is what we are used to," he told the BBC's Newsday programme.











						Covid: South Africa new cases surge as Omicron spreads
					

The new Omicron variant has now become dominant, the country's top medical scientists say.



					www.bbc.co.uk
				




I will want to check hospital data rather than rely on descriptions of a 'slight increase'. And if there continue to be no red flags in regards dramatically different proportion of hospitalisations, then fears of incredible health service pressures will come down to the usual factors we've seen with other variants - it will still be a terrible situation if very large numbers of people catch the virus, so I get most concerned about transmissibility and immune escape rather than the variant being more directly deadly to each individual. And thats the same as the concerns of UK authorities at this stage, the usual numbers game, the usual implications.


----------



## 2hats (Dec 2, 2021)

From ECDC Threat Assessment Brief - Implications of the further emergence and spread of the SARS-CoV-2 B.1.1.529 variant of concern (Omicron) for the EU/EEA – first update, 2 Dec 2021.


> The rapid increase of cases, the increase of the effective reproductive number Rt, and the pace of replacement of the Delta VOC by the Omicron VOC in South Africa all suggest that this variant is more transmissible than the Delta VOC, but robust evidence is still lacking and there remains a high uncertainty. Limited evidence gathered from initial cases reported from EU/EEA countries to date also suggests that Omicron may be associated with high transmissibility as high attack rates have been reported among some household contacts.


----------



## elbows (Dec 2, 2021)

Well this is also a sign that not enough testing is being done, but even so.


----------



## elbows (Dec 2, 2021)

2hats said:


> From ECDC Threat Assessment Brief - Implications of the further emergence and spread of the SARS-CoV-2 B.1.1.529 variant of concern (Omicron) for the EU/EEA – first update, 2 Dec 2021.


Ah its been ages since I looked at any ECDC pandemic documents. Some more quotes from that one:



> Current evidence on transmissibility, severity, and immune escape is highly uncertain for the Omicron VOC. However, preliminary data from South Africa suggest that it may have a substantial growth advantage over the Delta VOC. If this is the case, mathematical modelling indicates that the Omicron VOC is expected to cause over half of all SARS-CoV-2 infections in the EU/EEA within the next few months. The greater Omicron's growth advantage over the Delta VOC and the greater its circulation in the EU/EEA, the shorter the expected time until the Omicron VOC causes the majority of all SARS-CoV-2 infections.





> Based on the currently available limited evidence, and considering the high level of uncertainty, the overall level of risk for EU/EEA countries associated with the further emergence and spread of the SARS-CoV-2 Omicron VOC is assessed as HIGH TO VERY HIGH.





> To date, the Omicron VOC has already been introduced into many EU/EEA countries. Given the current limited evidence around this new variant and the concerns about its immune escape properties in relation to available COVID-19 vaccines and treatments, a multi-layered approach to delay the spread of this VOC in the EU/EEA is needed.
> Due to the ongoing circulation of the Delta VOC, EU/EEA countries are urged to give utmost priority towards the vaccination of people initially targeted by COVID-19 vaccination programmes who remain unvaccinated or who are not yet fully vaccinated. Countries should consider a booster dose for people aged 40 years and older, first targeting the most vulnerable and the elderly, and could then consider a booster dose for all adults aged 18 years and older at least six months after completion of the primary series.





> Non-pharmaceutical interventions (NPIs) that have proven to be very effective in reducing transmission of infection should continue to be implemented by countries based on an assessment of their epidemiological situation regarding the Delta VOC, and taking into account the uncertainty of the situation regarding the Omicron VOC. Physical distancing measures, ensuring adequate ventilation in closed spaces, the maintenance of hand and respiratory hygiene measures, the appropriate use of face masks, and staying home when ill all remain relevant.





> Enhanced contact tracing measures such as backward contact tracing and stricter management of contacts could help slow the establishment of the Omicron VOC in the country.
> Genomic surveillance remains of the utmost importance for early detection of the presence of the variant, to enable the following of epidemiological trends and guide containment measures.





> Temporary travel-related measures should be carefully considered in light of the latest epidemiological situation, and should be regularly reviewed as new evidence emerges. Such measures might include the testing and quarantining of travellers who have recently returned from affected countries and sequencing cases identified among travellers. Public information around the emerging situation and the public health measures in place for returning travellers from affected areas are important to raise awareness and support the effective implementation of these measures. However, given the increasing number of cases and clusters in the EU/EEA without a travel history or contact with travel-related cases, it is likely that within the coming weeks the effectiveness of travel-related measures will significantly decrease, and countries should prepare for a rapid and measured de-escalation of such measures.


----------



## elbows (Dec 2, 2021)




----------



## 2hats (Dec 2, 2021)

Preprint of an initial study (NICD/Stellenbosch/others) which suggests that risk of reinfection by omicron for those with natural immunity only (acquired via infection by beta or delta) is 3x higher than for previous VOC.


> Population-level evidence suggests that the Omicron variant is associated with substantial ability to evade immunity from prior infection.







DOI: 10.1101/2021.11.11.21266068.


----------



## weltweit (Dec 2, 2021)

I know Johnston doesn't want the blame for Omicron restrictions over Christmas, but how likely do people think it is that there will be greater restrictions over the Christmas / NY period? 

I suppose we have to wait for the assessments on its virulence.


----------



## elbows (Dec 2, 2021)

Its hard to say. Even without Omicron I would not have wanted to bet against some additional restrictions during winter, although authorities would probably have tried to wait till after Christmas before doing them, making some use of the effect of school holidays in the meantime. And the effects of the booster campaign and prior infections might have meant they got away with only basic stuff rather than the stronger things people often think of when they hear the word restrictions.

With Omicron, it would probably require amost all of the news about Omicrons properties to be very good news in order for the modellers to not come up with results that are extremely worrying to the authorities. But even if all the news is very bad, with resulting scary modelling about the potential consequences of another wave, the timing may yet allow the government to avoid the heavier measures until we progress into January. But the high rates of Delta infection that have been allowed to persist in the UK are an additional complication, robbing authorities of some of the wiggle room that would otherwise be available if an Omicron wave started from scratch rather than building on top of the ugly Delta picture. However the declines seen in hospitalisations, presumably as a result of the young ages of those getting infected the most recently, and also as the result of the booster effects, reintroduces a bit of wiggle room on some key fronts.

So I wouldnt bet on many more restrictions in December, although I could end up saying something different in a weeks time. If the estimates of this variants properties turn out to be especially grim, or the real-world UK data starts to show new alarming properties, even this government might yet feel compelled to act in December. But school holidays arent too many weeks away and the government may fancy their chances of at least being able to drag things out beyond Christmas.


----------



## Raheem (Dec 2, 2021)

Regardless of the impact of omicron, the government has followed a pattern of delaying as much as they can, and now they also seem to be abandoning the line that they are "following the science". I would expect the intention is to delay past Christmas in all eventualities.


----------



## weltweit (Dec 2, 2021)

Hi elbows yes those are pretty much my feelings. My son and his mum are planning to visit family in Spain and I am a bit worried about their return trip in case either of them contracts covid and fail their last minute test while they are there. Nothing I can do about it though.


----------



## elbows (Dec 2, 2021)

Plus dont forget there is already one announced measure that authomatically ramps up if Omicron starts to make up a more notable proportion of cases here. That being the rules where you dont need to self isolate if you are deemed to be a close contact but are vaccinated - these rules that were part of the summer easing have been changed this week so that they do not apply if the person who tested positive is suspected to have the Omicron variant. So there will far be more people told to isolate if Omicron grows, and the relaxed version of those rules are dead if Omicron dominates because every case will be assumed to be Omicron at that point.


----------



## StoneRoad (Dec 2, 2021)

The gov't will be relying on the vaccines / boosters to do the heavy lifting.
Depiffle seems incapable of pre-empting problems and only reacting, and slowly at that.

Yeah, some harder restrictions - or actually enforcing the existing isolation / mask mandates & maybe extending them to something sensible ? well, I'm expecting something after chrimble.


----------



## elbows (Dec 2, 2021)

The authorities will also be interested to see what impact the Omicron news and peoples sense of winter caution has on behaviour and the spread of Delta in the coming weeks.


----------



## wemakeyousoundb (Dec 2, 2021)

Which date is the "every kid goes back to school" U-turn scheduled for in January, is it the 3rd?


----------



## zahir (Dec 3, 2021)

Suggestion here of omicron leading to increased hospitalisation of children


----------



## zahir (Dec 3, 2021)

Thread


----------



## zahir (Dec 3, 2021)

elbows (or anyone else) does the thread above sound accurate?


----------



## Raheem (Dec 3, 2021)

Hope fucking not, because if it's not some sort of nonsense or false alarm we're going to be locked down soon, hard and for a long time.

(ETA: er, and obviously because I don't want children to be hospitalised with Covid.)


----------



## zahir (Dec 3, 2021)

Yes, I'm not sure what to make of it tbh.


----------



## teuchter (Dec 3, 2021)

That thread looks a bit sketchy to me.


----------



## Raheem (Dec 3, 2021)

teuchter said:


> That thread looks a bit sketchy to me.


He seems to have got the data from another Twitter account, and it's not clear where they got it.


----------



## 8ball (Dec 3, 2021)

elbows said:


> The authorities will also be interested to see what impact the Omicron news and peoples sense of winter caution has on behaviour and the spread of Delta in the coming weeks.



My feeling is that a good proportion of people have had enough of it, and Johnson will be forced to take stronger measures.


----------



## 2hats (Dec 3, 2021)

The graphed data are genuine; those are slides from a NICD presentation. Paediatric admissions are certainly up but proportions could be skewed as children may be more likely to be admitted as a precaution. As with other aspects of omicron this needs some more time to clarify.


----------



## Raheem (Dec 3, 2021)

Ok, but why would children be more likely to be admitted as a precaution?

Don't answer. I should be in bed.


----------



## 8ball (Dec 3, 2021)

Raheem said:


> Ok, but why would children be more likely to be admitted as a precaution?
> 
> Don't answer. I should be in bed.



That occurred to me too.


----------



## MrCurry (Dec 3, 2021)

If omicron is affecting the young proportionately more than previous variants have, is that an indication that those with stronger immune systems might be more vulnerable to serious illness from it, or is that too simplistic?


----------



## LDC (Dec 3, 2021)

Raheem said:


> Ok, but why would children be more likely to be admitted as a precaution?
> 
> Don't answer. I should be in bed.



Children go downhill quickly and sometimes scarily so. Little bodies good at compensating until suddenly they're not. Also hard to get good history of how they feel etc. sometimes.


----------



## Numbers (Dec 3, 2021)

8ball said:


> That occurred to me too.


That they should be in bed?


----------



## zahir (Dec 3, 2021)

This South African press report looks less alarmist.









						Covid patients aged under 2 have highest admission rate in South African epicentre
					

Increase in admissions among very young 'could be precautionary', says doctor




					www.thenationalnews.com
				





> There were about 455 admissions from November 11 to 28 in the Gauteng city of Tshwane, where eight people have died, Dr Jassat said during a televised government media briefing on Monday.
> In Tshwane, which has recorded the highest increases in admissions, there has been “a very sharp increase”, particularly in the past 10 days, she said.
> “When you look at the numbers of admissions by age, what we normally see is a large number of admissions in older people,” she added.
> “But in this early resurgence in Tshwane, we are seeing most admissions in the 0-2 age group.
> ...


----------



## zahir (Dec 3, 2021)




----------



## elbows (Dec 3, 2021)

2hats said:


> The graphed data are genuine; those are slides from a NICD presentation. Paediatric admissions are certainly up but proportions could be skewed as children may be more likely to be admitted as a precaution. As with other aspects of omicron this needs some more time to clarify.



Yes and people should also be made aware that we heard similar things when Delta took off in India earlier in 2021.

There are a bunch of factors that can lead to such reports, very much including the age groups most affected by spiralling infection rates at the time. Concerns about children have extra power to them that people understandably latch onto and amplify. Authorities may even be tempted to make use of this if they are facing a situation where the population dont seem to be taking things seriously enough.

None of that excludes the possibility that a variant may have a different impact on the young, but with Covid in general the risks are so extremely heavily linked to increasing age that even a fair shift in the underlying reality will still leave the older members of society most at risk.

Also the ages of people being vaccinated makes a difference to that picture. Where vaccines protect the older people, its going to skew the proportions so that younger, unvaccinated people start to make up a greater proportion of those requiring hospital treatment.


----------



## elbows (Dec 3, 2021)

Another reason we might not be best placed to fit such emerging details into our existing understanding of the pandemic is that frankly the situation with children in the UK has been rather underplayed so far.

For example, last time I did the figures (going up to 27th November), in England there had been 5765 hospital admissions/diagnoses of children aged 0-5, and 6074 in those aged 6-17. I dont have death figures to hand but I believe it may be over 100 for the UK so far.

Also the demographics for South Africa are fairly different to ours, and I lack knowledge about which groups were largely spared being infected in past waves there.

None of this means I am saying there is nothing of note to see in the data and reports from South Africa. I'm just drawing attention to other aspects to get a more rounded picture. There is nothing I can say that can short-cut the waiting game in regards discovering the reality of what Omicron is bringing to the pandemic.


----------



## elbows (Dec 3, 2021)

Todays Indie SAGE:



A bunch of the Omicron slides from it which I screengrabbed. I've put them in spoilers since there are quite a lot of them.

The young admissions data is most certainly of concern, though I wont be able to build on those concerns too much until/unless the same pattern is repeated elsewhere or more clinical info emerges.



Spoiler


----------



## Supine (Dec 3, 2021)

Risk Assessment released


----------



## 2hats (Dec 3, 2021)

SARS-CoV-2 variants of concern and variants under investigation in England Variant of concern: Omicron, VOC21NOV-01 (B.1.1.529) Technical briefing 30.


----------



## elbows (Dec 3, 2021)

Covid in Scotland: Omicron cases linked to Steps concert in Glasgow
					

The number of cases in Scotland increases to 29, including six linked to a Steps concert in Glasgow.



					www.bbc.co.uk


----------



## steeplejack (Dec 3, 2021)

fuck's sakes.

will this ever, ever end?


----------



## Steel Icarus (Dec 3, 2021)

8ball said:


> I think "mostly harmless" is a long way from most current estimations.





steeplejack said:


> fuck's sakes.
> 
> will this ever, ever end?


Of course. All things must pass.


----------



## elbows (Dec 3, 2021)

SAGE meeting minutes from 29th November (the ones that were leaked to the BBC some days ago).



			https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1037831/SAGE_97_Minutes_29_November_2021.pdf
		




> Even if there continues to be good protection against severe disease for individuals from vaccination (including boosters), any significant reduction in protection against infection could still result in a very large wave of infections. This would in turn lead to potentially high numbers of hospitalisations even with protection against severe disease being less affected. The size of this wave remains highly uncertain but may be of a scale that requires very stringent response measures to avoid unsustainable pressure on the NHS. If vaccine efficacy is substantially reduced, then a wave of severe disease should be expected.





> It is important to be prepared for a potentially very significant wave of infections with associated hospitalisations now, ahead of data being available.


----------



## 2hats (Dec 3, 2021)

2hats said:


> SARS-CoV-2 variants of concern and variants under investigation in England Variant of concern: Omicron, VOC21NOV-01 (B.1.1.529) Technical briefing 30.


(Fig. 10, p. 28) PCR SGTF (probably => omicron) notably rising fastest in SE, London and E Midlands.


----------



## gentlegreen (Dec 3, 2021)

so ordinarily the PCR spits out "positive or negative" and they don't pay attention to the distribution of markers ?

The cat is definitely out of the bag ... presumably to be confirmed by some sequencing of old samples ?


----------



## Badgers (Dec 3, 2021)

steeplejack said:


> fuck's sakes.
> 
> will this ever, ever end?


Smallpox did


----------



## gentlegreen (Dec 3, 2021)

Badgers said:


> Smallpox did


polio is close to ending - if it wasn't for some very extreme antivaxxers ...


----------



## elbows (Dec 3, 2021)

gentlegreen said:


> so ordinarily the PCR spits out "positive or negative" and they don't pay attention to the distribution of markers ?
> 
> The cat is definitely out of the bag ... presumably to be confirmed by some sequencing of old samples ?


They've been doing genomic sequencing on a proportion of samples for a very long time. One of the resons it would have been better to have less cases every day would be that then we could have sequened a far higher proportion of them.

Even if we sequenced every sample there are still some delays in getting that full picture, so the use of checking for things like S gene dropout that a bunch of the standard PCR labs can check for is something we've used before to get a quicker picture of a new variant taking over.


----------



## Cloo (Dec 3, 2021)

Well, that all sucks. But what's also going suck now is all the twats going 'Ohhh, so they've _conveniently _got another dangerous "variant" now and of course they'll be one next year and the year after that. Ohhh, how convenient'


----------



## weltweit (Dec 3, 2021)

Update on Omicron
					

On 26 November 2021, WHO designated the variant B.1.1.529 a variant of concern, named Omicron, on the advice of WHO’s Technical Advisory Group on Virus Evolution (TAG-VE).  This decision was based on the evidence presented to the TAG-VE that Omicron has several mutations that may have an impact...




					www.who.int


----------



## elbows (Dec 3, 2021)

WHO 'dont panic' comments seem useless to me, and have the potential to be counterproductive in two different directions. I'm not impressed by that bit, though warnings to prepare are much more sensible.









						Covid: Don't panic about Omicron variant, WHO says
					

The World Health Organization urges people to be cautious and prepare for the Omicron variant.



					www.bbc.co.uk


----------



## Riklet (Dec 3, 2021)

Cloo said:


> Well, that all sucks. But what's also going suck now is all the twats going 'Ohhh, so they've _conveniently _got another dangerous "variant" now and of course they'll be one next year and the year after that. Ohhh, how convenient'



Yeah at work my boss was making comments along the lines of "Omicron just before Ghislaine Maxwell's trial.. how convenient" Gawd.

It's worrying the number of cases found in the UK. Either cos we are looking harder or we have more community transmission. Sucks though. Can already see my holiday to Portugal in January not happening now...


----------



## kenny g (Dec 4, 2021)

MrCurry said:


> Deffo a good idea to have a thread dedicated to this one variant, IMHO.
> 
> I’m worried now about my 80+ parents, who after weathering the early part of the pandemic by shielding and allowing others to do shopping for them have, post vaccination, returned to going to the supermarket once a week, plus other shops.
> 
> The sooner we have confirmed info on how much Omicron defeats the current vaccine, the better, as even if I start lobbying them to isolate I know they‘re going to resist.  Nothing was helped by the Daily Mail (their favourite source of propagandist disinformation) having the headline “Experts say jabs WILL work on variant” on the front page yesterday.  Simultaneously technically correct and massively misleading, in the truest DM tradition.


My parents are 80 and active and when you reach that age the risk benefit analysis from isolating becomes complicated and definitely one for people to do themselves. I fully understand my dad wanting to have a social life and won't stand in his way.


----------



## MrCurry (Dec 4, 2021)

kenny g said:


> My parents are 80 and active and when you reach that age the risk benefit analysis from isolating becomes complicated and definitely one for people to do themselves. I fully understand my dad wanting to have a social life and won't stand in his way.


Yeah, I understand their view, which is that something is going to kill them before too long, so they may as well keep doing the things they enjoy while they still can. Like you say, it’s complicated.  I just don’t think they take decisions based on good info.

My dad will say things like “it said in the paper there’s only two cases of this new variant in the U.K., and neither is anywhere near us”, as though the reporting in the Daily Mail is a live readout of the current location of every copy of the virus on that particular day.

They also seem to think that wearing masks in shops gives them total protection.


----------



## Boru (Dec 4, 2021)

Ireland announcedd new restrictions yesterday evening in light of recent developments.. not quiet a lockdown but significant restrictions heading for Christmas.
Fresh restrictions after 'stark' NPHET advice


----------



## Cloo (Dec 4, 2021)

kenny g said:


> My parents are 80 and active and when you reach that age the risk benefit analysis from isolating becomes complicated and definitely one for people to do themselves. I fully understand my dad wanting to have a social life and won't stand in his way.


My parents are in their 70s and and I know my dad's view is that he'll take his chances because he's had his life and it's not fair younger people should have their lives on hold to protect him. But of course, not everyone feels the same.


----------



## weepiper (Dec 4, 2021)

Well, this is pretty alarming.


----------



## StoneRoad (Dec 4, 2021)

Yeah, I'm not looking forward to the next few weeks and months.

I don't think vaccinations alone, or even with masks & social distancing, will keep this variant from pushing a huge wave of infections. However much depiffle wants not to, something more serious in terms of measures are going to be needed.

Also reinforces the point that high case rates encourage mutations when there hasn't been enough vaccinations.


----------



## Pickman's model (Dec 4, 2021)

I thought they were being premature at work when they took down the one way system signs etc some weeks back


----------



## _Russ_ (Dec 4, 2021)

weepiper said:


> Well, this is pretty alarming.



If that is true and Omicron also turns out to cause serious illness in the vaccinated then we are truly fucked, the quote of 80-90 people being positive gives me some hope that it has some incorrect info in it. (its either 80 or 90 or the writer doesnt know, so the writer may have other stuff wrong)


----------



## cupid_stunt (Dec 4, 2021)

_Russ_ said:


> If that is true and Omicron also turns out to cause serious illness in the vaccinated then we are truly fucked, the quote of 80-90 people being positive gives me some hope that it has some incorrect info in it. *(its either 80 or 90* or the writer doesnt know, so the writer may have other stuff wrong)



BIB, why do you think that? It could be any number between 80 & 90.


----------



## xenon (Dec 4, 2021)

The news reports on that super spreader incident also said simptoms were mild. No one of that lot has been hospitalised.


----------



## _Russ_ (Dec 4, 2021)

cupid_stunt said:


> BIB, why do you think that? It could be any number between 80 & 90.


I've tried the find the mention of that number range in the story she links to (reuters)
 but can't find it, im not sure where that comes from


Xenon, got a link to when the party happened?


----------



## 2hats (Dec 4, 2021)

> Viral genomes deduced from these 2 SARS-CoV-2‒positive cases differed only by 1 nt. Retrospective investigation, including closed-circuit television camera footage, confirmed that neither case-patient left their room during the quarantine period. No items were shared between rooms, and other persons did not enter either room. The only time the 2 quarantined persons opened their respective doors was to collect of food that was placed immediately outside each room door. The only other time they might have opened their doors would be for RT-PCRs, which were conducted in 3-day intervals. However, because these 2 case-patients arrived 1 day apart, it is unlikely that they would be tested on the same day. *Airborne transmission across the corridor is the most probable mode of transmission.*











						Probable Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel, Hong Kong, China, November 2021
					

Probable Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel, Hong Kong, China




					wwwnc.cdc.gov


----------



## MrCurry (Dec 4, 2021)

2hats said:


> Probable Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel, Hong Kong, China, November 2021
> 
> 
> Probable Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel, Hong Kong, China
> ...


Presumably they can’t rule out surface borne transmission from the food and utensils which were being delivered to their doors? Even if the people handling those items in the quarantine centre are being tested, there must be a supply chain which physically handles food before it arrives there?


----------



## xenon (Dec 4, 2021)

_Russ_ said:


> I've tried the find the mention of that number range in the story she links to (reuters)
> but can't find it, im not sure where that comes from
> 
> 
> Xenon, got a link to when the party happened?



Nov 26th according to this.








						Omicron outbreak at Norway Christmas party is biggest outside South Africa, authorities say
					

At least 13 people in Oslo have been infected with the Omicron variant of the coronavirus following a corporate Christmas party described as a "superspreader event," and their numbers could rise to over 60 cases, authorities said on Friday.




					edition.cnn.com
				




Granted if people are going to be hospitalised with covid19, it can happen a week or 2 after initial infection IIRC. And by definition it's likely most attending were of working age.

But it could also just be that omicron is more transmissible but no more deadly. A problem in itself I know, as a small percentage of a huge number of cases could still cause too much pressure on health services.

tl/dr no point fretting about it being more dangerous than delta til more is known.


----------



## cupid_stunt (Dec 4, 2021)

75 new cases found in England, bringing the total across the UK to 134. 

* BBC TV News


----------



## cuppa tee (Dec 4, 2021)

2hats said:


> Probable Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel, Hong Kong, China, November 2021
> 
> 
> Probable Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel, Hong Kong, China
> ...



heres another theory, number 2 picked it up in the airport terminal.


----------



## zahir (Dec 4, 2021)

A summary of where we're up to with omicron









						Rupert Beale · On Omicron · LRB 4 December 2021
					

Since Delta, every variant from Epsilon to Kappa has been downgraded, with Lambda and Mu still designated as merely '...




					www.lrb.co.uk


----------



## 2hats (Dec 4, 2021)

Fresh from the 'mutations' thread, for those who don't subscribe.








						Omicron variant may have picked up a piece of common-cold virus
					

The Omicron variant of the virus that causes COVID-19 likely acquired at least one of its mutations by picking up a snippet of genetic material from another virus - possibly one that causes the common cold - present in the same infected cells, according to researchers.




					www.reuters.com


----------



## elbows (Dec 4, 2021)

2hats said:


> Fresh from the 'mutations' thread, for those who don't subscribe.
> 
> 
> 
> ...


Ah, as you may recall I've been waiting for any signs of recombination for ages, perhaps this is the first clear sign of such things.

I suppose this will increase speculation about both increased transmissibility and also the whole 'mild' thing. I dont think I'll be able to tell the difference between good news, bad news or a mix of bad and good news on this front for a while yet. I also end up wondering whether it may have anything to do with the hospitalised age patterns that have shown up in South Africa data.


----------



## Cloo (Dec 4, 2021)

xenon said:


> The news reports on that super spreader incident also said simptoms were mild. No one of that lot has been hospitalised.


Let's hope but there's a bit of lag for hospitalisation. I guess the issue is that even if it is mild and hospitalises, say half as many people, if it infects 5 times as many then we're pretty fucked.


----------



## 2hats (Dec 4, 2021)

cuppa tee said:


> heres another theory, number 2 picked it up in the airport terminal.


Maybe you missed the fact that the SARS-CoV-2 genomes of each patient, who arrived on different days, differed by a single nucleotide?


----------



## cuppa tee (Dec 4, 2021)

2hats said:


> Maybe you missed the fact that the SARS-CoV-2 genomes of each patient, who arrived on different days, differed by a single nucleotide?


I don’t even know what that means tbh.


----------



## 2hats (Dec 4, 2021)

cuppa tee said:


> I don’t even know what that means tbh.


The implication of such a small difference (the smallest possible) is that it is extremely likely that one infected the other.


----------



## cuppa tee (Dec 4, 2021)

2hats said:


> The implication of such a small difference (the smallest possible) is that it is extremely likely that one infected the other.



it actually freaks me out that we (not me obvs) are capable of measuring something so tiny with anything approaching accuracy 🙁


----------



## Aladdin (Dec 4, 2021)

cuppa tee said:


> it actually freaks me out that we (not me obvs) are capable of measuring something so tiny with anything approaching accuracy 🙁




Makes me have even more faith in science.


----------



## 2hats (Dec 4, 2021)

MrCurry said:


> Presumably they can’t rule out surface borne transmission from the food and utensils which were being delivered to their doors? Even if the people handling those items in the quarantine centre are being tested, there must be a supply chain which physically handles food before it arrives there?


The clear (genomic) implication is that one traveller was infected by the other.


----------



## kenny g (Dec 4, 2021)

MrCurry said:


> Yeah, I understand their view, which is that something is going to kill them before too long, so they may as well keep doing the things they enjoy while they still can. Like you say, it’s complicated.  I just don’t think they take decisions based on good info.
> 
> My dad will say things like “it said in the paper there’s only two cases of this new variant in the U.K., and neither is anywhere near us”, as though the reporting in the Daily Mail is a live readout of the current location of every copy of the virus on that particular day.
> 
> They also seem to think that wearing masks in shops gives them total protection.


Maybe because that is easier than saying "I am likely to have at most ten years of good life ahead of me so I may as well not spend three of it cooped up in a shell".


----------



## kenny g (Dec 4, 2021)

I have my faith in the O being amazingly transmissible and relatively safe. Call me an optimist.


----------



## elbows (Dec 4, 2021)

> Just over 100 of the 120 people who participated were infected with corona during the evening.
> 
> So far, 13 cases have been confirmed to become ill by the new variant omikron.





> A staff party for the Norwegian energy company Scatec has come into the spotlight as Europe's first super-spreader event for the new corona variant omikron.
> 
> On Friday, just over a week ago, Scatec invited 120 of its employees to a Christmas dinner at Louise Restaurang och Bar in Oslo. According to the company, infection control measures had been taken and all present were vaccinated and tested for covid-19.
> 
> Despite this, almost 100 people were infected that evening. Exactly how many of the infected belong to Scatec's staff is not known. The evening ended in a public area with other restaurant guests.





> The person who is believed to have caused the spread of infection is an employee at Scatec who returned from South Africa a few days earlier.
> 
> Scatec spokesman Stian Tvede Karlsen tells the New York Times that the person, who was the first to test positive for covid-19, came home to Norway from a business trip before the new variant from South Africa was on everyone's lips.





> - This wave seems to go much faster than the delta wave, and we thought that the delta wave was very fast. It's incredible, says Juliet Pulliam, head of epidemiological modeling and analysis at Stellenbosch University in South Africa, to the American media company NPR.
> 
> An analysis that she and her colleagues have done shows that the omicron variant is extremely contagious and seems to have a greater ability to get past the immune system than the delta variant has.
> 
> - There is a great deal of uncertainty in the analysis, but I would say that it is probable, Pulliam explains to NPR.



Machine translated from Så blev julbordet ett superspridarevent


----------



## elbows (Dec 4, 2021)




----------



## mx wcfc (Dec 4, 2021)

elbows said:


>



Why wait till sodding Tuesday - it's just like delta - stand back, hold the door wide open, whilst acting tough.

The fuckers learn nothing.


----------



## MrCurry (Dec 4, 2021)

2hats said:


> The clear (genomic) implication is that one traveller was infected by the other.


So that result wouldn’t be seen if they had both been infected by a single third party?


----------



## Steel Icarus (Dec 4, 2021)

mx wcfc said:


> Why wait till sodding Tuesday - it's just like delta - stand back, hold the door wide open, whilst acting tough.
> 
> The fuckers learn nothing.


Mrs SI thinks they can't as it has to go through parliament. I don't think it does. Who's right?


----------



## weltweit (Dec 4, 2021)

Well I imagine the airlines need a bit of warning, and the people who will be arranging quarantine etc ..


----------



## mx wcfc (Dec 4, 2021)

They don't have to do those things if they don't want to.  They will make excuses,


----------



## elbows (Dec 4, 2021)

S☼I said:


> Mrs SI thinks they can't as it has to go through parliament. I don't think it does. Who's right?


I'm not too knowledeable about such matters but I think the travel-related stuff doesnt require a vote. I say that because I dont recall votes whenever they've changed the red list and other travel rules in the past. And they had votes on November 30th when they wanted to change domestic stuff in response to Omicron - they had a vote for changing the self-isolation rules to incorporate Omicron stuff, and a vote for the new mask rules.


----------



## LDC (Dec 4, 2021)

S☼I said:


> Mrs SI thinks they can't as it has to go through parliament. I don't think it does. Who's right?



I'm pretty sure you are.





__





						The Health Protection (Coronavirus, International Travel) (England) Regulations 2020 (revoked)
					

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .




					www.legislation.gov.uk


----------



## MrSki (Dec 4, 2021)

The vote for the new mask rules was after the rules came into affect. 4am in the morning & vote was not till later that afternoon.


----------



## elbows (Dec 4, 2021)

LynnDoyleCooper said:


> I'm pretty sure you are.
> 
> 
> 
> ...


I think that one got revoked and replaced with this one earlier in 2021. I havent tried to wade through it and see if it requires further changes or already has built in mechanisms to change certain details without needing to change the legislation.





__





						The Health Protection (Coronavirus, International Travel and Operator Liability) (England) Regulations 2021
					

These Regulations replace the Health Protection (Coronavirus, International Travel) (England) Regulations 2020 (“the International Travel Regulations”), the Health Protection (Coronavirus, Public Health Information for International Passengers) (England) Regulations 2020 and the Health...




					www.legislation.gov.uk


----------



## 2hats (Dec 4, 2021)

MrCurry said:


> So that result wouldn’t be seen if they had both been infected by a single third party?


Far less likely. The incubation windows don't allow much wriggle room, even for quarantine hotel staff, who are reported to have repeatedly tested negative anyway (sounds like food was left for the quarantinees; not clear on details of PCR procedure but again could have been self-sampling with no contact, besides which, the report infers it was performed on different days for each).


----------



## elbows (Dec 5, 2021)

Speaking of incubation windows:



> On Saturday, On Saturday Downing Street announced that it was introducing pre-departure tests for people travelling to the UK. From 4am on Tuesday, travellers will have to complete a lateral flow or PCR test 48 hours before entering the country. Nigeria has been added to the red list, and from 4am on Monday arrivals will have to quarantine in hotels. Officials said the moves came as evidence emerged that the Omicron strain had been reported in more than 40 countries, with apparent community transmission in places such as Norway. *They also said there was evidence that the incubation period was shorter than for other variants.*











						UK’s progress on Covid now squandered, warns top scientist
					

Sir Jeremy Farrar, director of Wellcome Trust, suggests emergence of Omicron variant means pandemic is far from over




					www.theguardian.com


----------



## kenny g (Dec 5, 2021)

S☼I said:


> Mrs SI thinks they can't as it has to go through parliament. I don't think it does. Who's right?


It doesn't have to go through parliament. Amusingly enough considering your board name. Under the health act the secretary of state can sign off an SI ( statutory instrument) without parliamentary pre approval. Look at the intro to the recent mask SI.

Or this intro where it is laid before parliament but there is no requirement for approval. The Health Protection (Coronavirus, International Travel and Operator Liability) (England) Regulations 2021


----------



## LDC (Dec 5, 2021)

elbows said:


> I think that one got revoked and replaced with this one earlier in 2021. I havent tried to wade through it and see if it requires further changes or already has built in mechanisms to change certain details without needing to change the legislation.
> 
> 
> 
> ...



Ah yeah, even says 'revoked' in the title!


----------



## Aladdin (Dec 5, 2021)

Our Tanaiste Leo Veradkar has announced that the pandemic is far from over and we can expect variants and restrictions for the next 5 years.
He also said we should do everything we can to curb spread so we can have a really good summer in 2022.









						Varadkar says we need to make the most of summer, next winter could be difficult
					

“I’m determined that should not be the case next summer, that we should open safely if we can and not have the toughest restrictions in Europe in the summer of 2022."




					www.google.com
				



🤔

I'm not convinced summer next year will be any better than now.


----------



## kabbes (Dec 5, 2021)

Can I fact-check something that is slightly confusing me?

On the one hand, we have talk of Omicron "outcompeting" Delta.  Whether it will replace or supplant it in the population.
On the other hand, though, we have the evidence that antibodies produced against Delta (be they organic or vaccine-induced) may not be effective against Omicron. 

So question 1 -- if Delta antibodies are ineffective against Omicron then presumably that's also true in reverse?
Question 2 -- leading on from that, if their antibodies are mutually ineffective then why would one replace the other?  Surely both can circulate in the population unimpeded by the other?  You could quite legitimately get Delta and then Omicron or Omicron and then Delta.


----------



## Supine (Dec 5, 2021)

Q1 - the premise is probably wrong. There is evidence that antibodies may be less effective. Certainly not ineffective. 

Q2 - Both can circulate. If omicron can spread more effectively it starts to win the race because more people get it. So the numbers go up quicker than for delta. Also, if there is more reinfection it has a wider range of hosts available which also helps it.


----------



## kabbes (Dec 5, 2021)

Supine said:


> Q2 - Both can circulate. If omicron can spread more effectively it starts to win the race because more people get it. So the numbers go up quicker than for delta. Also, if there is more reinfection it has a wider range of hosts available which also helps it.


Why is it a “race” though, if antibodies don’t provide mutual protection?  (Accepting that this is not necessarily actually the case). It’s then no more a race than COVID races against flu.


----------



## Supine (Dec 5, 2021)

kabbes said:


> Why is it a “race” though, if antibodies don’t provide mutual protection?  (Accepting that this is not necessarily actually the case). It’s then no more a race than COVID races against flu.



Its not a race for covid, it just floats around and replicates. Antibodies will neutralise it, perhaps to differing levels.


----------



## LDC (Dec 5, 2021)

kabbes said:


> Can I fact-check something that is slightly confusing me?
> 
> On the one hand, we have talk of Omicron "outcompeting" Delta.  Whether it will replace or supplant it in the population.
> On the other hand, though, we have the evidence that antibodies produced against Delta (be they organic or vaccine-induced) may not be effective against Omicron.
> ...



_I think _(iirc from listening to an interview with an immunologist recently) then the bit I highlighted is actually possible - quick re-infection and _possibly_ concurrent infections with both.

The rest just makes my head feel like it's going to explode.


----------



## kabbes (Dec 5, 2021)

Supine said:


> Its not a race for covid, it just floats around and replicates. Antibodies will neutralise it, perhaps to differing levels.


I think you're not grasping what I'm saying.  Or possibly vice versa.

If antibodies don't mutually "work" to eliminate both variants then from _our _point of view, these are essentially two different diseases.  Omicron won't replace Delta because somebody who has already had Omicron can still get Delta.  This is fundamentally different to Alpha and Delta, whereby somebody who has had Delta now (basically) can't get Alpha.  In the latter case, Delta outcompeted Alpha and Alpha disappeared.  However, in the former case, there is nothing to stop Omicron and Delta co-existing.

Now, if antibodies _do_ mutually "work" to eliminate both variants then fine, the competition happens and only one variant wins.  But this seems to be far from certain right now.  The hope is there, but not the sure knowledge.

And sure, you get an interesting non-linear dynamic system akin to a multiple predator-prey model where the antibodies are partially mutually effective.  In this case, my expectation is that there is no stationary point to the system, and each will see flare ups over time.  But if this happens, we are effectively looking at a long-term two-variant system, not a system in which one variant replaces the other.


----------



## xenon (Dec 5, 2021)

kabbes said:


> Why is it a “race” though, if antibodies don’t provide mutual protection?  (Accepting that this is not necessarily actually the case). It’s then no more a race than COVID races against flu.



Not sure I understand your question.

AIUI the idea. if a large section of the population has delta antibodies, however gained. There is obviously an increasingly  smaller  susceptible body of  hosts for it to infect.

Omicron turns up and these antibodies can't completely defeat it, so it has a vastly greater susceptible host population. If other features of it, viral load, upper airway reproduction means it can also spread more easily, that would also give it an advantage in overtaking delta.


----------



## xenon (Dec 5, 2021)

You can presumably simultaniously have antibodies that can fight off delta and omicron. Even if these delta antibodies fade after some time, delta could have already run out of enough hosts to efficiently circulate by then.


----------



## kabbes (Dec 5, 2021)

xenon said:


> Not sure I understand your question.
> 
> AIUI the idea. if a large section of the population has delta antibodies, however gained. There is obviously an increasingly  smaller  susceptible body of  hosts for it to infect.
> 
> Omicron turns up and these antibodies can't completely defeat it, so it has a vastly greater susceptible host population. If other features of it, viral load, upper airway reproduction means it can also spread more easily, that would also give it an advantage in overtaking delta.


But if antibodies against Omicron aren't (strongly) effective against Delta (and why would they be, if the reverse isn't true?), the fact that somebody has had Omicron doesn't stop them carrying on getting Delta.  In that case, Omicron is no more a limiting factor against the spread of Delta than the 'flu is.  What you're saying only works in the one-way situation in which Omicron antibodies stop Delta but Delta antibodies don't stop Omicron.


----------



## kabbes (Dec 5, 2021)

kabbes said:


> What you're saying only works in the one-way situation in which Omicron antibodies stop Delta but Delta antibodies don't stop Omicron.


This is the crux of it, for me.  A lot of what is being written about Omicron replacing Delta implicitly makes the assumption that there is this one-way relationship.


----------



## Aladdin (Dec 5, 2021)

None of this sounds good to me...
If Omicron can spread rapidly and mutates further as it spreads, how fucked are we? "We" being those most vulnerable like the elderly and immunocompromised?


----------



## xenon (Dec 5, 2021)

kabbes said:


> But if antibodies against Omicron aren't (strongly) effective against Delta (and why would they be, if the reverse isn't true?), the fact that somebody has had Omicron doesn't stop them carrying on getting Delta.  In that case, Omicron is no more a limiting factor against the spread of Delta than the 'flu is.  What you're saying only works in the one-way situation in which Omicron antibodies stop Delta but Delta antibodies don't stop Omicron.



But we're not starting from 0. There's already a defence against delta. The defence needed to fight omicron might not work against it but it's too late for delta.

I mean  in a perfect lab scenario. There'll always be pockets of unprotected population obviously.


----------



## kabbes (Dec 5, 2021)

xenon said:


> But we're not starting from 0. There's already a defence against delta. The defence needed to fight omicron might not work against it but it's too late for delta.
> 
> I mean  in a perfect lab scenario. There'll always be pockets of unprotected population obviously.


I'm really not seeing much evidence that Delta is done.  50,000+ infections a day in this country alone would tend to argue against that scenario.


----------



## xenon (Dec 5, 2021)

Actually I wonder can you have both variants at the same time.


----------



## kabbes (Dec 5, 2021)

xenon said:


> Actually I wonder can you have both variants at the same time.


Yes, this is what I am wondering.  If not, why not?  Although I am aware that understanding the impact of multiple pathologies in the same individual is another level of complexity again.  You also need to consider all the other pathogens and other microbial thingies that are present too -- bacteria, fungi, other viruses etc.  Not straightforward!


----------



## xenon (Dec 5, 2021)

kabbes said:


> I'm really not seeing much evidence that Delta is done.  50,000+ infections a day in this country alone would tend to argue against that scenario.



Sure, but over the medium term. Mind you, there could be the Pi varient by then.


----------



## zahir (Dec 5, 2021)

Thread


----------



## xenon (Dec 5, 2021)

Musst admit I've tended to figuratively picture it like lots of blue dots swarming around.  Blue being delta.
Once everything's turned blue, Red (omicron) comes along, swarms much quicker and in wider dispersal patterns and blue gets taken over.

Not sure if that helps anyone else though...


----------



## StoneRoad (Dec 5, 2021)

xenon said:


> Actually I wonder can you have both variants at the same time.


There were several cases of "orginal" and "delta" in the same individual.

I'm now worrying that we'll have a large omicron wave this winter that is largely uncontrolled by the vaccines.
If omicron evades the vaccines, then the boffins need to be doing the required tweaking asap.


----------



## elbows (Dec 5, 2021)

LynnDoyleCooper said:


> _I think _(iirc from listening to an interview with an immunologist recently) then the bit I highlighted is actually possible - quick re-infection and _possibly_ concurrent infections with both.
> 
> The rest just makes my head feel like it's going to explode.


The way I think about it is by not focussing so much on whether that can happen in some instances, but rather how often it happens, whether it makes up a large part of the picture or is just a sideshow.

There is much that I do not claim to know, and I treat assumptions as mere placeholders that I will only make use of where there would otherwise be a complete void.

I dont like to make assumptions about whether a strain will dominate until the signs are much clearer in real data. But so far I tend to think about momentum - dominant strains gain a hell of a lot of momentum in order to get to that position, they outcompete other strains in ways that have not been subtle so far.

I understand the logic of kabbes questions about this and I dont have many answers, other than to think about that momentum and not to consider immunity in a simplistic way. There are multiple levels of immune defense and probably some overlap which should not be ignored, even when variants are quite different. The overlap may not be enough to prevent a nasty new wave and lots of health care pressure, but it can still be enough to allow the new strain to dominate at the expense of previous strains.

Consider the story of flu for the first two thirds of the 20th century. H2N2 was different enough from H1N1 to cause a new pandemic, and yet it also dominated and caused the previous strain to dissapear. Likewise H3N2s arrival led to the demise of H2N2. The story loses its simplicity after that because H1N1 came back in the 1970's (quite possibly due to human error) and we've had two major strains of influenza A co-existing ever since, but if people look for explanations about the story of flu strains in the 20th century then maybe it will still help with the current questions.


----------



## elbows (Dec 5, 2021)

zahir said:


> Thread



Thanks for that. I did read that hospital report last night and would describe it as a familiar scene - some good news that should be tempered by the fact its still too early in that wave to draw safe conclusions, and that a small percentage of a very large number can still be incredibly bad news.


----------



## Supine (Dec 5, 2021)

kabbes said:


> I think you're not grasping what I'm saying.  Or possibly vice versa.
> 
> If antibodies don't mutually "work" to eliminate both variants then from _our _point of view, these are essentially two different diseases.  Omicron won't replace Delta because somebody who has already had Omicron can still get Delta.  This is fundamentally different to Alpha and Delta, whereby somebody who has had Delta now (basically) can't get Alpha.  In the latter case, Delta outcompeted Alpha and Alpha disappeared.  However, in the former case, there is nothing to stop Omicron and Delta co-existing.
> 
> ...



I think I get what your saying but to get to the answer you need to get into the next level of complexity regarding immune systems. Not my area of expertise but I’ll give it a bash! Bored on a train so why not.

Its too simplistic to talk about antibodies for a particular strain of covid. The immune system recognises lots of little bits of covid.  You could have 2, 10, 100 bits of the covid shape which are recognised and antibodies created. When covid mutates some of these shapes will disappear and therefore the memory of what they look like is redundant.

This is why you sometimes hear talk of a broader immune response post natural infection because the immune system will be recognising shapes in the main protein and not just the spike. Current vaccines only use the spike shape to train the immune system. Some of the newer vaccines will be using inactivated whole covid to train the immune system so it will be interesting to see how well they do.

Back to the race, if your body recognises 39 bits of covid and omicron comes along with shape changes you might get a reduction in recognised shapes from 39 down to 19 or 10 or 6. Who knows! The point is that the less shapes recognised the less efficient the immune response would be. So far the spike hasnt changed enough to stop vaccines working efficiently. Omricon has people worried because of the number of shape differences. It will naturally start to become the dominant type because it has a competitive advantage. Also need to remember that omicron isnt a fixed mutation and is already changing as mistakes happen during replication all the time. There is already a family branch of omicron that does not have the s gene dropout. That appears to be something that comes and goes over time.

So yeah, its not a one variant scenario or two types living side by side. Its a constantly changing outlook and when the next significant changes occur it will be designated Pi variant. We all need to accept annual jabs, with the latest variants encoded to fine tune the immune response over time.

Not sure that answers all of your questions but maybe a start?


----------



## elbows (Dec 5, 2021)

Plus there is plenty of theory that is only being put to the test properly by this pandemic. I believe some experts think there is a risk of trying to be too clever for our own good when it comes to tweaking the vaccines to act against specific new strains, due to the complexities of the immune system and some counter-intuitive possibilities.

Original antigenic sin is just one example and only time will truly demonstrate whether that idea is actually applicable to this virus and whether our response has the potential to make things worse.

Plus one of the many reasons I have to wait to see what happens elsewhere with Omicron is due to differences in previous wave variants in South Africa compared to a country like the UK. They had a beta wave in the past, we didnt.


----------



## kabbes (Dec 5, 2021)

Thanks both. That does make sense, and I guess we’ll see over time what the dominant features are of the particular circumstances we are in that determine else happens on this occasion.


----------



## Supine (Dec 5, 2021)

Just on the subject of on-going changing here is the current ‘family tree’ for the omicron clade. As you can see it is evolving in multiple ways already (most being insignificant luckily).  I recommend the nextstrain. org website if you want to get into the detail of mutations.


----------



## elbows (Dec 5, 2021)

Other things to keep in mind include that studies into immunity and SARS-CoV-2 are inevitably biased towards using the aspects of our immune system that they find reasonably easy to measure. Hence the emphasis on antibody levels in the blood, which is far from the whole immune system story.

As far as I know there are still plenty of outstanding questions when it comes to immune response to even more disparate viruses. For example there are some studies which imply there may be some cross-reactive antibodies generated from either the pandemic virus or a bunch of the other human coronaviruses that were around long before this pandemic. I dont think they've found strong evidence that recent infection with one of the other coronaviruses confers protection against infection or severe disease of the Covid-19 variety, but it could still be the case, especially if the phenomenon is somewhat brief and transient. Indeed that possibility was on the list of possible explanations for why some countries did not suffer as great a healthcare burden in the first wave, if they had had a large wave of a normal human coronavirus with just the right pre-pandemic timing that a chunk of their population ended up with better, but temporary, defences against the arrival of the pandemic.

The transient nature of some of this stuff is also worth consuidering when seeking explanations for why a new strain can dominate at the expense of the previously dominant strain - the momentum of the new strain and the huge numbers affected could massively rob the previous strain of opportunities for a time, and during that time the old strain runs out of sufficient hosts.

But then again I would caution that the transient nature of the immune response may receive an undue degree of attention because that waning form of immunity is most strongly associated with the aspects of our immune response that are easiest to measure (eg via the blood), and the longer-lasting forms of protection are much harder to measure and obtain masses of data about.


----------



## _Russ_ (Dec 5, 2021)

Please take the example below as what it is, a single case that is still early in its trajectory and could well go in a different direction


----------



## Supine (Dec 5, 2021)

Slightly mind bending thread on transmission advantage


----------



## Aladdin (Dec 5, 2021)

_Russ_ said:


> Please take the example below as what it is, a single case that is still early in its trajectory and could well go in a different direction





And he probably has no immune issues or underlying health problems.


----------



## teuchter (Dec 5, 2021)

_Russ_ said:


> Please take the example below as what it is, a single case that is still early in its trajectory and could well go in a different direction



So basically information which is of no use to anyone.


----------



## gentlegreen (Dec 5, 2021)

Fairly standard for John Invermectin Campbell


----------



## _Russ_ (Dec 5, 2021)

teuchter said:


> So basically information which is of no use to anyone.


Oh you speak for everyone?
The abundance of comments that add fuck all to the discussion is getting a bit boring


----------



## kabbes (Dec 5, 2021)

Supine said:


> Slightly mind bending thread on transmission advantage



That really puts the advantage of omicron over delta into perspective. Over five days, based on current immunity levels, they think it likely grows about 4 times faster.


----------



## elbows (Dec 5, 2021)

kabbes said:


> That really puts the advantage of omicron over delta into perspective. Over five days, based on current immunity levels, they think it likely grows about 4 times faster.


Although they expect the existing immunity picture in each country to make quite a difference, so I'll be waiting for UK-specific data to firm up in the next week or two before I judge the extent to which the shit will hit the fan here.

My default assumption is that it will be grim and will necessitate the imposition of strong measures, but I'm always ready to change my tune on that.


----------



## elbows (Dec 5, 2021)

I'm not a big fan of the headline framing of this article, because unlike the arrival of previous variants, this time the government have not pretended that we are actually trying to contain this variant, and have been more honest that these measures are only to slow its spread. And buying time for more boosters is a sensibe thing to do, its just a shame they didnt bother doing more on the domestic measures front too.









						Covid: Travel changes too late to halt potential new wave - scientist
					

The return of pre-departure Covid tests for travellers to the UK will come into force on Tuesday.



					www.bbc.co.uk


----------



## kabbes (Dec 5, 2021)

elbows said:


> Although they expect the existing immunity picture in each country to make quite a difference, so I'll be waiting for UK-specific data to firm up in the next week or two before I judge the extent to which the shit will hit the fan here.
> 
> My default assumption is that it will be grim and will necessitate the imposition of strong measures, but I'm always ready to change my tune on that.


It's highly uncertain at the moment, but one of the estimates in that thread did try to take account of the existing immunity context of the UK.  If I remember rightly, it was a slightly lower estimate (but with a huge range of uncertainty)


----------



## teuchter (Dec 5, 2021)

_Russ_ said:


> Oh you speak for everyone?
> The abundance of *comments that add fuck all to the discussion* is getting a bit boring


In my view your post containing that video falls into this category but you are free to explain how you think it is a useful contribution.


----------



## elbows (Dec 5, 2021)

kabbes said:


> It's highly uncertain at the moment, but one of the estimates in that thread did try to take account of the existing immunity context of the UK.  If I remember rightly, it was a slightly lower estimate (but with a huge range of uncertainty)


Yes, I'm waiting for more of that S-gene dropout data from the UK to emerge before I put weight in the number deduced by that means.


----------



## 2hats (Dec 5, 2021)

Very early UK (and EU) sequencing data _might_ suggest a <3-day doubling rate (in a population with delta dominant and relatively high vaccine-induced immunity). However, one should bear in mind there could be a sequence over-sampling bias. Equally there could be under-sampling as non-SGTF omicron 'family' (sub-)variants are definitely out there.


----------



## ska invita (Dec 5, 2021)

teuchter said:


> In my view your post containing that video falls into this category but you are free to explain how you think it is a useful contribution.


Russ is a troll, should be banned long ago


----------



## elbows (Dec 5, 2021)

I tend to associate those sort of doubling time with even the most stupid regimes being forced to act in a pandemic.


----------



## Supine (Dec 5, 2021)

Strewth


----------



## kabbes (Dec 5, 2021)

What the...


----------



## StoneRoad (Dec 5, 2021)

kabbes said:


> What the...


Nothing good !


----------



## elbows (Dec 6, 2021)

Bits I've cherrypicked from the South African presidents statement today:



> Over the last week, the number of daily infections has increased five-fold. Nearly a quarter of all COVID-19 tests now come back positive. Compare this to two weeks ago, when the proportion of positive tests was sitting at around 2%.





> The massive surge in infections means that, in addition to vaccination, we need to be far more diligent in reducing our contact with people outside our household. Social distancing is difficult as the festive season approaches, but the evidence shows that gatherings – mainly those held indoors – carry the greatest risk of transmission. Many people have been disappointed by the cancellation of some big events in recent days, but it is by far the safest and most responsible thing to do now.
> 
> Fortunately, we all know what we need to do, such as wearing masks, social distancing and avoiding crowds. Now we just need to make sure that we do these things more consistently and without exception.





> As we work with greater urgency to increase vaccination rates, we need to significantly up our game on prevention measures to ensure our collective safety.
> 
> We should not wait for new regulations before we reduce the size of the gatherings, as research has shown this to be an effective means of reducing the spread of the virus.
> 
> ...







__





						From the desk of the President, Monday, 6 December 2021 | The Presidency
					






					www.thepresidency.gov.za


----------



## _Russ_ (Dec 6, 2021)

> Over the last week, the number of daily infections has increased five-fold. Nearly a quarter of all COVID-19 tests now come back positive. Compare this to two weeks ago, when the proportion of positive tests was sitting at around 2%.



Just as (another) Illustration of how shit we've behaved in this Pandemic, there were 2 weeks in the second half of october where the positivity rate in Wales was at the levels reported in the massive surge going on now In South Africa (24%)...difference being we did fuck all to bring it down, no increased measures, everything stayed open and the  people of Wales  wandered around like it was all over


----------



## elbows (Dec 6, 2021)




----------



## elbows (Dec 6, 2021)

Already mentioned shorter incubation window possibilities but just to touch on that again.


----------



## weltweit (Dec 6, 2021)

Why do I feel a little like the rabbit in the headlights where Omicron is concerned?


----------



## Indeliblelink (Dec 6, 2021)




----------



## Steel Icarus (Dec 6, 2021)

This is what frustrates me so much
We can see what might be coming
Nobody gives a fuck


----------



## weltweit (Dec 6, 2021)

S☼I said:


> This is what frustrates me so much
> We can see what might be coming
> Nobody gives a fuck


Do you think Government should do a lockdown?


----------



## Steel Icarus (Dec 7, 2021)

weltweit said:


> Do you think Government should do a lockdown?


Yeah


----------



## Ming (Dec 7, 2021)

S☼I said:


> Yeah


Agree. But the horse may have bolted. We'll know better in a few weeks when the data's in and they've run the numbers obviously. I think humanity has really fucked this one up. Leaving largely unvaccinated populations in poor countries to give the virus plenty of opportunity to mutate.


----------



## cupid_stunt (Dec 7, 2021)

So, we can expect Omicron to become the dominant variant within a few weeks, although on the plus side, with the usual caveats, there seems an increasing number of experts expressing the view that it looks fairly mild, with symptoms more like other coronaviruses that get lumped into just the 'common cold', at least in those that have had it before or been vaccinated, which gives us some hope.



> With the caveat that until scientists get more data, there is a lot of speculation around, but *Dr Jeffrey Barrett*, director of the Covid-19 genomics initiative at the Wellcome Sanger Institute, has agreed this morning with those suggesting that Omicron would take over from Delta in the UK as the dominant variant of coronavirus “within a matter of weeks”.
> 
> PA Media quotes him telling the BBC Radio 4 Today programme: “I think we can now say that this variant is spreading faster in the UK than the Delta variant at the same time, and that’s something that I think was unclear until very recently. I am pretty confident that it’s going to take over probably in a matter of weeks.”
> 
> ...











						Fury in UK after video about No 10 party; early signs Omicron more transmissible – as it happened
					

Early indications Omicron more transmissible than Delta, says Boris Johnson; Nicola Sturgeon says staff should work from home until mid-January




					www.theguardian.com


----------



## ska invita (Dec 7, 2021)

cupid_stunt said:


> So, we can expect Omicron to become the dominant variant within a few weeks, although on the plus side, with the usual caveats, there seems an increasing number of experts expressing the view that it looks fairly mild, with symptoms more like other coronaviruses that get lumped into just the 'common cold', at least in those that have had it before or been vaccinated, which gives us some hope.


if that is true and it becomes truly dominant and really is mild might this be a way out of this covid hellhole no? in fact it would be good if it spreads and dominates? or does its spread create more chances of nastier variants?


----------



## gentlegreen (Dec 7, 2021)

ska invita said:


> if that is true and it becomes truly dominant and really is mild might this be a way out of this covid hellhole no? in fact it would be good if it spreads and dominates?


Assuming it gives good cross-immunisation against more unpleasant strains...
That said, I ain't taking my mask off any time soon ...


----------



## cupid_stunt (Dec 7, 2021)

ska invita said:


> if that is true and it becomes truly dominant and really is mild might this be a way out of this covid hellhole no? in fact it would be good if it spreads and dominates? or does its spread create more chances of nastier variants?



It could do, but...


----------



## cupid_stunt (Dec 7, 2021)

Another update, again suggesting it is mild. 



> Prof *Tim Spector*, from the Covid Zoe app, said that in about 10 days’ time the UK could have more cases of Omicron than some countries it had put on the travel red list.
> 
> The professor of genetic epidemiology at King’s College London told BBC Breakfast: “The official estimates are about 350-odd Omicron cases, and because the current testing is missing a lot of those, it’s probably at least 1,000 to 2,000 I would guess at the moment.
> 
> ...











						Fury in UK after video about No 10 party; early signs Omicron more transmissible – as it happened
					

Early indications Omicron more transmissible than Delta, says Boris Johnson; Nicola Sturgeon says staff should work from home until mid-January




					www.theguardian.com


----------



## bluescreen (Dec 7, 2021)

But it only needs a small percentage (of the massively more widely infected population) to suffer badly for the Omicron variant to be a big problem.


----------



## zahir (Dec 7, 2021)

Omicron Post #4
					

Previous Omicron updates: #1, #2, #3. Last weekly non-Omicron update. An introductory word: Thanks to Dominic Cummings, I have a lot of new readers, many from the United Kingdom, so I want to welco…




					thezvi.wordpress.com
				





> Omicron spreads far more rapidly than Delta and is going to take over.
> This will come at us fast. Omicron will be the majority strain by the end of January. This happening by end of year is on the table.
> Omicron re-infects those who have already been sick, or breaks through to those who have been vaccinated, much more than Delta.
> Previous infection continues to protect against severe disease, hospitalization and death.
> ...


----------



## Monkeygrinder's Organ (Dec 7, 2021)

ska invita said:


> if that is true and it becomes truly dominant and really is mild might this be a way out of this covid hellhole no? in fact it would be good if it spreads and dominates? or does its spread create more chances of nastier variants?



I guess if it is mild (big if obviously) in general the question is if that's still true for older or otherwise vulnerable people?


----------



## cupid_stunt (Dec 7, 2021)

bluescreen said:


> But it only needs a small percentage (of the massively more widely infected population) to suffer badly for the Omicron variant to be a big problem.



Indeed, although if the vaccine boosters hold up to it, hopefully not.


----------



## elbows (Dec 7, 2021)

Vaccines arent enough to stop the 'small percentage of a large number' thing from still having big implications, which is one of the reasons I keep saying we shouldnt rely on vaccines to carry all the weight of the pandemic. SAGE are meeting very infrequenctly these days, but we know from previous planning and modelling of variants that increased transmissibility is expected to have big implications for hospital pressure, and that increased transmission bothers many experts more than various changes to pure 'deadliness'.

The 'mild' stuff still requires quite a bit more time to unpick, especially in a vaccine era. I dont mind people using this as a source of hope, as long as it isnt used as an excuse to err on the side of recklessness and to delay doing the things that should be done.

I am nowhere close to being able to tell whether Omicron is pure bad news or a mix of bad news and good news.

In terms of the UK picture, we were only just getting to the point where stronger clues would emerge as to whether we were going to get through this winter without Delta causing enough problems that further measures would be required. And now it is not clear to me that we will get to see that picture emerge cleanly, due to the timing of the rise of Omicron.


----------



## elbows (Dec 7, 2021)

And then after writing that I groaned when I saw this:



> We have some more from the prime minister's official spokesman.
> 
> He says there is "no hard agreement on the level of transmissibility" and the impact of Omicron will "depend on the severity".



I am not alone:


----------



## elbows (Dec 7, 2021)




----------



## StoneRoad (Dec 7, 2021)

DePiffle dragging his heels, and expecting the vaccines to do all the work, especially as Omicron is already here & there is community transmission with the added benefit of it being winter here ...
is totally #world-beating

[I predict that the 3.6 Rt that SA is probably experiencing, is going to convert to at least 5 Rt with our being in winter]


----------



## elbows (Dec 7, 2021)




----------



## elbows (Dec 7, 2021)

There were too many tweets in this thread for me to be posting them all, so I'm just posting the end of this particular thread that was in response to Christina Pagels 'toy' modelling exercise.


----------



## elbows (Dec 7, 2021)




----------



## bluescreen (Dec 7, 2021)

This has got me scared in a way I haven't been before, as we have a government and press and large part of the population who think: Oh this variant is milder and will take over, we can all relax now, it's just like the common cold. And they're all saying this at a time when A&E depts are already being overrun and scheduled operations being cancelled on a grand scale.


----------



## weepiper (Dec 7, 2021)

Mood music from the Scottish Government is fairly grim.









						Sturgeon warns of 'rapid' rise in Omicron cases
					

Scotland's Covid restrictions to be reviewed daily as first minister warns that Omicron is a "significant challenge".



					www.bbc.co.uk
				












						Covid in Scotland: Take a test every time you leave home, says Swinney
					

Evidence of a negative test for Covid-19 can now be used as an alternative to a vaccine passport.



					www.bbc.co.uk


----------



## elbows (Dec 7, 2021)

Also see the stuff Sturgeon has said that I just psoted on the main UK thread. I am recommending people change their behaviours now, and prepare for disruption.

       #43,561      

Ah thanks for that weepiper, your post appreared while I was typing this message.


----------



## 8ball (Dec 7, 2021)

S☼I said:


> This is what frustrates me so much
> We can see what might be coming
> Nobody gives a fuck



It's a very "February 2020" feeling.


----------



## Brainaddict (Dec 7, 2021)

I don't for a moment think the govt has the stomach for a full lockdown, but there's a lot they could do to slow the spread short of a lockdown - ban large gatherings, enforce mask wearing everywhere indoors, close cinemas and gig venues. But as usual they just don't care enough.


----------



## Pickman's model (Dec 7, 2021)

Brainaddict said:


> I don't for a moment think the govt has the stomach for a full lockdown, but there's a lot they could do to slow the spread short of a lockdown - ban large gatherings, enforce mask wearing everywhere indoors, close cinemas and gig venues. But as usual they just don't care enough.


no, they care loads: but they care more - much more - about the economy than they do about people's health


----------



## elbows (Dec 7, 2021)

> Back to the situation in the UK now. A leading scientist says it is "extremely likely" the UK will get a "very large wave of infections" as a result of the Omicron variant.
> 
> Prof Andrew Haryward, a member of the government's New and Emerging Respiratory Virus Threats Advisory Group, tells BBC Radio 4's World at One programme that evidence from South Africa and the UK suggests cases of Omicron are doubling every two or three days.
> 
> By contrast, when cases of Delta have increased recently, the doubling time was two or three weeks, he says. This means Omicron can "very rapidly" replace and overtake Delta, which is currently dominant in the UK, he adds.





> The speed of its spread may mean cases peak before there is the opportunity to increase immunity through booster jabs - and immunity may also be weaker against the new variant so the only remaining option is more social distancing measures, the professor of infectious diseases says.
> 
> He adds that it's too early to say Omicron is milder than previous variants and its effect on the elderly population remains to be seen.
> 
> ...



Thats from the 14:33 entry on the BBC live updates page. https://www.bbc.co.uk/news/live/59559623


----------



## manji (Dec 7, 2021)

I know friends that were terrified a year ago and when lockdown was relaxed continued to avoid gigs, football etc. this time round are completely blasé. I really don’t understand it


----------



## elbows (Dec 7, 2021)

Pickman's model said:


> no, they care loads: but they care more - much more - about the economy than they do about people's health


They care about the economy in a superficial and counterproductive way too, since late action means longer periods of restrictions. And when health care capacity is exceeded this does rather tend to suppress economic activity for a whole bunch of reasons.


----------



## Pickman's model (Dec 7, 2021)

elbows said:


> They care about the economy in a superficial and counterproductive way too, since late action means longer periods of restrictions. And when health care capacity is exceeded this does rather tend to suppress economic activity for a whole bunch of reasons.


i never said they were competent. just that they care much more about the economy than about people's health


----------



## elbows (Dec 7, 2021)

manji said:


> I know friends that were terrified a year ago and when lockdown was relaxed continued to avoid gigs, football etc. this time round are completely blasé. I really don’t understand it


The initial shock wore off, the media have been talking shit for a long time, people were encouraged to have oversimplistic expectations about vaccines and the wrong ideas about 'how long a pandemic lasts'.


----------



## StoneRoad (Dec 7, 2021)

I am absolutely dreading the next few weeks. DePiffle's doing only a little to actually mitigate the potential risks.

Personally, I'm boosted, as are my close family, live in an area with very high vaccination rates, and currently - at least - a low case rate. And I can WFH, get deliveries [weather permitting !]

But I regularly see people ignoring the basic safety precautions ... as in they think it is all over.
It is most definitely not all over.


----------



## Boru (Dec 7, 2021)

And more developments just published on the guardian.. an undetectable stealth version..








						Scientists find ‘stealth’ version of Omicron that may be harder to track
					

Variant lacks feature that allows probable cases to be distinguished among positive PCR tests




					www.theguardian.com


----------



## Brainaddict (Dec 7, 2021)

manji said:


> I know friends that were terrified a year ago and when lockdown was relaxed continued to avoid gigs, football etc. this time round are completely blasé. I really don’t understand it


To be fair, they have been vaccinated since then. Even if you know that vaccines don't solve all problems, there's still a line of argument that says this virus will be circulating forever now, and there's got to be a point at which we start living our normal lives again, even if there is some risk. (This is a plausible line of argument for ordinary people btw but not for the govt, who know that health services are in danger of being overwhelmed).


----------



## elbows (Dec 7, 2021)

Boru said:


> And more developments just published on the guardian.. an undetectable stealth version..
> 
> 
> 
> ...


Thats the second time in recent days the Guardian have made a big deal about holes in our ability to estimate Omicron case numbers via S-gene dropout. Previously they were focussing on the fact that only a percentage of our PCR labs have the ability to detect s gene dropout, with coverage especially poor for the South West.

It would be better if we could see something closer to the complete picture without these issues, but I think there is still likely to be enough data that we get a good enough idea about this variants potential and spread. And its looking likely to spread so quickly that I dont feel like I desperately need that complete picture, so I'm not especially alarmed by these Guardian stories. The properties of the variant itself are of huge concern to me, not these angles by the Guardian.

I suppose there is a small risk that some people could misinterpret the Guardians headline - PCR tests still detect positive cases that are infected with that version of Omicron, they just cant be used to tell its Omicron in particular as opposed to another variant, if the Omicron in question is the version that doesnt have the s-gene dropout.


----------



## 2hats (Dec 7, 2021)

elbows said:


>



More tellingly (Denmark sequences a much higher proportion of cases than any other country, ie ~57% to Sweden's ~38% and the UK's ~16% **, so is far less confounded by SGTP or SGTF assumptions):


(** Of course, as omicron exponentiates all these proportions will significantly drop without additional capacity).


----------



## Boru (Dec 7, 2021)

elbows said:


> Thats the second time in recent days the Guardian have made a big deal about holes in our ability to estimate Omicron case numbers via S-gene dropout.



I did think there was a level of sensationalism to the story but it is still a surprise development to me. I feel we are progressively moving towards a new world of 'living with covid', and whatever ramifications that may have for the world.


----------



## Supine (Dec 7, 2021)

Boru said:


> And more developments just published on the guardian.. an undetectable stealth version..
> 
> 
> 
> ...



Guardian playing catch-up. I mentioned that on urban over a week ago!


----------



## 8ball (Dec 7, 2021)

elbows said:


> They care about the economy in a superficial and counterproductive way too, since late action means longer periods of restrictions. And when health care capacity is exceeded this does rather tend to suppress economic activity for a whole bunch of reasons.



Yeah.  I'm thinking my economic activity might soon be heavily curtailed by this.


----------



## planetgeli (Dec 7, 2021)

elbows said:


> I suppose there is a small risk that some people could misinterpret the Guardians headline - PCR tests still detect positive cases that are infected with that version of Omicron, they just cant be used to tell its Omicron in particular as opposed to another variant, if the Omicron in question is the version that doesnt have the s-gene dropout.



I wouldn't say small risk. That's exactly (wrongly) how I interpreted that headline until I read your well explained post. It's a very badly written headline.


----------



## 2hats (Dec 7, 2021)

Boru said:


> And more developments just published on the guardian.. an undetectable stealth version..
> 
> 
> 
> ...


Sequences with 69-70del missing were seen in the earliest samples (very small numbers). It's just that late last night the original omicron lineage was sub-divided into two recognised sub-lineages. There are further sub-variants (with a few point mutations differing). If any of those prove to be biologically significant (right now one _might_ be), or have phylogenetic utility, then there will probably be some further re-classification shortly. But they are all omicron (just like all AY.* are essentially delta). The only difference here is whether you can infer proportions from PCR SGTF, which is still a useful indication of trend, where omicron SGTP numbers are small-to-negligible (eg the UK, at the time of writing).


----------



## Supine (Dec 7, 2021)

Guardian getting corrected by experts


----------



## elbows (Dec 7, 2021)

planetgeli said:


> I wouldn't say small risk. That's exactly (wrongly) how I interpreted that headline until I read your well explained post. It's a very badly written headline.


Yeah I was being too charitable to the Guardian with my use of the word small.


----------



## elbows (Dec 7, 2021)




----------



## 2hats (Dec 7, 2021)

Preliminary omicron vaccine neutralisation results (Sigal et al). Here performed with Pfizer/BioNTech vaccine induced sera. The apparent raw neutralisation reduction is around 40-fold compared to original D614G. Other observations - omicron is still using the ACE2 receptor. Omicron does not escape from hybrid immunity (previous infection plus vaccination).


----------



## elbows (Dec 7, 2021)

Yeah I just came to post a tweet or two about that:


----------



## elbows (Dec 7, 2021)




----------



## 2hats (Dec 7, 2021)

Note that the Sigal lab studies were performed in a BSL-3 with live virus. Also bear in mind that antigenic imprinting can modulate subsequent immunoresponses.


----------



## teuchter (Dec 8, 2021)

I've made the mistake of reading an Omicron thread on another forum, where people are saying it doesn't matter if millions of people become infected and lots of people are hospitalised - there will be a week or two which will be horrendous but after that it'll be fine, everyone will be immune and the pandemic will be over.


----------



## LDC (Dec 8, 2021)

teuchter said:


> I've made the mistake of reading an Omicron thread on another forum, where people are saying it doesn't matter if millions of people become infected and lots of people are hospitalised - there will be a week or two which will be horrendous but after that it'll be fine, everyone will be immune and the pandemic will be over.



Shit. That's were we all went wrong right at the beginning then... just do nothing, have a bad fortnight, but then it's all OK! Have you pointed out to these people they need to urgently get in touch with the WHO etc. to let them know they have the answer we're all been searching for?


----------



## Monkeygrinder's Organ (Dec 8, 2021)

Other forums are best avoided to be honest. Bunch of idiots.


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## LDC (Dec 8, 2021)

So, doubling every 2-3 days here in the UK. Anyone got the modelling for what that looks like in various scenarios?


----------



## prunus (Dec 8, 2021)

LynnDoyleCooper said:


> So, doubling every 2-3 days here in the UK. Anyone got the modelling for what that looks like in various scenarios?



100k cases a day by Christmas. 1 million a day a week and a half later unless lockdown brought in.


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## gentlegreen (Dec 8, 2021)

How about getting *slightly *infected ? (fully-vaxxed and masked)
One of the reasons I got my flu jab this year was because it dawned on me that I might have previously been getting inoculating doses of flu that stopped me getting ill very often ... I certainly never got "colds" per se and when I *was *sick, it was 4 days off work ...


----------



## Supine (Dec 8, 2021)

LynnDoyleCooper said:


> So, doubling every 2-3 days here in the UK. Anyone got the modelling for what that looks like in various scenarios?



There is this. But a few days old…


----------



## LDC (Dec 8, 2021)

gentlegreen said:


> How about getting *slightly *infected ? (fully-vaxxed and masked)
> One of the reasons I got my flu jab this year was because it dawned on me that I might have previously been getting inoculating doses of flu that stopped me getting ill very often ... I certainly never got "colds" per se and when I *was *sick, it was 4 days off work ...



Not sure I get what you mean, or are asking?


----------



## gentlegreen (Dec 8, 2021)

LynnDoyleCooper said:


> Not sure I get what you mean, or are asking?


After 2 years without catching anything, I'm torn about ever going unmasked around other people ...

As and when a mild form of covid shows up, or it becomes seasonal, presumably vaccination will reduce to once a year combined with flu and the rest of the time we will be expected to just catch it ?


----------



## LDC (Dec 8, 2021)

Supine said:


> There is this. But a few days old…




Thanks both, but is there the Imperial or LSHTM modelling there has been before?


----------



## Flavour (Dec 8, 2021)

I am supposed to be flying to the UK from Italy on December 19th. (I had a similar drama last Christmas where I got stuck in Amsterdam due to flight cancellations). Wonder if I will be able to come back this year, or, more aptly, if I _should_. Perhaps not a good idea.


----------



## elbows (Dec 8, 2021)

LynnDoyleCooper said:


> Thanks both, but is there the Imperial or LSHTM modelling there has been before?


I'm guessing some modelling showing scenarios under different ranges of increased transmissibility and immune escape have been done in recent days, and probably formed part of a presentation given to Johnson yesterday. Exactly when that stuff will be made public remains to be seen, possibly more quickly than usual if new measures are announced today, although there may still be some publication lag.


----------



## cupid_stunt (Dec 8, 2021)

elbows said:


> I'm guessing some modelling showing scenarios under different ranges of increased transmissibility and immune escape have been done in recent days, and probably formed part of a presentation given to Johnson yesterday. Exactly when that stuff will be made public remains to be seen, possibly more quickly than usual if new measures are announced today, although there may still be some publication lag.



There's a Downing Street press conference today - SEE HERE.


----------



## elbows (Dec 8, 2021)

Given the need to keep people engaged with vaccination programmes and not fall foul of utter defeatism, I was expecting some sugarcoating of the Omicron situation. However I consider the WHO's sugarcoating to be a bit too much, although only time will tell whether I find cause to have massive rants about some of these words or whether the gap between reality and rhetoric doesnt turn out to be too extreme:









						Covid: Vaccines should work against Omicron variant, WHO says
					

A small study in South Africa suggests the new variant could partially evade the Pfizer jab.



					www.bbc.co.uk
				




I dont have enough data or strong enough evidence to have a high degree of confidence in my own ability to judge what the mix of good and bad news with Omicron really is at this stage. Not all of the tentative clues are as negative as might have been expected. But if we read between the lines of the actions that national authorities feel the need to take now, there is quite a gap between that and the 'reassuring, dont panic' sentiments from the WHO in recent days. Its obvious which side I will err on, the cautious side!


----------



## elbows (Dec 8, 2021)




----------



## elbows (Dec 8, 2021)

LynnDoyleCooper said:


> Thanks both, but is there the Imperial or LSHTM modelling there has been before?


SAGE meeting details leaked to the BBC again (the late November meeting minutes were also leaked). Not as good as having modelling graphs published but contains some strong clues about what some modelling probably showed. Article headline features a watered down estimate compared to the body of the article:



> The scientists say it is "highly likely" Omicron will account for the majority of new coronavirus infections in the UK within "a few weeks".
> 
> And they say the peak of the wave is "highly likely to be higher" than 1,000-2,000 Omicron hospital admissions per day without new rules to slow the spread of rising infections.











						Covid: Omicron hospital admissions could reach 1,000 a day - scientific advisers
					

The BBC has seen minutes of a meeting of scientific advisers which warn of NHS pressure from Omicron.



					www.bbc.co.uk


----------



## BigMoaner (Dec 8, 2021)

My work, big uni, told to work from home Tom till fn


----------



## weltweit (Dec 8, 2021)

WHO on the news saying DONT WAIT till your hospitals are full from Omicron, act now, don't wait!


----------



## Ming (Dec 8, 2021)

It does sound like a transformer though.


----------



## BigMoaner (Dec 8, 2021)

is this ever going to end


----------



## Numbers (Dec 8, 2021)

BigMoaner said:


> is this ever going to end


Not for a few more years by the looks of it.


----------



## 8ball (Dec 9, 2021)

Numbers said:


> Not for a few more years by the looks of it.



Well, for the richer part of the world, maybe in a couple of years.  Sadly, it’s not going to be an even thing.


----------



## elbows (Dec 9, 2021)




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## Pickman's model (Dec 9, 2021)

BigMoaner said:


> is this ever going to end


it's as long as a piece of string


----------



## 8ball (Dec 9, 2021)

Pickman's model said:


> it's as long as a piece of string



11 centimetres?
I could have sworn it's been longer.


----------



## Pickman's model (Dec 9, 2021)

Ming said:


> It does sound like a transformer though.


----------



## nosos (Dec 9, 2021)

Who is cancelling Christmas travel plans? I can't see how this won't have much worse by Christmas


----------



## Pickman's model (Dec 9, 2021)

BigMoaner said:


> My work, big uni, told to work from home Tom till fn


where i am we've got to risk the lurgy continue coming in


----------



## Pickman's model (Dec 9, 2021)

nosos said:


> Who is cancelling Christmas travel plans? I can't see how this won't have much worse by Christmas


it will be much worse and the government is going to cancel christmas plans


----------



## elbows (Dec 9, 2021)

SAGE meeting of 7th Deember minutes are available. The BBC received a leak of these recently and so I already discussed possible hospitalisation numbers. The whole thing is worth a read, here I am just quoting some stuff I found especially noteworthy.









						SAGE 98 minutes: Coronavirus (COVID-19) response, 7 December 2021
					






					www.gov.uk
				






> 11. The impact of changes in transmissibility and immune escape on overall numbers of admissions is likely to be much more significant than the impact of any changes in severity (high confidence).





> 12. There are other impacts from high levels of incidence aside from hospitalisations and deaths, including the morbidity burden in those who are not hospitalised and workforce absences. With very rapid doubling times a large wave could occur leading to synchronous absences from work.





> 14. The faster the growth in infections at the point measures are introduced, the more admissions will increase in the period between action being taken and the number of admissions being affected. With lags of the order of two or more weeks, and doubling times of the order of three days, it is likely that, once hospitalisations begin to increase at a rate similar to that of cases, four doublings (a 16-fold increase) or more could already be “in the system” before interventions that slow infections are reflected in hospitalisations.





> 16. Given the rapid increase, decision makers will need to consider urgently which measures to introduce to slow the growth of infections if the aim is to reduce the likelihood of unsustainable pressure on the NHS. The effectiveness of these will be dependent on the measures chosen, and also on behavioural responses. Evidence suggests that measures could be reintroduced with expectation of a similar level of adherence as has been seen in the past. Adherence is likely to be higher if messaging and policy have clear rationales and are consistent. Consistency across the UK may help with messaging.





> 17. The generation time for Omicron is not known, but it is possible that it is shorter than for Delta, which would mean that case-based interventions (for example finding and isolating cases through contact tracing) become less effective because people become infectious sooner. This would increase the relative importance of population-based rather than case-based measures, namely measures which affect everyone, not just those who are confirmed as being infected.





> 20. Nosocomial transmission is likely to be an even greater risk as a result of Omicron, particularly as hospitalisations increase. Measures will need to be put in place to reduce this risk including measures to reduce the risk of healthcare workers becoming infected and infecting others, and measures to reduce the risk of transmission between patients. Other vulnerable settings (for example care homes and prisons) will also need particular attention. Reducing nosocomial spread will be even more difficult with a more highly transmissible variant.





> 22. Pharmaceutical interventions including antivirals will also continue to be important. Though antivirals should be used in combination where possible to reduce the risk of resistance developing, this will not be possible in the forthcoming wave of infections due to availability and lack of clinical trial data for combination approaches. Resistance monitoring, particularly in immunocompromised patients, will be needed and preparation should be made for combination therapies to be tested and rolled out as soon as practical.


----------



## andysays (Dec 9, 2021)

elbows said:


> SAGE meeting of 7th Deember minutes are available. The BBC received a leak of these recently and so I already discussed possible hospitalisation numbers. The whole thing is worth a read, here I am just quoting some stuff I found especially noteworthy.
> 
> 
> 
> ...


So presumably the new measures announced yesterday were decided after that assessment and advice was available.

They really haven't gone nearly far enough or fast enough, have they?


----------



## elbows (Dec 9, 2021)

andysays said:


> So presumably the new measures announced yesterday were decided after that assessment and advice was available.
> 
> They really haven't gone nearly far enough or fast enough, have they?



I'd say there is a very real risk of a very sharp, intense catastrophe.

That isnt the only possible outcome I have in mind, but I would rather fear the worst and then be delighted if I have to spend lots of time later explaining why it didnt happen. If it doesnt happen, we will likely learn much about the state of immunity in this country as a result of dodging such a potent bullet. Either that or us dodging the bullet in a different way, eg by people in their masses responding to the threat in a much stronger way than is currently evident or demanded by authorities.

The authorities rarely go fast enough of strong enough for my liking. They've gone a bit faster but weaker this time, and the theoretical risks posed by this variant means that they'd always have needed to go faster than previously in order to even come close to previous results (again, unless our immunity picture and Omicrons ability to blast past a big chunk of it turns out to be balanced so much more in our favour than experts dare presume at this stage).

I dont doubt that authorities will have to go much further if the picture continues along the same tracks SAGE are implying. But I cant predict when exactly, at least not many hours or days in advance of those moments arriving.


----------



## elbows (Dec 9, 2021)

In terms of possible sharpness of wave I'm not focussed on health issues exclusively either. There were various bullets we dodged in the past in terms of infrastructure and supplies due to staff sickness levels during wave peaks being high but still just within coping thresholds. I should not be complacent about whether that will remain the case in a very fast spreading wave.


----------



## elbows (Dec 9, 2021)

Oops there was one more quote from those SAGE minutes that I meant to include but missed out in my previous post about that:



> 19. Some international reports of ‘superspreading’ events (some of which include Omicron) also suggest a greater role for airborne transmission than has previously been the case, as it is less likely that Omicron could have spread to as many people as it has at those events by other routes (low confidence). This means that measures to reduce airborne spread such as ventilation, well-fitting masks and distancing or reduced density of people in indoor environments may be even more important.


----------



## elbows (Dec 9, 2021)

I've still not seen any graphs of modelling results yet LynnDoyleCooper but there is now a document about the SAGE modelling groups latest consensus statement:





__





						SPI-M-O: Consensus Statement on COVID-19, 7 December 2021
					






					www.gov.uk
				




I dont know which bits to quote to do it justice, so here is just a flimsy first attempt:



> 16. Initial preliminary modelling has been conducted by two academic groups to consider the potential implications of a variant with immune escape (from both vaccine-induced and natural immunity) and transmission advantage.
> 
> 17. Any wave of significant infection, almost irrespective of immune escape, will spill over into hospitalisations, and ultimately deaths. If initial estimates of transmission advantage and immune escape from South Africa are applicable to the UK population, there is the potential for a very substantial peak of infections much larger than occurred during the winter wave of January 2021. Even if severity of omicron were half that of delta, the sheer number of infections could lead to significantly more pressures on health and care settings; currently there is no strong evidence that omicron infections are either more or less severe than delta infections.
> 
> 18. If omicron’s immune escape reduces vaccine effectiveness against hospitalisation from, say, 96 per cent to 92 per cent, that would effectively double the number of vaccinated individuals who are not protected from hospitalisation.





> 23. Assuming that omicron has the same severity or pathogenicity as delta, all modelled scenarios from the three groups so far have qualitative similarities across sensitivities analysed, irrespective of immune escape and transmissibility assumptions made and the interplay between these. Even assuming the lower end of this observed growth rate, many scenarios see hospitalisations close to or going beyond previous peak levels, if there is no reduction in transmission. The situations where the peak of the epidemic is below 1,000 to 2,000 omicron hospital admissions per day (without intervention) require low immune escape and very high protection from boosters to be consistent with observed growth.
> 
> 24. The rapid rate of increase currently observed suggests that omicron-based hospital admissions alone could be of the order of 1,000 per day by the end of 2021.





> 28. Given the known data issues and potential for different test-seeking behaviours around the festive period, it is possible the scale of cases and hospitalisations over this period will be very difficult to track at a critical time for the epidemic.





> 30. The relative severity of omicron compared to delta remains unknown. Changes in the level of hospitalisations will broadly scale linearly with changes in severity, assuming no change in hospital capacity as admissions increase, and a marked decrease in severity is unlikely to offset the impact of a larger susceptible pool and or increased transmissibility; it would be easier to halve the number of infections than the infection hospitalisation rate (IHR).



They had another meeting yesterday, since the one this document covers, and I know nothing about that one yet.


----------



## nosos (Dec 9, 2021)

Pickman's model said:


> it will be much worse and the government is going to cancel christmas plans


I agree it's going to be much worse & peaking soon after Christmas. But I'm sceptical the Government will cancel Christmas plans unless there is a palace coup before then.


----------



## LDC (Dec 9, 2021)

elbows said:


> I've still not seen any graphs of modelling results yet LynnDoyleCooper but there is now a document about the SAGE modelling groups latest consensus statement:
> 
> 
> 
> ...



Thanks, really appreciated.


----------



## Pickman's model (Dec 9, 2021)

nosos said:


> I agree it's going to be much worse & peaking soon after Christmas. But I'm sceptical the Government will cancel Christmas plans unless there is a palace coup before then.


You're having a laugh, I think, if you believe it'll peak soon after Xmas


----------



## andysays (Dec 9, 2021)

Pickman's model said:


> You're having a laugh, I think, if you believe it'll peak soon after Xmas


TBF, they didn't specify which Xmas...


----------



## Pickman's model (Dec 9, 2021)

andysays said:


> TBF, they didn't specify which Xmas...


Have a well-earned pedant point


----------



## weltweit (Dec 9, 2021)

I am getting a little muddled about timelines. 

When did we first hear about Omicron? 

When did South Africa first classify it and when did they have the first surge of cases?

What was the time from infection to hospital deaths of delta? 

So when can South Africa expect their first deaths, if that is the MO of Omicron? 

And likewise, when can the UK expect them?


----------



## elbows (Dec 9, 2021)

weltweit said:


> I am getting a little muddled about timelines.
> 
> When did we first hear about Omicron?
> 
> ...



South Africa told the WHO about it on 24th November. We heard plenty about it on the 25th and it was named Omicron on the 26th. Overall covid case numbers in South Africa had already started rising notably, signalling a new wave, by the time they were in a position to inform the world about it.

I dont want to answer your other questions because I am tired and because infection to death time intervals vary across a range, and because not every case that is Omicron will be identified as Omicron, and because which age groups are first affected by large case numbers of the variant has an impact on initial death quantities and timing.


----------



## weltweit (Dec 9, 2021)

elbows said:


> South Africa told the WHO about it on 24th November. We heard plenty about it on the 25th and it was named Omicron on the 26th. Overall covid case numbers in South Africa had already started rising notably, signalling a new wave, by the time they were in a position to inform the world about it.


That recent oh, well. I am worrying ahead of myself then.


elbows said:


> I dont want to answer your other questions because I am tired


No worries, thanks for the above. 


elbows said:


> and because infection to death time intervals vary across a range, and because not every case that is Omicron will be identified as Omicron, and because which age groups are first affected by large case numbers of the variant has an impact on initial death quantities and timing.


Aha, thanks ..


----------



## elbows (Dec 9, 2021)

We are already into the period where worrying in a pro-active way is sensible. The estimated doubling time for this variant is very low and so its rise is expected to be rapid.


----------



## Hollis (Dec 9, 2021)

Far too much 'science' in here for me.. but I suspect the stuff about the future evolution of the virus towards the end of the article is interesting.. 

Beyond Omicron: what’s next for COVID’s viral evolution


----------



## wemakeyousoundb (Dec 9, 2021)

nosos said:


> Who is cancelling Christmas travel plans? I can't see how this won't have much worse by Christmas


I haven't yet because I don't want to disappoint my mum, but am pretty confident I will do the same as last year.


----------



## teuchter (Dec 10, 2021)

The news from Gauteng has gone a little quiet ... here is an updated version of that graph that appears not to show the exponential rise continuing at the same rate.



However as she points out, it could be related to testing capacity.


----------



## bluescreen (Dec 10, 2021)

Two hypotheses about why Omicron emerged in South Africa. Unsurprisingly, Merck deny it has anything to do with their clinical trials of molnupiravir, which began in October 2020. With luck, article should be free to read.




__





						Subscribe to read | Financial Times
					

News, analysis and comment from the Financial Times, the worldʼs leading global business publication




					www.ft.com


----------



## prunus (Dec 10, 2021)

bluescreen said:


> Two hypotheses about why Omicron emerged in South Africa. Unsurprisingly, Merck deny it has anything to do with their clinical trials of molnupiravir, which began in October 2020. With luck, article should be free to read.
> 
> 
> 
> ...



It's not unfortunately.  Would you mind, er, exerpting it here?


----------



## bluescreen (Dec 10, 2021)

prunus said:


> It's not unfortunately.  Would you mind, er, exerpting it here?


Sorry - their coronavirus stuff used to be open access. I don't think there's anything new, it's just in a handy article. It's a bit long, and there's graphs and all, and I don't know how to evade their naughty trackers. You could try archive.ph

Basically they're saying it has probably been around undetected for a year, as it bears more genetic similarity to older strains than to Beta and Delta. Suggestions are that either it came from chronic infection via someone with untreated HIV or evolution accelerated by the use of anti-Covid drugs. Crossover to animals then back again not ruled out but considered unlikely.


----------



## Supine (Dec 10, 2021)

bluescreen said:


> Two hypotheses about why Omicron emerged in South Africa. Unsurprisingly, Merck deny it has anything to do with their clinical trials of molnupiravir, which began in October 2020. With luck, article should be free to read.
> 
> 
> 
> ...



There is no evidence it started in South Africa.


----------



## platinumsage (Dec 10, 2021)

bluescreen said:


> Two hypotheses about why Omicron emerged in South Africa. Unsurprisingly, Merck deny it has anything to do with their clinical trials of molnupiravir, which began in October 2020. With luck, article should be free to read.
> 
> 
> 
> ...



The molnupiravir thing is not a hypothesis, it's just idle speculation.



Spoiler: FT article



Given that South Africa has faced the first wave of Omicron infections, it is likely that the variant traces its roots to somewhere in the region, said Richard Lessells, an infectious diseases physician at the University of KwaZulu-Natal in Durban.

A South African research team, which included Lessells, discovered an untreated HIV patient late last year who was infected with Covid-19 for more than six months and gave rise to a string of mutations that affected the spike protein, the part of the virus where most of Omicron’s adaptations are located. A UK study observed a similar process in a Covid patient with blood cancer.

The immune response of an untreated HIV patient would be “too weak to clear the virus but strong enough to drive the process of evolution”, explained Lessells. He said this process would allow coronavirus to mutate without being “picked up” as many of these patients are asymptomatic and therefore do not get tested.

“This evolutionary pathway is likely to be rare but it’s a plausible reason for the emergence of Omicron,” said Lessells. 

More than half of the world’s 37.7m HIV sufferers are in east and southern Africa. In South Africa alone, around 1.9m individuals have HIV that is undetected, untreated or poorly controlled, according to UNAIDs, the UN programme on HIV/Aids.

Jonathan Li, director of the Harvard/Brigham virology specialty laboratory in Boston, said it was “striking” that two variants of concern — Beta and Omicron — had arisen in southern Africa, a region with “large numbers of immunosuppressed individuals as a result of HIV infection”.

“The collision of high case numbers, low vaccine availability and decades of an HIV crisis means that the chance immunocompromised individuals have been carrying Covid for a while is very high,” said Otto. “It’s important to recognise that many of these health crises are not independent of one another.”

Another theory about how Omicron emerged in southern Africa has been advanced by William Haseltine, a virologist who has speculated that mutations could have been caused by Merck’s Covid-19 antiviral pill. He noted that South Africa was among the locations chosen for clinical trials of the drug molnupiravir, which began in October 2020.

UK and EU regulators have already authorised molnupiravir for emergency use but some scientists, including Haseltine, have warned that its mutagenic properties could, under certain circumstances, create more dangerous variants. These concerns were also raised by external experts at a US Food and Drug Administration meeting last week.

“That is a very heavily mutated virus and that is the kind of patterns you see with molnupiravir,” Haseltine told the Financial Times. “And the timing is right. I’m not saying it happened, but it could have happened.”

Merck told the FT that Haseltine’s “unfounded allegation has no scientific basis or merit”.

“There is no evidence to indicate that any antiviral agent has contributed to the emergence of circulating variants,” said a Merck spokeswoman.

As more genomes are sequenced worldwide, researchers are beginning to piece together the origins of Omicron. Each genome from areas with limited genomic surveillance coverage helps understand the “missing branches” of Omicron’s phylogenetic tree, said Lessells. More than 1,300 Omicron sequences have been uploaded to Gisaid, a global genomics repository, since November 22. 

Recent sequencing has shown the idea that Omicron was spreading undetected for some time in an area not sampled by genome testing to be “increasingly implausible”, according to Stuart Ray, professor of medicine at Johns Hopkins University.

“As we get more sequencing data, it is clear that the genomes are tightly clustered,” explained Ray. “There would be more diversity if it had been spreading undetected.”

The theory that the mutation arose in animals before being passed back to humans “is not completely implausible but there is very little reason to believe that happened”, Ray added. “When you look at the passage of human viruses in animals, they accumulate mutations that are suited to that host, not to humans.”

Back in South Africa, medics and scientists stressed that, regardless of how Omicron emerged, richer, western nations should learn the lessons of its evolution.

“We’ll never find patient zero,” said Prof Ian Sanne, director of the HIV research unit at the University of the Witwatersrand. “But we must prevent history from repeating itself.”

“For the pandemic to end, we have to...address all regions of the world at the same time. It worries me that Africa could be the last in line for an Omicron-specific vaccine, if it’s necessary.”


----------



## elbows (Dec 10, 2021)

Yeah we arent likely to get to the bottom of that variants exact origins, and much will likely remain in the realm of speculation rather than fact.

However its fair to say that more broadly, experts and authorities are aware of the potential role of immunocompromised patients and certain drug treatments in the evolution of viral strains with certain properties. Hence both SAGE and Whitty comments about antivirals in recent weeks.


----------



## elbows (Dec 10, 2021)

From the BBC live updates page: https://www.bbc.co.uk/news/live/uk-scotland-59607055



> The first minister says there are now 110 confirmed cases of Omicron.
> 
> Ten days ago there were nine, she says.
> 
> ...





> Ms Sturgeon says that the R number associated with Omicron is likely to be well over 2, close to 3.
> 
> She estimates the R number overall in Scotland is likely to rise above 2.
> 
> ...


----------



## cupid_stunt (Dec 10, 2021)

Here's the whole Telegraph article, with graphs - archive.ph


----------



## elbows (Dec 10, 2021)

Early estimates but worth highlighting:



			https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1040076/Technical_Briefing_31.pdf
		




> ▪ the risk of household transmission using routine testing data (adjusted odds ratio of transmission from an Omicron index case compared to a Delta index case 3.2 (95% CI 2.0-5.0))
> ▪ the risk of a close contact becoming a secondary case (adjusted odds ratio 2.09 (95% CI: 1.54-2.79))
> ▪ the household secondary attack rate using routine contact tracing data (Omicron, 21.6% (95% CI: 16.7%-27.4%), Delta 10.7% (95% CI: 10.5%-10.8%)





> The growth advantage is also visible in the community testing data. The proportion of cases with SGTF (now highly predictive of Omicron) continues to grow rapidly. The estimated growth rate of Omicron based on adjusted SGTF counts is 0.35 per day. If Omicron continues to grow at the present rate, Omicron case numbers are projected to reach parity with Delta cases in mid- December.





> There is currently no evidence of increased reinfection risk at the population level, but preliminary analyses indicate approximately three- to eight-fold increased risk of reinfection with the Omicron variant.





> The Variant Technical Group reviewed the available neutralisation data from published international and internal UK studies (UK Health Security Agency, University of Oxford). UK data will be published as soon as possible and cited here when available. Across 5 preliminary live virus studies (3 international and 2 UK), there was a 20- to 40-fold reduction in neutralising activity by Pfizer 2-dose vaccinee sera for Omicron compared to early pandemic viruses. There was at least 10 fold loss of activity when compared to Delta; in both UK studies this was over 20 fold. A greater reduction in activity was seen for AZ 2- dose sera, and for a high proportion of such sera, neutralising activity fell below the limit of quantification in the assay. An mRNA booster dose resulted in an increase in neutralising activity irrespective of primary vaccination type, including an increase in the proportion of samples that were above the limit of quantification. This is true regardless of which vaccine was used for the primary course. These data are from the early period after the booster and data are urgently required on the durability of neutralising activity.





> Early estimates of vaccine effectiveness (VE) against symptomatic infection find a significantly lower VE for against Omicron infection compared to Delta infection. Nevertheless, a moderate to high vaccine effectiveness of 70 to 75% is seen in the early period after a booster dose. With previous variants, vaccine effectiveness against severe disease, including hospitalisation and death, has been higher than effectiveness against mild disease. It will be a few weeks before effectiveness against severe disease with Omicron can be estimated, however based on this experience, this is likely to be substantially higher than the estimates against symptomatic disease. The duration of restored protection after mRNA boosting is not known at this juncture.



Updated variant risk assessment as a result:



			https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1040064/9_December-2021-risk-assessment-for-SARS_Omicron_VOC-21NOV-01_B.1.1.529.pdf


----------



## redsquirrel (Dec 10, 2021)

prunus said:


> It's not unfortunately.  Would you mind, er, exerpting it here?


As well as the achieve stuff or plugins, you can get round the FT paywall by opening a private browsing window and then putting the title into a google search


----------



## bluescreen (Dec 10, 2021)

Does anyone know if the risk of fomite transmission is increased with Omicron? Had a quick Google and couldn't find anything on it specifically.


----------



## _Russ_ (Dec 10, 2021)

I have no Expertise whatsoever but if the increased transmission of Omicron is because of changes in the spike protein as we are being told then I would assume that regardless of the delivery method the risk will be higher
Though of course its widely held that the main delivery method is via aerosol.


----------



## Supine (Dec 10, 2021)

bluescreen said:


> Does anyone know if the risk of fomite transmission is increased with Omicron? Had a quick Google and couldn't find anything on it specifically.



Nobody will know yet, but I wouldn’t image the latest changes are enough to fundamentally change this kind of thing. 

Luckily, it's bad enough with covid being airborne!!!


----------



## bluescreen (Dec 10, 2021)

Supine said:


> Nobody will know yet, but I wouldn’t image the latest changes are enough to fundamentally change this kind of thing.
> 
> Luckily, it's bad enough with covid being airborne!!!


Indeed! Thanks - I think there'll be a lot more mask-wearing but Joe Public hasn't been worrying about fomites as they seem pretty low risk with previous variants. Can't remember when I last saw someone using hand sanitiser.


----------



## gentlegreen (Dec 10, 2021)

I always slather on a generous amount before I grab the handle of a shopping basket.


----------



## cuppa tee (Dec 10, 2021)

gentlegreen said:


> I always slather on a generous amount before I grab the handle of a shopping basket.



could be wrong but after might be better.


----------



## gentlegreen (Dec 10, 2021)

cuppa tee said:


> could be wrong but after might be better.


I do it instead of wiping down the handle - and I always scrub up when I get home and I quarantine the shopping for a bit ...


----------



## StoneRoad (Dec 10, 2021)

I use hand santiser when I am out & about, and have touched surfaces such as door handles.
Also, I wash my hands when I get home, as well as cleaning touch points.


----------



## two sheds (Dec 10, 2021)

Yes I've not been out for a long while but I was opening doors with my elbow. Let's hope elbow transmission isn't a thing.


----------



## Monkeygrinder's Organ (Dec 10, 2021)

Has there been any proven transmission via surfaces at all yet?


----------



## l'Otters (Dec 11, 2021)

I use cotton gloves and hand sanitiser when out, wash hands with soap on arriving home - but more for general infections not particularly for covid. Don’t think any fomite transmission of covid has definitely been proved (doesn’t mean it doesn’t happen?) whereas the evidence on aerosol transmission has been clear for over well a year. 

Plenty of other unpleasant illnesses do transmit via surface contact tho so I’m still doing these things. Adopted them initially cos of covid.


----------



## teuchter (Dec 11, 2021)

Hand sanitiser everywhere annoys me a little now as its main purpose seems to be to allow people to feel as if they are doing something meaningful whilst completely ignoring ventilation.


----------



## Raheem (Dec 11, 2021)

Monkeygrinder's Organ said:


> Has there been any proven transmission via surfaces at all yet?


I don't think it is possible to take an individual case and prove transmission by a particular means. I believe the consensus is that you can catch Covid from surfaces, but that is likely to represent a small minority of cases.


----------



## gentlegreen (Dec 11, 2021)

It's my theory now that maybe in the days before handwashing, I may have got innoculated against minor viruses by inhaling or otherwise imbibing broken bits from public keyboards ...


----------



## kabbes (Dec 11, 2021)

teuchter said:


> Hand sanitiser everywhere annoys me a little now as its main purpose seems to be to allow people to feel as if they are doing something meaningful whilst completely ignoring ventilation.


I'm also concerned that a legacy of this pandemic will be a residual germophobia.  We used to view it as a sign of concern for people to constantly sanitise their hands, that this indicated an obsessive concern about an  excessively magnified risk, making it difficult for people to live their lives.  I wonder about the long-term effect of normalising this.


----------



## Monkeygrinder's Organ (Dec 11, 2021)

kabbes said:


> I'm also concerned that a legacy of this pandemic will be a residual germophobia.  We used to view it as a sign of concern for people to constantly sanitise their hands, that this indicated an obsessive concern about an  excessively magnified risk, making it difficult for people to live their lives.  I wonder about the long-term effect of normalising this.



I have one colleague who was pretty openly delighted that the hand sanitiser thing as she saw it vindicated her previous germ obsession.


----------



## 2hats (Dec 11, 2021)

Omicron and Delta could grow as separate epidemics with people infected by both, Sage warns
					

The minutes of a Sage meeting that informed government policy say both variants likely to remain common in the coming weeks




					inews.co.uk
				




Thought for the day:


----------



## SpookyFrank (Dec 11, 2021)

Monkeygrinder's Organ said:


> Has there been any proven transmission via surfaces at all yet?



Latest info seems to be that surface transmission is trivial relative to airborne droplet transmission.

So of course we're still spraying litres of toxic pink shite everywhere for cleaning tables and stuff but we're not enforcing masks.


----------



## LDC (Dec 11, 2021)

2hats said:


> Thought for the day:




Like _that'll _happen in the current mess of the NHS!


----------



## elbows (Dec 11, 2021)

LynnDoyleCooper I've not gone looking for the modelling myself yet but I see its now in the news:









						Covid: Omicron study suggests major wave in January
					

More stringent restrictions may be needed to prevent coronavirus from overwhelming hospitals, scientists say.



					www.bbc.co.uk
				






> The work by the London School of Hygiene and Tropical Medicine is not a crystal ball. It does not say what will happen with Omicron but gives a range of possible outcomes.





> In the most optimistic scenario the numbers being admitted to hospitals every day would be 40% lower than the peak last winter. In the most pessimistic scenario it would be nearly twice as high.
> 
> But the report said "the majority of scenarios" concluded that with current measures there would be more admissions than last winter.
> 
> Dr Davies said: "I think our projections are worrying, it doesn't paint an optimistic picture."


----------



## platinumsage (Dec 11, 2021)

Study: https://cmmid.github.io/topics/covid19/reports/omicron_england/report_11_dec_2021.pdf


----------



## platinumsage (Dec 11, 2021)

elbows said:


> In the most optimistic scenario the numbers being admitted to hospitals every day would be 40% lower than the peak last winter. In the most pessimistic scenario it would be nearly twice as high.
> 
> But the report said "the majority of scenarios" concluded that with current measures there would be more admissions than last winter.
> 
> Dr Davies said: "I think our projections are worrying, it doesn't paint an optimistic picture."



Previous such scenarios and projections for alpha turned out to be wildly inaccurate, with the more transmissible delta wave that came along delivering fewer hospitalizations than even the most optimistic of scenarios modeled for alpha. So when someone says "even in the most optimistic scenario" it should really be read as "in our most optimistic scenario, from our pessimistic model"


----------



## elbows (Dec 11, 2021)

What would you have them do differently? I recall from the past that you didnt like the vaccine assumptions used, and its fair enough to debate what the realistic parameters for those should be. But when it comes to whether the model itself is pessimistic, I note that they do try to test and adjust their model via things like fitting their model to real data observed in the past (and there are graphs of them doing that in this latest document, using real data from the entire pandemic so far).

And its rare for me to expect the reality to match any of the modelling projections because they have very little chance of making the correct assumptions about how peoples behaviours/the result of restrictions will change at different moments in time. Plus the modelling usually involves dates for new restrictions being imposed that dont end up perfectly mirroring the dates government actually do those things.

I am broadly content with pessimistic or realistic modelling because they end up affecting behaviour in ways that reduces the pandemic burden. 'self defeating prophecy' stuff which allows some people to indulge in stupid narratives but the modelling and its effects ultimately end up serving the cause of public health in a manner I highly approve of.


----------



## platinumsage (Dec 11, 2021)

elbows said:


> What would you have them do differently? I recall from the past that you didnt like the vaccine assumptions used, and its fair enough to debate what the realistic parameters for those should be. But when it comes to whether the model itself is pessimistic, I note that they do try to test and adjust their model via things like fitting their model to real data observed in the past (and there are graphs of them doing that in this latest document, using real data from the entire pandemic so far).



I was going to mention their vaccine efficacy figures for hospitalisation and death (falling to 66% for the unboosted in the most optimistic of the two scenerios) in Table 1. These seem to be plucked from thin air, but I wasn't sure it worth arguing on here.


----------



## teuchter (Dec 11, 2021)

platinumsage said:


> Previous such scenarios and projections for alpha turned out to be wildly inaccurate, with the more transmissible delta wave that came along delivering fewer hospitalizations than even the most optimistic of scenarios modeled for alpha. So when someone says "even in the most optimistic scenario" it should really be read as "in our most optimistic scenario, from our pessimistic model"


Is it not more the case that prrdictions were made for what would happen without restrictions, restrictions were then put in in a half baked way, and we never got to see what would have actually happened without them.


----------



## elbows (Dec 11, 2021)

platinumsage said:


> I was going to mention their vaccine efficacy figures for hospitalisation and death (falling to 66% for the unboosted in the most optimistic of the two scenerios) in Table 1. These seem to be plucked from thin air, but I wasn't sure it worth arguing on here.



I cant say how close to reality they will be, but they arent plucked from thin air:



> Neutralisation studies on Omicron are ongoing, so we rely on a combination of estimates of the fold reduction in neutralisation titre for previous variants of concern (VOCs) as well as early studies explicitly considering Omicron neutralisation (1–5) to inform our assumptions about the level of immune escape Omicron might possess. The largest drop in neutralisation titre (8.8 fold) was estimated for the Beta VOC (20), with a 3.9 fold reduction for the Delta variant, compared to the ancestral SARS-CoV-2 virus. We consider two scenarios for the immune escape of Omicron relative to Delta: 5.1-fold (escape low, EL) and 12.8-fold (escape high, EH) reductions compared to our existing assumptions for Delta (19). Since the Delta variant was estimated to have a 3.9 fold reduction in neutralisation compared to the ancestral SARS-CoV-2 virus, these assumptions correspond to overall fold reductions of approximately 20 and 50-fold between the ancestral SARS-CoV-2 virus and the Omicron variant.





> We use the relationship between mean neutralisation titre and protective efficacy from Khoury et al. (7) to arrive at assumptions for vaccine efficacy against infection with Omicron, given each drop in neutralisation. We then use Khoury et al.’s modelled relationship between efficacy against any infection and efficacy against severe infection to generate vaccine effectiveness estimates against severe outcomes (Fig. 1c). For the effectiveness of booster vaccinations against Omicron, we base two main scenarios on two studies which measured increases in neutralisation titres following the second dose of the primary vaccination course and after booster vaccinations with the Moderna (2.5-fold) and Sinovac (4.9-fold) vaccines (20). We assume that protection against infection for individuals who have received a primary course of the AstraZeneca COVID-19 vaccine before being boosted with either full-dose Pfizer or half-dose Moderna (the current policy in England) is initially increased to the same levels as Pfizer/Moderna, before using the relationship in Fig. 1c to scale protection against infection to protection against severe outcomes (hospitalisation and death). We assume that individuals in the recovered disease state who have previously been infected with SARS-CoV-2 have the same level of protection against Omicron as individuals who have received two doses of Pfizer/Moderna. Our estimates for vaccine protection against different outcomes for the Delta variant and for the various Omicron scenarios are shown in Table 1.





> These estimates are broadly in line with early vaccine effectiveness estimates against Omicron and Delta from the UK’s Health Security Agency (21), with the exception that our assumptions for dose 2 AstraZeneca vaccine protection against Omicron disease are high in comparison (we assume 38.2% and 23.3% protection against disease, whereas the UKHSA study’s highest estimate for protection against Omicron disease with two doses of AstraZeneca is 5.9%).


I have mentioned in other posts some acknowledged limitations with the UKHSA AZ estimates that they mention in that last bit, so I'm not surprised they have used higher ones for that.


----------



## platinumsage (Dec 11, 2021)

teuchter said:


> Is it not more the case that prrdictions were made for what would happen without restrictions, restrictions were then put in in a half baked way, and we never got to see what would have actually happened without them.



The models included restrictions, the reality of transmissibility and restrictions was worse than modeled, but the outcome in terms of cases and deaths was better than their most optimistic scenario. I’d dig it out and match it up to what actually happened again, but I don’t think there’s much appetite for criticism of SAGE on here.


----------



## platinumsage (Dec 11, 2021)

elbows said:


> before using the relationship in Fig. 1c to scale protection against infection to protection against severe outcomes (hospitalisation and death).



^^ that's what plucking from thin air looks like


----------



## elbows (Dec 11, 2021)

Its what uncertain science looks like, have you got a better methodology they could use instead? Would you rather they pluck optimistic stuff from thin air instead? And this isnt SAGE, although obviously they are one of the sources SAGE relies on and there is overlap between people in the academic institutions and members of SAGE.

Please do dig the old stuff out, so we can evaluate your criticisms of past modelling.


----------



## platinumsage (Dec 11, 2021)

elbows said:


> Its what uncertain science looks like, have you got a better methodology they could use instead? Would you rather they pluck optimistic stuff from thin air instead? And this isnt SAGE, although obviously they are one of the sources SAGE relies on and there is overlap between people in the academic institutions and members of SAGE.



A good starting point would be to use the protection against hospitalisation and death figures for delta in the main model. There's currently no evidence to suggest the figures for omicron will be lower. They could always produce a secondary set of scenarios using stepwise reductions in those figures.


----------



## platinumsage (Dec 11, 2021)

elbows said:


> Please do dig the old stuff out, so we can evaluate your criticisms of past modelling.



No. Last time I did something like that you said "I am not interested in playing this stupid game with you" so I'll try and stick to reddit for that stuff.


----------



## elbows (Dec 11, 2021)

I'd agree that evidence isnt there yet but I also think its reasonable for them to assume it could be lower, especially if its only a little lower. Especially given that even a small reduction can make quite a difference to the numbers.

But yes, I'd have nothing against a larger number of scenarios being presented in modelling reports. Including more optimistic ones. But then it comes down to what some people will want build off the back of more optimistic scenarios being presented at this time. An excuse to do less at this stage? That carries its own risk, better safe than sorry is a reasonable approach given the stakes.


----------



## elbows (Dec 11, 2021)

platinumsage said:


> No. Last time I did something like that you said "I am not interested in playing this stupid game with you" so I'll try and stick to reddit for that stuff.


I'll do it myself then when I find time. I expect I'll be able to build a case that you are misrepresenting the limitations of past modelling in order to serve your dubious agenda.


----------



## gentlegreen (Dec 11, 2021)

.


----------



## platinumsage (Dec 11, 2021)

elbows said:


> But yes, I'd have nothing against a larger number of scenarios being presented in modelling reports. Including more optimistic ones. But then it comes down to what some people will want build off the back of more optimistic scenarios being presented at this time. An excuse to do less at this stage? That carries its own risk, better safe than sorry is a reasonable approach given the stakes.



This is the problem. Their output is presented as covering a range of scenarios, and the impression given is that that this is the range of likely scenarios, whereas it's actually a subset of pessimistic scenarios.


----------



## teuchter (Dec 11, 2021)

I'd also be very interested to see a proper direct comparison between modelled and actual outcomes for previous waves.


----------



## elbows (Dec 11, 2021)

platinumsage said:


> This is the problem. Their output is presented as covering a range of scenarios, and the impression given is that that this is the range of likely scenarios, whereas it's actually a subset of pessimistic scenarios.


Does that mean that you think I wont be able to find any modelling scenarios that showed better outcomes than actually turned out to be the case?

I'll probably start looking at this with the most recent (before Omicron) modelling first - ie first I will look at the modelling of the Delta wave post-'freedom day' and compare it to what actually happened. I know that some modelling they did before the summer relaxation of measures showed worse outcomes than happened, in great part because their scenarios included a return to greater levels of normal behaviour than was initially actually the case. But I think they did a set of modelling after that reality had become clearer, I will check.


----------



## elbows (Dec 11, 2021)

teuchter said:


> I'd also be very interested to see a proper direct comparison between modelled and actual outcomes for previous waves.


Well you know I wont be able to take a proper academic stab at that, just cruder attempts at such stuff. But I'd be surprised if there have been no academic papers on that theme, though whether I have time to find any of them is another question.


----------



## Supine (Dec 11, 2021)

teuchter said:


> I'd also be very interested to see a proper direct comparison between modelled and actual outcomes for previous waves.



If you fancy something to read this paper compares a couple of models used on the Spanish covid data. 






						Predictive Mathematical Models of the Short-Term and Long-Term Growth of the COVID-19 Pandemic
					

The prediction of the dynamics of the COVID-19 outbreak and the corresponding needs of the health care system (COVID-19 patients’ admissions, the number of critically ill patients, need for intensive care units, etc.) is based on the combination of a limited growth model (Verhulst model) and a...




					www.hindawi.com


----------



## 2hats (Dec 11, 2021)

In part-answer, some models actually didn't perform too badly - for a given set of conditions the relevant scenario offered largely played out with a not unreasonable level of concordance.








						Bad data and flawed models? Fact-checking a case against lockdowns
					

Was the government’s decision to implement lockdowns to combat COVID-19 based on faulty evidence? Philippe van Basshuysen (Leibniz University Hannover and LSE) and Lucie White (Leibniz University H…




					blogs.lse.ac.uk
				




Related, though not directly addressing the question, you might find this interesting.
'_Two perspectives on the use of modelling during the pandemic_', (SPI-M).


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## teuchter (Dec 11, 2021)

elbows said:


> Well you know I wont be able to take a proper academic stab at that, just cruder attempts at such stuff. But I'd be surprised if there have been no academic papers on that theme, though whether I have time to find any of them is another question.


It's one of the things i keep seeing elsewhere, said by those who think the whole covid thing has just been a fuss about nothing with everyone drummed into paranoia by the government/scientists/communists/big pharma or whatever. It's stated as fact that all the previous alarming projections presented to the public turned out to bear no resemblance to what actually happened. But I've not had the time or skills or energy to go back through it and try and get a handle on how true that is - ie is it complete nonsense, or slightly true, or kind of true but only if you ignore X or Y.


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## elbows (Dec 11, 2021)

Well I certainly dont intend to spend any time looking at it from the fucking stupid angle of those people. There is no huge need to study the detail when it comes to that since the number of deaths seen in the waves, number of hospitalisations etc was quite sufficient to see why the initial waves were a big deal that governments could not ignore. We saw how awful things were getting before lockdown and massive behavioural changes kicked in. And many of the real data totals got rather large despite the fact that rather strict measures were eventually implemented each time. But the extremists who try to suggest all the modelling was just propaganda also tend to be in complete denial about whats shown by actual data that measures what happened, giving me little reason to attempt to argue sincerely with them about detail of modelling.

Plus when it comes to the detail, its not like any of the modelling exercises said 'this is what is going to happen', they are mostly all exercises in what sorts of curves, peaks and and totals you get when you change various modelling input parameters. Done so that policy makers get an idea of what sort of effects they might expect if they implement various strengths of measures, and what to expect with variants with different transmission, immune escape levels, different pace of return to normal behaviours by the population, different amounts of waning immunity over time etc etc. Or stuff designed to see what sort of reasonable worst case scenarios need to be planned for in advance, eg in advance of winter. As such I've alway struggled to know which bits of modelling documents to quote, and have ended up posting numerous graphs and explanations as a result, as well as going on about confidence intervals and paying attention to ranges rather than single numbers.

Anyway since the latest modelling we hae seen this time around is from the London School of Hygiene and Tropic Medicine, I decided the first summer 2021 modelling I would look at was from them ( https://assets.publishing.service.g...rior_to_delayed_step_4.2__7_July_2021__1_.pdf ). Here is my summary of my opinion about it now that we have the benefit of data hindsight in regards most of that period:

Some of the scenarios they presented did a reasonably good job of coming out with total estimated numbers of infections, hospitalisations and deaths for the July-December 2021 period that are in the same realm as the real totals for the period have turned out to be for England. Some other scenarios/demonstrations of what happens when you change one or two parameters were wider of the mark when it came to totals, but thats normal enough and demonstrates that they covered a fair range of different possibilities in both directions, not just the most extremely bad ones, although there were certainly a lot of those included. In terms of the peak levels their modelling came out with, as opposed to totals, they tended to came out with peak levels that were notably higher than what actually happened. And they didnt really get the curve shape of what was seen from July to December right either, although their modelling that included what effects waning vaccine effectiveness could have did manage to better hint at the later curve shape and later persistence of the wave. But it still featured a larger initial peak and smaller resurgence relative to that peak than was actually seen. However those same scenarios where they included assumptions about waning effects of vaccines were really far wide of the mark when it came to the various totals for the whole period. But thats not too surprising given that they said in the document that their method of accounting for waning probably wasnt very good and would need later refinement. The scenarios that featured totals that ended up close to the real totals seen managed this despite getting the peak sizes and shape of wave wrong because two wrongs ended up making a right - in reality the first summer peak wasnt as high as their modelling tended to show, but after those peaks the wave then persisted at higher levels than their model showed.

Trying to put that into words fairly turned out to be way more tedious than the process of re-reading that modelling document and comparing it to actual data and forming my conclusions in my mind. And it starts to remind me of all the other sorts of blah blah blah I inevitably end up coming out with when I try to describe modelling exercises in any detail. Partly because sometimes the tables of numbers and the graphs are a better way to put it than all these words, but also because they cover so many scenarios and 'what ifs when different parameters are changed' that I'm not reviewing one thing, I'm not comparing an attempt at a single prediction with what actually happened, so I cant come out with a single judgement and neat description of how well they managed.

I'm certainly happy to point out that I think modelling is more challenging now than it once was. At the start of the pandemic the assumptions about population susceptibility were really straightforward. These days there are so many more uncertain input parameters, such as all manner of aspect of the effects of vaccines, and properties of variants. And they certainly dont have any magic ways to make all the right guesses and assumptions about those, they just want to pick a useful range of possibilities for those and then model what the implications are of those different possibilities.


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## weltweit (Dec 12, 2021)

I don't like the uncertainty, as soon as we have some facts about Omicron I will be happier.


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## elbows (Dec 12, 2021)

weltweit said:


> I don't like the uncertainty, as soon as we have some facts about Omicron I will be happier.



There are a larger number of uncertainties this time. A lot of what will be learnt will be based on studying the real data that emerges as more people get infected, and some of these pictures will take some time to emerge sufficiently. South Africa can offer some clues ahead of the UK situation being able to do so, but there is also some wariness about whether everything obsered in South Africa will hold fully true in the UK context. This is for a number of reasons including different demographics and different sizes and features of past waves in the two countries.

Modelling is only as good as the assumptions fed into it, so even when I am a fan of the utility of these models, I have to take them with an even larger pinch of salt this time. The people doing them know this all too well, and expect to have to update their stuff as more data emerges and better estimates of various things can be fed into the models. And I dont think certain possibilities are probed at all in the modelling we've seen this time so far, eg seeing what happens when different levels of clinical severity (and hospitalisation ratios) for Omicron are fed into those models. But perhaps some other groups modelling that has been looked at by authorities but not seen by us yet does look at that side of things. Even if they have, it wont tell us anything about what the actual clinical picture of this variant is, only what sort of thing happens to the numbers if they play around with these values/guesses.

The current modelling only offers me vague clues about how strong the further restrictions will actually need to be. It offers clues about what sort of scale of challenges they have to consider to be possible at this stage of great uncertainty about many things. Real data that arrives once the wave is larger will provide a far more substantial guide, but unless it tells a happy story it will arrive too late for authorities to act on it with the right strength of measures at the right time.


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## cupid_stunt (Dec 12, 2021)

Nadhim Zahawi  interviewed on Sky News' Trevor Phillips on Sunday show - 1/3rd of cases in London are now omicron, and we now know that there are omicron cases in hospital too.


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## teuchter (Dec 12, 2021)

elbows said:


> Some of the scenarios they presented did a reasonably good job of coming out with total estimated numbers of infections, hospitalisations and deaths for the July-December 2021 period that are in the same realm as the real totals for the period have turned out to be for England. Some other scenarios/demonstrations of what happens when you change one or two parameters were wider of the mark when it came to totals, but thats normal enough and demonstrates that they covered a fair range of different possibilities in both directions, not just the most extremely bad ones, although there were certainly a lot of those included. In terms of the peak levels their modelling came out with, as opposed to totals, they tended to came out with peak levels that were notably higher than what actually happened. And they didnt really get the curve shape of what was seen from July to December right either, although their modelling that included what effects waning vaccine effectiveness could have did manage to better hint at the later curve shape and later persistence of the wave. But it still featured a larger initial peak and smaller resurgence relative to that peak than was actually seen. However those same scenarios where they included assumptions about waning effects of vaccines were really far wide of the mark when it came to the various totals for the whole period. But thats not too surprising given that they said in the document that their method of accounting for waning probably wasnt very good and would need later refinement. The scenarios that featured totals that ended up close to the real totals seen managed this despite getting the peak sizes and shape of wave wrong because two wrongs ended up making a right - in reality the first summer peak wasnt as high as their modelling tended to show, but after those peaks the wave then persisted at higher levels than their model showed.


 That seems a fair summary. I have taken some of the graphs in the document you linked to, these ones on page 16:



And roughly overlaid the "reality" graphs from the gov.uk dashboard with the scales more or less adjusted to be the same and it looks like this:



What's interesting to me is that there is a second 'hump' around November that their "scenario 2" line predicts, and it's also visible in the real data, and they have got the timing pretty much right, even if the magnitude and overall direction of travel is different.
(maybe this should be in the nerdy details thread instead)


----------



## Badgers (Dec 12, 2021)




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## Pickman's model (Dec 12, 2021)

Badgers said:


>



This will end well


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## elbows (Dec 12, 2021)

teuchter said:


> (maybe this should be in the nerdy details thread instead)


Yeah I think that if I feel the need to look at other models from the past I will try to stick the detail in that thread instead, as I'm not sure there will be much that is highly relevant to whats happening with Omicron now. I'll just say that the graphs you posted were ones I think they chose in order to demonstrate the large degree of uncertainty, how far apart two different modelling scenarios for that period could be. Some of the later ones, especially ones with waning included, show the later bump in a slightly more obvious way. Also note that models sometimes get the timing of some phenomenon right because they've likely got school holiday timing baked into them, and in this case they might have been reasonable in their assumptions of the timing of waning if not the magnitude. I dont know as they got the strength of seasonal factors right though, and I wouldnt be surprised if they failed to anticipate the strength of effects seen earlier via 'the pingdemic' (large numbers self isolating acting as a sort of equivalent to a mini lockdown during a crucial period).

And just to repeat a point one last time, part of the utility of such modelling for authorities is not as a prediction of what will happen, but as a guide as to what sort of effects you'd see if you change some parameters, whether they be parameters relating to restrictions and behaviour, or examples of what happens if the properties of a variant and vaccines protection against it turn out to have changed in particular ways. If I were making big decisions I'd want to see such examples, even though they are not a guide as to what those variant properties actually are in reality.


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## SpookyFrank (Dec 12, 2021)

teuchter said:


> I'd also be very interested to see a proper direct comparison between modelled and actual outcomes for previous waves.



Not really possible as the outcome of those waves was affected by measures taken in response to the modelling.


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## Monkeygrinder's Organ (Dec 12, 2021)

SpookyFrank said:


> Not really possible as the outcome of those waves was affected by measures taken in response to the modelling.



A mathematical model could be recalculated retrospectively based on those effects though couldn't it? If you have a formula including measure X you could plug that in even if you didn't calculate it for the eventual actual value at the time.


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## teuchter (Dec 12, 2021)

A claim here that it's peaked in Gauteng


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## magneze (Dec 12, 2021)

🤞


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## Mr.Bishie (Dec 12, 2021)

magneze said:


> 🤞


Innit?!! So hope this cunting virus has fucked itself with the 30 spike mutation!


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## SpookyFrank (Dec 12, 2021)

teuchter said:


> A claim here that it's peaked in Gauteng




No restrictions needed anywhere is not a claim that can be made based on that data. We desperately needed more restrictions _before_ Omicron showed up ffs.


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## elbows (Dec 12, 2021)

teuchter said:


> A claim here that it's peaked in Gauteng



I dont know what to make of South Africa case data for several reasons that are covered here in this reply to Scott:


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## teuchter (Dec 12, 2021)

SpookyFrank said:


> No restrictions needed anywhere is not a claim that can be made based on that data. We desperately needed more restrictions _before_ Omicron showed up ffs.



Yes, the fact that he makes that claim makes me disinclined to trust him in general.


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## elbows (Dec 12, 2021)

The media arent so hot at reporting all the key points from modelling documents. For example with the latest Omicron modelling we saw, in addition to not bothering to detail the confidence intervals, they also neglected to mention that the modelling people didnt find that speeding up the booster campaign made much difference to the pandemic numbers for this wave. The percentage of people who take up the booster offer does make a notable difference to their results though. And its always possible one of their assumptions in this regard is faulty, for example they've assumed that the most at risk people have been prioritised for boosters and will already have received them, but I'm not sure thats actually reflected in the real world booster data, there are some alarming gaps.


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## _Russ_ (Dec 12, 2021)

> for example they've assumed that the most at risk people have been prioritised for boosters and will already have received them, but I'm not sure thats actually reflected in the real world booster data, there are some alarming gaps.




UK clinics defy guidance and give under-40s their Covid booster jabs now


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## elbows (Dec 12, 2021)

teuchter said:


> A claim here that it's peaked in Gauteng




Look away now if you dont want to see what happened next.


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## Ax^ (Dec 12, 2021)

is johnson due on at 8 


operation distract from the christmas parties still on going


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## elbows (Dec 12, 2021)

So yeah like I pointed to earlier, South Africa have some data delay issues. And even if they didnt have particular data issues right now, we can see from past pattern of daily figures that they have data-related dips at fairly frequent intervals that should be taken into account when considering both an individual days figures and those figures short-term effect on 7 day averages.


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## Ax^ (Dec 12, 2021)

jesus is he wearing one of prince philips old suits

he looks like he has covid again


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## Ax^ (Dec 12, 2021)

now if you  did a lot of cocaine at a christmas party thats how your eyes and bags would look like


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## weltweit (Dec 12, 2021)

Glad we all got our boosters already. 

The queues might be something.


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## Ax^ (Dec 12, 2021)

any one under 40 :/


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## weltweit (Dec 12, 2021)

Covid: First people in UK hospitals with Omicron variant
					

The variant accounts for a third of infections in London, Education Secretary Nadhim Zahawi says.



					www.bbc.co.uk
				






> Dr Susan Hopkins, chief medical adviser for the UK Health Security Agency, said she expected to see an increase in the number of people in hospital with Omicron infection.





> It is not clear if those people who are in hospital with Omicron are there because of the virus or for other reasons.





> She said there had not been a report of a death from the variant in the UK yet, although she pointed out that it had only been identified two weeks ago. It is two weeks after infection that you would expect to see people admitted to hospital, with deaths coming after that.


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## teuchter (Dec 13, 2021)

elbows said:


> Look away now if you dont want to see what happened next.



He says that previous waves haven't reached more than 30% of the population anywhere - is that true and is it particular to Covid?


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## BigMoaner (Dec 13, 2021)

anyone else getting those slow pangs of covid fear/anxiety. they had gone from my life for months. rearing up again. mainly around somehow sometime losing my job, and then everything will massively fall apart for me.


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## ska invita (Dec 13, 2021)

BigMoaner said:


> anyone else getting those slow pangs of covid fear/anxiety. they had gone from my life for months. rearing up again. mainly around somehow sometime losing my job, and then everything will massively fall apart for me.



Why might you lose your job Moaner?


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## elbows (Dec 13, 2021)

teuchter said:


> He says that previous waves haven't reached more than 30% of the population anywhere - is that true and is it particular to Covid?


There are problems giving a straightforward answer to that.

For example there is the question of how such things are measured and/or estimated. Its not going to be through routine testing of people for current infection, because there are massive undercounts in that data and testing was especially limited in many places in the first wave. So its going to be estimated via things like antibody testing of blood donors. And the samples may be biased in various ways as a result.

Its also going to vary depending on how much you zoom in, either on subsets of the population or by zooming into a narrower geographical area.

And of course there is the fact that most places had to take extreme measures to reduce the number of people getting infected, in order to stop hospitals being overwhelmed. But obviously there are variations on this theme, especially during the vaccine era where we've seen how many millions of people in the UK have shown up via testing as having caught the virus in the Delta wave over a substantial period of time. That level of infection has been considered tolerable due to the changed hospitalisation ratio that vaccines brought over this time period against the strain dominant at the time.

So when it comes to comparisons with other diseases, we have to take into account what mitigations against the disease were actually bothered with when it came to other diseases vs covid. And we also have to consider the lack of mass testing for most diseases in normal times, meaning most data about how many people were infected with other diseases are vague estimates or assumptions.

When it comes to Covid and your question, I suppose I would suggest studying Manaus as an example where a very large proportion of people were thought to have caught it in their first wave, and where there was a fair amount of reporting on this detail later once the hoped-for herd immunity in that area did not turn out to save them from future woe.

eg look at various detail here: Covid-19: Is Manaus the final nail in the coffin for natural herd immunity?


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## cupid_stunt (Dec 13, 2021)

According to Johnson, yeah I know, the UK has at least one death from omicron.









						Boris Johnson says at least one person has died with Omicron Covid variant
					

The Prime Minister confirmed 'sadly at least one patient has been confirmed to have died with Omicron' - and refused to rule out more restrictions by Christmas




					www.mirror.co.uk


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## elbows (Dec 13, 2021)

Also teuchter consider looking at the detail from seroprevalence studies from New York, eg:



> *Results: *The seroprevalence among 45 367 participants was 23.6% (95% confidence interval, 23.2%-24.0%). High seroprevalence (>30%) was observed among black and Hispanic individuals, people from high poverty neighborhoods, and people in healthcare or essential worker industry sectors. COVID-19 symptom history was associated with seropositivity (adjusted relative risk, 2.76; 95% confidence interval, 2.65-2.88). Other risk factors included sex, age, race/ethnicity, residential area, employment sector, working outside the home, contact with a COVID-19 case, obesity, and increasing numbers of household members.











						Seroprevalence of Severe Acute Respiratory Syndrome Coronavirus 2 Following the Largest Initial Epidemic Wave in the United States: Findings From New York City, 13 May to 21 July 2020 - PubMed
					

Based on a large serosurvey in a single US jurisdiction, we estimate that just under one-quarter of NYC adults were infected in the first few months of the COVID-19 epidemic. Given disparities in infection risk, effective interventions for at-risk groups are needed during ongoing transmission.




					pubmed.ncbi.nlm.nih.gov


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## Numbers (Dec 13, 2021)

BigMoaner said:


> anyone else getting those slow pangs of covid fear/anxiety. they had gone from my life for months. rearing up again. mainly around somehow sometime losing my job, and then everything will massively fall apart for me.


I worry about my job a bit, what I do can be done from anywhere in the world and for a lot cheaper too, this was the case pre Covie too tho'.


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## elbows (Dec 13, 2021)

Another angle to consider teuchter is modelling of diseases, and attempts to ascertain what use things like R0 estimates are when making public health decisions. Because there is considered to be a relationship between things like R and the attack rate.

eg: Unraveling R0: Considerations for Public Health Applications



> The overall attack rate, the percentage of individuals who will get sick during an outbreak in a given population, may be the one disease characteristic of most interest to public health authorities, and the attack rate is the characteristic that appears to be most plausibly predicted by using estimates of _R_0.



With that in mind, I doubt it is a good idea to go looking for overly simplistic assumptions about a single maximum potential attack rate for Covid, given large differences between variants. Although care should also be taken to appreciate the difference between R0 and other versions of R.


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## elbows (Dec 13, 2021)

A little bit of early vaccine-status data for Omicron cases discovered in Denmark so far. I would want to be aware of far more details about their vaccination programme, vaccines used and schedule between doses, booster campaign etc, as well as details of demographics of Omicron cases in Denmark so far, before trying to apply any conclusions from this data to other countries.



From a report at https://files.ssi.dk/covid19/omikron/statusrapport/rapport-omikronvarianten-12122021-k29d


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## BigMoaner (Dec 13, 2021)

ska invita said:


> Why might you lose your job Moaner?


i work at a uni. i dunno, continued covid means they can't recruit as many students (nearly half are recruited from overseas)/hold as many events etc, therefore profits fall, therefore cuts.

i'm 90% sure it won't happen, but that doesn't stop the occasional pang of worry.


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## weepiper (Dec 13, 2021)

First hospitalisations yesterday and first death today seems... not good.


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## Pickman's model (Dec 13, 2021)

popped into a bookshop at lunchtime and chatted to the owner about the virus for a bit. they were quite sure there'd not be a lockdown over this one. me, i think they might be too optimistic. certainly if we're looking at say 75-100k infections a day and a 1-2% hospitalisation rate i feel a lockdown's on the cards.


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## Raheem (Dec 13, 2021)

weepiper said:


> First hospitalisations yesterday and first death today seems... not good.


No, although we shouldn't take too much from one case.


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## ska invita (Dec 13, 2021)

Pickman's model said:


> popped into a bookshop at lunchtime and chatted to the owner about the virus for a bit. they were quite sure there'd not be a lockdown over this one. me, i think they might be too optimistic. certainly if we're looking at say 75-100k infections a day and a 1-2% hospitalisation rate i feel a lockdown's on the cards.


One projection was a million cases by the end of the month then two million not long after that!! cant see how you cant have a lockdown , adn that from Sajid Javid!!








						Rapid infection rate of omicron Covid variant is causing concern, as UK braces for 1 million cases
					

"The omicron data is enormously worrying," immunologist Danny Altmann told CNBC, pointing to the U.K's 2.5-day doubling time of cases.




					www.cnbc.com
				




There should be one now of course, but just as last December, everything most be open so xmas trade can happen.

Id bet on a January lockdown


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## Pickman's model (Dec 13, 2021)

ska invita said:


> One projection was a million cases by the end of the month then two million not long after that!! cant see how you cant have a lockdown , adn that from Sajid Javid!!
> 
> 
> 
> ...


yeh january suits me better than december - i hope spooks reading this can pass that up the ladder


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## LDC (Dec 13, 2021)

Fucking BBC presenters hanging on to this 'causes mild disease' thing. FFS.


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## Raheem (Dec 13, 2021)

ska invita said:


> Id bet on a January lockdown


Reckon the government is with you, but omicron may have an opinion.


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## ska invita (Dec 13, 2021)

Raheem said:


> Reckon the government is with you, but omicron may have an opinion.



the government dont care about the viruses opinon
this is when we came out of lockdown last year so as to "do xmas"


100% theyre doing the same thing again


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## StoneRoad (Dec 13, 2021)

ska invita said:


> the government dont care about the viruses opinon
> this is when we came out of lockdown last year so as to "do xmas"
> View attachment 300640
> 
> 100% theyre doing the same thing again


"they" don't care, as long as you "spend, SpEnD ! SPEND !!!" in the lead up to the so-called festive period. That's hat their paymasters want to happen.

I know from a few years spent working in shops, almost 3/4 of turnover happens in the last 1/4 of the year [made up from the late October to Early January period].


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## ska invita (Dec 13, 2021)

StoneRoad said:


> I know from a few years spent working in shops, almost 3/4 of turnover happens in the last 1/4 of the year [made up from the late October to Early January period].


well exactly - some retailers loses money all year and make all profits over this periid
it would be a financial disaster to shut down the economy at this time of year, which also means jobs and livelihoods
i dont think its a straightforward call to make
*but *its clear their decisions are made to be popular (save xmas etc), to not spend state money, and to downplay risks that lead to this moment in first place - theres a lot more that could be done right now without shutting shops


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## prunus (Dec 13, 2021)

weepiper said:


> First hospitalisations yesterday and first death today seems... not good.



It’s entirely expected and doesn’t change the outlook at all.


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## Raheem (Dec 13, 2021)

prunus said:


> It’s entirely expected and doesn’t change the outlook at all.


I don't think it's expected that a death would typically be one day after a hospital admission. It can happen, but it's not just the usual way of things.

Otoh, I don't think it's clear that the hospital admission was one day prior. It could have been, but it may have been somebody already admitted testing positive for omicron.


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## elbows (Dec 13, 2021)

They are bound to go on about deaths especially at the moment to try to counteract some of the simplistic sentiments that may have built up as a result of the talk of it being mild.


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## Smangus (Dec 13, 2021)

I have a colleague at work who's son is  a doctor in a London hospital. They have been told all operations are cancelled and that to expect a lockdown in Jan.


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## prunus (Dec 13, 2021)

Raheem said:


> I don't think it's expected that a death would typically be one day after a hospital admission. It can happen, but it's not just the usual way of things.
> 
> Otoh, I don't think it's clear that the hospital admission was one day prior. It could have been, but it may have been somebody already admitted testing positive for omicron.



Was it one day post admission? I hadn’t read that. All the hospitalisations tested positive before or on admission (ie it wasn’t somebody already admitted testing positive for omicron.)

What I meant was, hospitalisations and deaths from omicron are entirely expected and the fact that they’re happening shouldn’t change one’s assessment of the danger.


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## elbows (Dec 13, 2021)

prunus said:


> What I meant was, hospitalisations and deaths from omicron are entirely expected and the fact that they’re happening shouldn’t change one’s assessment of the danger.


Depends how far wide of the mark some peoples assessment of Omicron has been so far.


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## prunus (Dec 13, 2021)

elbows said:


> Depends how far wide of the mark some peoples assessment of Omicron has been so far.



Fair! Shouldn’t change a sensible data-driven assessment then perhaps!


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## SpookyFrank (Dec 13, 2021)

weltweit said:


> Glad we all got our boosters already.
> 
> The queues might be something.



Nobody can book at the moment because the whole system is borked by massive demand. Likely result of Johnson's 'massive acceleration' will therefore be, um, fewer people getting boosters.


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## andysays (Dec 13, 2021)

prunus said:


> Was it one day post admission? I hadn’t read that. All the hospitalisations tested positive before or on admission (ie it wasn’t somebody already admitted testing positive for omicron.)
> 
> What I meant was, hospitalisations and deaths from omicron are entirely expected and the fact that they’re happening shouldn’t change one’s assessment of the danger.


I think that's the point Raheem was making - it's not clear that this particular death is someone who was admitted the day before.

All we really know is that the first known admissions to hospital with Omicron happened yesterday, and the first known death with Omicron happened today, and I suspect they're unlikely to release any more specific info than that, TBH.

But the wider point about which there should be no doubt is that the situation is quickly getting worse, including hospital admissions and now at least one known death and probably some which have not yet been identified as Omicron.


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## andysays (Dec 13, 2021)

SpookyFrank said:


> Nobody can book at the moment because the whole system is borked by massive demand. Likely result of Johnson's 'massive acceleration' will therefore be, um, fewer people getting boosters.


There are still walk-in vaccinations available, but I fear the high demand will discourage some of those who perhaps need the booster the most, and mean that those who are more able to travel further and/or queue for hours will be more likely to get it.


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## weltweit (Dec 13, 2021)

SpookyFrank said:


> Nobody can book at the moment because the whole system is borked by massive demand. Likely result of Johnson's 'massive acceleration' will therefore be, um, fewer people getting boosters.


For me and my son we didn't book, we just checked the centres we were going to were doing "walk ins" and then just went there and got jabbed.


----------



## SpookyFrank (Dec 13, 2021)

weltweit said:


> For me and my son we didn't book, we just checked the centres we were going to were doing "walk ins" and then just went there and got jabbed.



Local walk in centre for us started turning people away at 1pm because they're only open til 5 and the queue was four hours long.


----------



## weltweit (Dec 13, 2021)

SpookyFrank said:


> Local walk in centre for us started turning people away at 1pm because they're only open til 5 and the queue was four hours long.


Oh, ok .. we went pre Boris announcement, the queues were much more manageable and we went both of us mid morning.


----------



## elbows (Dec 13, 2021)

andysays said:


> I think that's the point Raheem was making - it's not clear that this particular death is someone who was admitted the day before.
> 
> All we really know is that the first known admissions to hospital with Omicron happened yesterday, and the first known death with Omicron happened today, and I suspect they're unlikely to release any more specific info than that, TBH.
> 
> But the wider point about which there should be no doubt is that the situation is quickly getting worse, including hospital admissions and now at least one known death and probably some which have not yet been identified as Omicron.


Yes and even when comments to the public about these figures are made in a timely way, the data still isnt always timely and is certainly an incomplete picture.

Plus when it comes to deaths, plenty of them dont happen in hospital. I dont think the NHS England hospital death total has even quite reached 100,000 yet, at least not the version that only includes people in hospital that tested positive.


----------



## elbows (Dec 13, 2021)




----------



## xenon (Dec 13, 2021)

andysays said:


> There are still walk-in vaccinations available, but I fear the high demand will discourage some of those who perhaps need the booster the most, and mean that those who are more able to travel further and/or queue for hours will be more likely to get it.



The nearest walk in place here is only jabbing people who've had their second jab prior to July. So no garantee you'll get one if you turn up, queueing in the rain.

I'm booked there for 22nd but may try this Friday.


----------



## weltweit (Dec 13, 2021)

Wondering if there will be any requirement to separate delta and omicron patients in hospital given that delta patients can also get omicron?


----------



## Pickman's model (Dec 13, 2021)

weltweit said:


> Wondering if there will be any requirement to separate delta and omicron patients in hospital given that delta patients can also get omicron?


Yeh there is, it's in beta mode at the moment


----------



## Riklet (Dec 13, 2021)

weltweit said:


> Wondering if there will be any requirement to separate delta and omicron patients in hospital given that delta patients can also get omicron?



Unlikely.  Also, we don't know that's true at all for a start.  Especially while already infected.  In fact, it's rather unlikely.  This seems to be a media misrepresentation of the fact that prior infection with delta provides little protection against omicron and recent covid convalescents in South Africa have caught omicron in significant numbers.

I remember reading that when you are actually infected with a virus you are often highly protected against being ill with another virus at the same time, not sure of the ins and outs of this or evidence however.


----------



## elbows (Dec 13, 2021)

Regarding South Africas data issues.


----------



## kabbes (Dec 13, 2021)

elbows said:


>



Isn't this what I was asking about before?


----------



## elbows (Dec 13, 2021)

Yeah thats part of the reason why I posted it. Havent always got the time or the will to go back and find and quote the previous strands of the conversation.


----------



## weltweit (Dec 13, 2021)

With Boris's December booster initiative it seems the UK is taking a strong stance on Omicron and taking some action now - rather than waiting to see the severity of the resulting illness.

What I can't find is other countries taking similar actions. 

Anyone spotted other countries taking action?


----------



## 2hats (Dec 13, 2021)

weltweit said:


> Anyone spotted other countries taking action?


Israel throughout August/September/October.


----------



## weltweit (Dec 13, 2021)

2hats said:


> Israel throughout August/September/October.


Surely they couldn't have known about Omicron back then 2hats?


----------



## Yossarian (Dec 13, 2021)

weltweit said:


> With Boris's December booster initiative it seems the UK is taking a strong stance on Omicron and taking some action now - rather than waiting to see the severity of the resulting illness.
> 
> What I can't find is other countries taking similar actions.
> 
> Anyone spotted other countries taking action?



Booster campaigns are getting stepped up all over the place though Johnson, uncharacteristically, does seem to be acting with more urgency than other leaders - might be connected to his government's heavy reliance on the AstraZeneca shot in the initial vaccination campaign.


----------



## teuchter (Dec 13, 2021)

weltweit said:


> With Boris's December booster initiative it seems the UK is taking a strong stance on Omicron and taking some action now - rather than waiting to see the severity of the resulting illness.
> 
> What I can't find is other countries taking similar actions.
> 
> Anyone spotted other countries taking action?


The UK is not really taking especially strong action as far as I can see.


----------



## teuchter (Dec 13, 2021)

The South African chap has modified his words a bit but despite the issues with the reported numbers there, he still seems to be confident that they are about to peak (rather than have already peaked).


----------



## Raheem (Dec 13, 2021)

Yossarian said:


> Booster campaigns are getting stepped up all over the place though Johnson, uncharacteristically, does seem to be acting with more urgency than other leaders - might be connected to his government's heavy reliance on the AstraZeneca shot in the initial vaccination campaign.


Johnson seems to be wanting to present boosters as a response to the wave that is now beginning. A race between the vaccine and the virus, we are told.

But, even if you buy the line that two doses offers really weak protection against omicron but the third somehow makes all the difference, vaccinating everyone in December is really only worthwhile if you're expecting the wave to hit in maybe February (given that they are not really going to get it done by the end of Dec, and there's also two or three weeks for vaccination to take effect).

I think it may well be about doing something as a noisy and expensive alternative to actually doing something.

ETA: Notice how we've heard the rationale for this plan from Johnson and Javid but not, as yet, from a government scientist.


----------



## Yossarian (Dec 14, 2021)

teuchter said:


> The South African chap has modified his words a bit but despite the issues with the reported numbers there, he still seems to be confident that they are about to peak (rather than have already peaked).




I wouldn't put too much faith in Streicher's predictions - he's getting quoted widely but he's only Dr. Streicher because he has a PhD in engineering. He's also a member of an anti-lockdown, anti-vaxxer group, and has been incorrectly predicting the peak of the pandemic since at least June 2020.









						Panda's Dr Streicher insists W Cape Covid-19 death peak will be 23 June -7 July
					

Dr Piet Streicher, a member of Pandemic Data and Analytics says looking at the trends the province is close to peak mortality rate.




					www.capetalk.co.za


----------



## teuchter (Dec 14, 2021)

Yossarian said:


> I wouldn't put too much faith in Streicher's predictions - he's getting quoted widely but he's only Dr. Streicher because he has a PhD in engineering. He's also a member of an anti-lockdown, anti-vaxxer group, and has been incorrectly predicting the peak of the pandemic since at least June 2020.
> 
> 
> 
> ...


Thanks, I already had a sense from the way he writes that he might not be entirely reliable, and I am interested to see what happens in SA in the next week or so, and what will happen to his confidently worded tweets if the numbers start to disagree with his predictions.


----------



## weltweit (Dec 14, 2021)

There are a lot of posts on a google search in South Africa saying Omicron severity is mild as if to say don't worry. But it hasn't infected people long enough to be able to know what the severity is yet. We have to wait a good couple of weeks more until we can see the real evidence.


----------



## Yossarian (Dec 14, 2021)

teuchter said:


> Thanks, I already had a sense from the way he writes that he might not be entirely reliable, and I am interested to see what happens in SA in the next week or so, and what will happen to his confidently worded tweets if the numbers start to disagree with his predictions.



There might be a stopped-clock-is-sometimes-right thing going on, but the organisation he's a part of definitely looks like Loon Central, with lots of "masks are bad, ivermectin is good" stuff.





__





						PANDA - PANDA’s analysis of the human & economic cost of lockdowns
					

Pandemics ~ Data & Analysis (PANDA) is a multidisciplinary initiative seeking to inform policy relating to the Covid-19 pandemic and lockdown. PANDA’s technical team of actuaries, data analysts, lawyers, economists and medical professionals brings to bear knowledge from various fields to...




					www.pandata.org


----------



## 2hats (Dec 14, 2021)

weltweit said:


> Surely they couldn't have known about Omicron back then 2hats?


Booster programme was started in response to delta.


----------



## elbows (Dec 14, 2021)

weltweit said:


> There are a lot of posts on a google search in South Africa saying Omicron severity is mild as if to say don't worry. But it hasn't infected people long enough to be able to know what the severity is yet. We have to wait a good couple of weeks more until we can see the real evidence.


The BBC is increasingly reporting on the 'mild in South Africa' story this week. Sources referenced by our media continue to include the doctor who made a big point of going on about how mild it is there all throughout their Omicron wave so far, but also at least one other medical professional, and there may also be some actual hospital detail data (eg percentage requiring oxygen).

As time goes on, my main caveat becomes that we need to see what that looks like in the UK context, rather than that not enough time has passed in South Africa to judge. Not that I can rule out other potential distortions of the Soouth Africa picture seen, such as deliberate bullshit and the recent problems with some of their data systems. And I am tending to disregard the death data for this wave in South Africa so far, because it looks to me like South Africa is one of the countries where it is still necessary to use excess death estimates rather than official death numbers, due to various phenomenon leading to large official undercounting.

Personally my instincts are still to rant and rave about the potential recklessness of 'mild in South Africa' stories, but I certainly dont rule out the possibility that this could end up being a mistake on my part, and that such stories were actually valid. I will just have to resist jumping to conclusions at this stage because UK context is quite different in some key respects, so will just have to see what the health realities of Omicron turn out to be in the UK, regardless of what the picture in South Africa actually is. And I dont believe authorities can really rely on the 'mild' stuff when planning a response. Its better to plan for the worst and then be delighted if it turns out we can relax more later on, with the added benefit that if we turn out to have overreacted to this variant, we'll at least have done things as a result that help reduce the ongoing burden from the delta variant during the difficult winter period.


----------



## LDC (Dec 14, 2021)

teuchter said:


> The South African chap has modified his words a bit but despite the issues with the reported numbers there, he still seems to be confident that they are about to peak (rather than have already peaked).




Maybe check your sources are OK before posting something like that?


----------



## teuchter (Dec 14, 2021)

LynnDoyleCooper said:


> Maybe check your sources are OK before posting something like that?


I don't think there is anything wrong in looking at some of the info that people with a different view are focusing on. As far as I can see he is not presenting falsified data.


----------



## elbows (Dec 14, 2021)

Early indications that Omicron may affect the value of F, the frequency with which I struggle to resist saying fuck off teuchter.

Yes, at this stage of waves I tend to get a bit more aggressive, my tolerance towards certain forms of wriggling reduces notably.

And yes I sometimes resort to posting stuff I dont agreee with either and then examine and pick at it. In this case I was annoyed that you posted yet another of his tweets because we already had an initial one posted in this thread, and then me posting a follow-up one where he was forced to change some of his analysis because he had previously used data that was blatantly likely to be an incomplete guide at that moment, was bound to be overridden by subsequent data. And since their view on when cases may peak in that region does not seem to have changed across these tweets, I dont see the point in keep sharing subsequent tweets.

If this Omicron wave turns out to really suck then I doubt I will in future be prepared to put up with some of the shit I've had to try and listen to and respond to reasonably throughout much of this year. Instead I will try to build a casde that my position is reasonable, not extreme, and that many who consider their approaach to be balanced and centrist are actually leading us repeatedly into massive waves of disruption and death. At this stage of the pandemic I'd much rather be wrong instead, and right now I do not exclude either possibility so will just have to wait and see.


----------



## LDC (Dec 14, 2021)

teuchter said:


> I don't think there is anything wrong in looking at some of the info that people with a different view are focusing on. As far as I can see he is not presenting falsified data.



No, not at all, but adding something to your post saying his timeline has been full of that all the way through the pandemic might be helpful and give a bit of context/raised eyebrow skepticism to his claims now.


----------



## teuchter (Dec 14, 2021)

There are obvious reasons why what's happening in SA now is of intense interest. I certainly am interested in seeing what is changing day by day there, and therefore I'm keeping an eye out for any easily digestible numbers. I also posted a Christina Pagel tweet with the same observation - that the case numbers in Gauteng seemed to have stopped following the fast exponential rise. I followed that with another one explaining this might be due to data issues. The Streicher tweets since then have included graphs which (as far as I can make out) have taken into account the data reporting issues, and it appears that it doesn't really change the picture of what looks like a significant slow-down in cases compared to the early fears. That to me is pretty important information, while of course remembering that we can't be sure it will translate to the same picture in the UK. So I have posted it on this thread. If anyone has alternative, better sources of graphs illustrating the ongoing situation in SA feel free to stick them up.

For the record I think the UK should have brought in greater restrictions this week, because of the potential for things to go very badly wrong very quickly in the more pessimistic scenarios. I won't change my view on that even if a week from now it's become clear that Omicron is nowhere near the threat that was feared.


----------



## teuchter (Dec 14, 2021)

LynnDoyleCooper said:


> No, not at all, but adding something to your post saying his timeline has been full of that all the way through the pandemic might be helpful and give a bit of context/raised eyebrow skepticism to his claims now.


See my post 502.

I've not followed him through the pandemic; I'd never heard of him until a couple of days ago.


----------



## elbows (Dec 14, 2021)

I'm pleased to hear your remarks on what you think should have been done this time.

And I should point out that part of the reason I get especially tetchy at times like this is nothing to do with what individuals are saying, its because I get very nervous and depressed waiting to see what the reality will turn out to be like. And obviously this time around this comes on the back of many 2021 pandemic attitudes having done my head in for a long time already.


----------



## elbows (Dec 14, 2021)

And there is the problem with potential good news at moments like this - we cant actually do much useful with any possible good news, due to differences in timing between when we need to act and when the true picture will be revealed. Whereas we really do have to act on potential bad news long before the underlying reality is clear. Its all rather draining and robs me of the ability to balance my natural instincts with something more optimistic.


----------



## SpookyFrank (Dec 14, 2021)

teuchter said:


> I don't think there is anything wrong in looking at some of the info that people with a different view are focusing on. As far as I can see he is not presenting falsified data.



His interpretation of those data though, namely that they somehow argue for the removal of all restrictions everywhere immediately, stinks of bad faith and vested interest.


----------



## SpookyFrank (Dec 14, 2021)

elbows said:


> And there is the problem with potential good news at moments like this - we cant actually do much useful with any possible good news, due to differences in timing between when we need to act and when the true picture will be revealed. Whereas we really do have to act on potential bad news long before the underlying reality is clear. Its all rather draining and robs me of the ability to balance my natural instincts with something more optimistic.



If there was good news after we brought in restrictions we would have the latitude to ease those restrictions. If we do nothing and then we get bad news, there's nowhere to go. 

And given that the transmissibility (is that a word?) of Omicron seems unambiguously high, I can't really see where good news might come from.


----------



## weltweit (Dec 14, 2021)

I don't know if people rate this guy, I found it interesting about Omicron.


----------



## elbows (Dec 15, 2021)

SpookyFrank said:


> And given that the transmissibility (is that a word?) of Omicron seems unambiguously high, I can't really see where good news might come from.


Even the fucking Telegraph are scraping the bottom of the barrel, in that on todays front page they've had to resort to calling pandemic penis Robert Dingwall a government advisor.

Of somewhat more substance they've got some numbers from an early study that I havent seen yet which apparently says, based on analysis of 78,000 Omicron cases in South Africa, Omicron has a 29% lower hospitalisation risk than the Wuhan strain, and a 23% lower hospitalisation risk than the Delta strain. Should those estimates turn out to be a fair reflection of disease severity, those are not the sort of decreases I would consider to be sufficient to deliver really good news, given the expected number of infections. But different countries also have different thresholds and capacitiesfor admitting people to hospital in the first place, different experiences in the pandemic waves, as well as different demographics, differences in vaccine programmes etc. The same study also talks of 5% of patients being admitted to ICU as opposed to 22% for Delta, but again I havent looked at any detail and I'd need to check how such figures compare with things like Delta ICU cases in the UK.


----------



## l'Otters (Dec 15, 2021)

Not sure if this belongs on another thread, or has already been covered on this one and I didn't pick up on it, but: 

Can all PCR tests be checked for omicron? 
Is this what's happening now? 
Or is it expected to be happening very  soon?

Reason for asking this today is I got a covid track n trace notification this morning; it's telling me I don't need to isolate because I've had vaccines (the page where you get asked that Q only has options for none/one/two; I've had three) - I understand this will change soon and I'd be instructed to isolate _if_ it was a confirmed omicron case. 

I'm cancelling this week's plans that involved leaving my house anyway but I'm curious how this plan is going to work out.


----------



## elbows (Dec 15, 2021)

For those trying to interpret data from South Africa, there is a lot of info in this twitter thread, though I'm only quoting a couple of the tweets the others are of interest. Also sounds like there is a public holiday there tomorrow.


----------



## 2hats (Dec 15, 2021)

elbows said:


> Of somewhat more substance they've got some numbers from an early study that I havent seen yet which apparently says, based on analysis of 78,000 Omicron cases in South Africa, Omicron has a 29% lower hospitalisation risk than the Wuhan strain, and a 23% lower hospitalisation risk than the Delta strain.


The Discovery Health analysis? Note that that study also suggests 20% greater risk of hospitalisation of under-18s relative to the first wave. Two-dose Pfizer 70% effective at reducing omicron-related hospital admissions (down from 93% for delta).








Unfortunately one should be cautious drawing too many conclusions from the SA data and applying them to the UK because of the population pyramid (median age 27 v 41) and the widespread (>70%) recently acquired natural immunity from two 'waves' of antigenically diverse and significantly immune evasive variants (first beta, then delta).


----------



## elbows (Dec 15, 2021)

l'Otters said:


> Not sure if this belongs on another thread, or has already been covered on this one and I didn't pick up on it, but:
> 
> Can all PCR tests be checked for omicron?
> Is this what's happening now?
> ...


There is only a certain capacity to do proper genomic sequencing of PCR test results, and when case numbers are high the percentage they can test in this way is low. And it ended up low throughout much of the Delta wave that has dragged on for months, because the case numbers in that wave were consistently high.

They have another shortcut method to estimate which cases are Omicron, looking for S gene target droputs, but not all of the labs in the country can use that method either. But still a significantly greater proportion of samples than can be checked in that way than can be genomically sequenced, and I think the results are also much quicker.

In regards the Omicron self-isolation rules you describe, they already changed them since they first rushed them in. So the Omicron-specific stuff is gone, and if it hadnt been removed then I expect they would soon have been assuming that every case could be Omicron, so every close contact would have eventually ended up being told to isolate rather than authorities trying to work out Omicrom suspicions in each particular case.

Likely flaws with the new version of these rules include the fact it will likely be weaker at reducing the spread of infections, and also it wont be surprising if there are ongoing shortages of LFT deliveries and the tests not being in the right hands of all those who will need such tests in order to follow these rules. Advantages to the new rule include less staff being off work.



> From Tuesday 14 December, people who are fully vaccinated and identified as a contact of someone with COVID-19 – whether Omicron or not – should take an NHS rapid lateral flow test every day for 7 days to help slow the spread of COVID-19.
> 
> The practical move comes as Omicron infections are rising significantly in the UK and it is expected to become the dominant strain in the UK by mid-December. It aims to reduce pressures on people’s everyday lives by replacing the requirement for Omicron contacts to isolate for 10 days, while protecting the public by identifying asymptomatic cases and stopping the chains of transmission. Testing daily will also help us understand how and where the virus is spreading.











						Daily rapid testing for COVID-19 contacts launches this week
					

From Tuesday, fully vaccinated contacts of a COVID-19 case should take a daily lateral flow test for 7 days to slow the spread of the virus.




					www.gov.uk


----------



## elbows (Dec 15, 2021)

2hats said:


> The Discovery Health analysis? Note that that study also suggests 20% greater risk of hospitalisation of under-18s relative to the first wave. Two-dose Pfizer 70% effective at reducing omicron-related hospital admissions (down from 93% for delta).
> 
> 
> 
> ...


Thanks for finding the stufy and drawing attention to important detail. I'll take a look now.

Yeah I cant draw firm conclusions from South Africas data & analysis for the reasons you mention. I sporadically try to point out that South Africa had a Beta wave rather than an Alpha wave and that I dont like to make assumptions about any difference that and the size and timing of their waves may have compared to the UK. Likewise when it comes to vaccination, not just the differing rates of vaccination in the population but also the types of vaccines and dosing schedules they used compared to the UK.

Sounds like I'll have to keep an eye on UK hospitalisation rates by age group in the weeks ahead. Well I say the UK but I mostly mean England as thats the hospitalisation age data I am used to locating on a routine basis.


----------



## Aladdin (Dec 15, 2021)

Apparently cases of omicron went from 1% of cases to 14% in one week here in Ireland. 

That to me sounds like a massive jump. So by next week can we assume cases will be at 28% and by new years day will be 56% and by 7th Jan 100% ?

And if we currently have 4500 cases a day and 14% today was  630 and  this virus doubles its rate every 2 days...then by 9th Jan everyone on the island of Ireland will have been infected. 😳

And if hospitalisations are 25% less than currently.... they are 45 a day here at the moment. So lets say it goes to 11 a day...but omicron is 6 times more transmissable so lets make that 66 a day ...
And deaths here are 0.2% of hospitalisations...80 people a week...with delta....
And deaths predicted at 0.1% of population with omicron..that's 5500 deaths here....in the space of 6 weeks....

Wiith only 350 ICU beds in the entire country.

We are basically fucked. Omicron may well be mild but it will take people. Those who are most vulnerable and unvaccinated with underlying conditions.

Fuck.

It just does not look good...from the perspwctive of someone with underlying conditions and ectremely vulnerable despite vaccinations. Let alone someone who might not he able to be vaccinated.😳


----------



## redsquirrel (Dec 15, 2021)

Sugar Kane said:


> Apparently cases of omicron went from 1% of cases to 14% in one week here in Ireland.
> 
> That to me sounds like a massive jump. So by next week can we assume cases will be at 28% and by new years day will be 56% and by 7th Jan 100% ?


No. I mean it is possible (although highly unlikely) that the numbers could work out that way but you should not assume a linear extrapolation of the %.

There are a whole heap of factors to consider but a much more likely scenario for the % would be an S-curve like in figure (d) in this tweet


The % of omicron will increase slowly at first, then very fast and then slow down again.

So while I think there is plenty to be worried about - and I certainly want to see governments take more mitigating actions - a lot of the assumption you are making probably don't hold and some of the working is not correct.


----------



## Supine (Dec 15, 2021)

Sugar Kane said:


> Apparently cases of omicron went from 1% of cases to 14% in one week here in Ireland.
> 
> That to me sounds like a massive jump. So by next week can we assume cases will be at 28% and by new years day will be 56% and by 7th Jan 100% ?
> 
> ...



You can’t use those predictions. But it isn’t looking good.


----------



## andysays (Dec 15, 2021)

redsquirrel said:


> No. I mean it is possible (although highly unlikely) that the numbers could work out that way but you should not assume a linear extrapolation of the %.
> 
> There are a whole heap of factors to consider but a much more likely scenario for the % would be an S-curve like in figure (d) in this tweet
> 
> ...



But in the short term of the next few weeks which Sugar Kane is referring to, the numbers (both the raw Covid numbers and the proportion due to Omicron) are likely to be going up rapidly and in fact more rapidly than ATM.

It's going to be a while before we start to see the tailing off of the rate shown in those graphs, which suggest one variant being essentially replaced by another rather than, say, Delta and Omicron co-existing in some sort of balance or equilibrium.


----------



## redsquirrel (Dec 15, 2021)

andysays said:


> But in the short term of the next few weeks which Sugar Kane is referring to, the numbers (both the raw Covid numbers and the proportion due to Omicron) are likely to be going up rapidly and in fact more rapidly than ATM.


Sugar Kane's prediction for the rate in increase in % Omicron is probably an underestimate, you'll go from ~15% to ~85% much faster.


----------



## andysays (Dec 15, 2021)

redsquirrel said:


> Sugar Kane's prediction for the rate in increase in % Omicron is probably an underestimate, you'll go from ~15% to ~85% much faster.


I didn't properly take in your point about not assuming linear extrapolation


----------



## teuchter (Dec 15, 2021)

Looks to me like Denmark is the country to keep an eye on for signs of a peak, maybe more so than South Africa as it is more similar to the UK in terms of demographics.


----------



## teuchter (Dec 15, 2021)

...although those graphs give what might be a misleading impression that Denmark is "ahead". These ones suggest Denmark and London are at a similar point.







__





						Subscribe to read | Financial Times
					

News, analysis and comment from the Financial Times, the worldʼs leading global business publication




					www.ft.com


----------



## bimble (Dec 15, 2021)

it's too early to have a clue about whether this version is equally likely to leave some people with post viral / long term symptoms isn't it.  
For the first time i'm thinking its probably more or less inevitable that i'll catch this at some point.


----------



## Numbers (Dec 15, 2021)

I get the feeling I've asked this question already but can't remember 
Can the current LFTs detect Omicron?


----------



## Supine (Dec 15, 2021)

Numbers said:


> I get the feeling I've asked this question already but can't remember
> Can the current LFTs detect Omicron?


Yes


----------



## elbows (Dec 15, 2021)

Sugar Kane said:


> Apparently cases of omicron went from 1% of cases to 14% in one week here in Ireland.
> 
> That to me sounds like a massive jump. So by next week can we assume cases will be at 28% and by new years day will be 56% and by 7th Jan 100% ?


In addition to the problems with making projections that are based on linear rather than exponential growth, at the moment there is no certainty about what will happen with existing Delta strain numbers. So authorities are only talking about Omicron becoming the majority of cases, not that all cases will become Omicron. So forget about the 100% thing for now.


----------



## elbows (Dec 15, 2021)

teuchter said:


> Looks to me like Denmark is the country to keep an eye on for signs of a peak, maybe more so than South Africa as it is more similar to the UK in terms of demographics.


Even if you find peaks quite quickly due to the speed of this variant, I would urge you to consider the age-based data that was really quite significant in the UK Delta wave, telling a somewhat different story.

By this I mean that the July peak in overall positive case numbers we had was driven by a younger age group, and did not end up mirroring the highest burden on hospitals, which came later.

I suppose peaks in various countries are still of some interest to me, but the data I am even more focussed on is what happens with Omicron numbers in older age groups. No doubt my graphs in the weeks to come will often focus on this.


----------



## Badgers (Dec 15, 2021)

Press conference at 5pm then...


----------



## MrCurry (Dec 15, 2021)

teuchter said:


> The South African chap has modified his words a bit but despite the issues with the reported numbers there, he still seems to be confident that they are about to peak (rather than have already peaked).



This fellow has just popped up on UnHerd TV on YouTube. I’ve not yet watched it, but based on past Freddie Sayers / UnHerd interviews I would guess it’s a going to be a detailed dive into and cross examination of his views. Might be of interest to some who either want to better understand or refute his viewpoint.


----------



## elbows (Dec 15, 2021)

No chance, I'll just get wound up and I'd rather just wait and see what actually happens. Omicron could end up being part of the pandemic exit story but the details could still be ugly and I'm in no mood to indulge certain optimistic versions of that right now, not at this precarious moment. I have no intention of trying to predict happy outcomes in advance, especially when there is always the risk it wont be a happy outcome. I'll be content to applaud the end only when hindsight and certainty allow.


----------



## LDC (Dec 15, 2021)

bimble said:


> it's too early to have a clue about whether this version is equally likely to leave some people with post viral / long term symptoms isn't it.



Why some people get post-viral fatigue and other related issues (even without a known viral infection) is very complicated and not well understood at all, even pre-covid.

If was a betting person I think the longer term symptoms some people get post-covid infection with Delta and other variants will be mirrored by Omicron. But yes, far too early to know, any data on that is likely months away.


----------



## TopCat (Dec 15, 2021)

Did the Boris just say 780,000 daily cases? Surely a Priti mistake?


----------



## 8ball (Dec 15, 2021)

TopCat said:


> Did the Boris just say 780,000 daily cases? Surely a Priti mistake?


78,000 is the number, I believe.

Though Boris might have said bloody anything.


----------



## TopCat (Dec 15, 2021)

8ball said:


> 78,000 I believe


Yes that’s what I know but did he say that? Rewind in a bit.


----------



## TopCat (Dec 15, 2021)

He is just talking shit now in response to Laura K


----------



## TopCat (Dec 15, 2021)

Robert Peston uppercutting Boris in the balls now.


----------



## elbows (Dec 15, 2021)

Johnson just got shitty about that.


----------



## 8ball (Dec 15, 2021)

TopCat said:


> Robert Peston uppercutting Boris in the balls now.



Well, that's something.  Wasn't too long ago he was so far up Boris Johnson's arse, he could see Laura Kuenssberg's feet.


----------



## TopCat (Dec 15, 2021)

I just watched the beginning again. He fucked it up. Definitely said there were 780,000 daily cases.


----------



## elbows (Dec 15, 2021)

TopCat said:


> I just watched the beginning again. He fucked it up. Definitely said there were 780,000 daily cases.


Yes. "with over 780,000 cases today" were the words used.


----------



## 8ball (Dec 15, 2021)

elbows said:


> Yes. "with over 780,000 cases today" were the words used.



That could easily shit up a few people.


----------



## TopCat (Dec 15, 2021)

8ball said:


> That could easily shit up a few people.


Thankfully I was up to date with the daily stats otherwise I would have had an arse / heart flutter moment.


----------



## cupid_stunt (Dec 15, 2021)

Everything is going to be OK.


----------



## TopCat (Dec 15, 2021)

cupid_stunt said:


> Everything is going to be OK.
> 
> View attachment 300965


YouTube research is so soothing.


----------



## Yossarian (Dec 15, 2021)

cupid_stunt said:


> Everything is going to be OK.
> 
> View attachment 300965



He should have just gone to Wuhan in 2019 and stopped the whole thing, the time-traveling twat.


----------



## Edie (Dec 15, 2021)

Wow infections are off the scale today!


----------



## cupid_stunt (Dec 15, 2021)

Yossarian said:


> He should have just gone to Wuhan in 2019 and stopped the whole thing, the time-traveling twat.



I think you mean 'she'.


----------



## LDC (Dec 15, 2021)

Edie said:


> Wow infections are off the scale today!






Sorry!


----------



## Pickman's model (Dec 15, 2021)

Edie said:


> Wow infections are off the scale today!


Yeh the only q now is lockdown pre- or post-xmas


----------



## Edie (Dec 15, 2021)

Pickman's model said:


> Yeh the only q now is lockdown pre- or post-xmas


Massively fingers crossed for after.


----------



## Pickman's model (Dec 15, 2021)

Edie said:


> Massively fingers crossed for after.


Yes.


----------



## Yossarian (Dec 15, 2021)

cupid_stunt said:


> I think you mean 'she'.



Oops - been watching from the start of the revived series now my son's old enough so I when I think Dr. Who I think Christopher Eccleston.


----------



## wemakeyousoundb (Dec 15, 2021)

Edie said:


> Massively fingers crossed for after.


I doubt Bojo will be the grinch 2 years in a row.


----------



## elbows (Dec 15, 2021)

Even without hospital consequences being on the dire end of things, and even without further restrictions imposed, and even with changes to self-isolation rules, the sheer number of infections will lead to massive disruption.


----------



## Badgers (Dec 15, 2021)

Edie said:


> Massively fingers crossed for after.


I feel the same for family reasons. However if there HAS to be a lock down then waiting till January (100k + cases a day) will have a different bad result. Especially for schools and hospitals.


----------



## Edie (Dec 15, 2021)

Badgers said:


> I feel the same for family reasons. However if there HAS to be a lock down then waiting till January (100k + cases a day) will have a different bad result. Especially for schools and hospitals.


This is true


----------



## _Russ_ (Dec 15, 2021)

Of course its needed now, but if a lockdown was announced to start tomorrow I reckon the only people that would pay any attention to it would be those that are for all intents and purposes doing it voluntarily already.


----------



## Supine (Dec 15, 2021)

_Russ_ said:


> Of course its needed now, but if a lockdown was announced to start tomorrow I reckon the only people that would pay any attention to it would be those that are for all intents and purposes doing it voluntarily already.



Rubbish. All evidence shows the majority of the country comply with rules when asked. Not everyone obviously, but the majority.


----------



## elbows (Dec 15, 2021)

Badgers said:


> I feel the same for family reasons. However if there HAS to be a lock down then waiting till January (100k + cases a day) will have a different bad result. Especially for schools and hospitals.


Regarding numbers and timing like that, and peoples response to this wave in terms of behaviours etc, here are some things I will highlight. I already ranted about the shitty 'analysis' bit of this article in the main UK thread so not repeating that here at this time.









						Covid-19: A record day for cases - what does it tell us?
					

Two epidemics at once and the threat to the NHS - three takeaways on the effect of Omicron.



					www.bbc.co.uk
				




The doubling time is only around 2 days, maybe a bit less, maybe now a bit more because of behavioural changes but we wont be able to see that in data properly straight away.

But there is an ongoing delta wave that Omicron sits on top of, so we cant just double todays total detected case figures every couple of days to estimate where we will be at for the rest of December. And behaviours and opportunities for Omicron will change further.

But we could use the numbers from that article, estimated 20,000 of todays figures being Omicron, and combine them with the doubling time in order to get a rough idea of Omicrons growth potential in the days ahead. It doesnt take very long at all for the Omicron cases to go over 100,000 if we do that exercise. And then add the 'relatively stable' delta case numbers back on top.

Other complications also mentioned in the article include that the testing capacity wont actually allow the same proportion of cases as are currently officially recorded to be detected in the daily data once the number and test demand goes above a certain level.



> If the two-day doubling continues, by Christmas day 640,000 Omicron infections would be being recorded and early in the new year the whole population will have been infected.
> 
> That said, the cases would never be spotted as testing capacity is limited to less than one million a day.
> 
> ...



In my book 'the whole population would have been infected by New Years day' stuff is not what will actually happen, things tend to be messier than that and some people will manage to hide from the virus this time around, or otherwise be protected, and others will never officially be recorded as having caught it in this wave. So I mention this stuff mostly to give an indication of what sort of timescales the simplistic version of the maths leads to within days.


----------



## smmudge (Dec 16, 2021)

Soo do we know... is the quick spread of omicron down to how quickly someone exposed then becomes infectious, or just how many more people one person will pass it on to.. or bit of both?


----------



## two sheds (Dec 16, 2021)

Omicron found to grow 70 times faster than Delta in bronchial tissue
					

Study of tubes between windpipe and lungs could help explain Covid variant’s rapid transmission




					www.theguardian.com
				




This could contribute.


----------



## existentialist (Dec 16, 2021)

_Russ_ said:


> Of course its needed now, but if a lockdown was announced to start tomorrow I reckon the only people that would pay any attention to it would be those that are for all intents and purposes doing it voluntarily already.


Well, yes. Because - unlike in many other countries, we don't even try to make it look like we're enforcing anything.

(TBF, Wales has had a better record on this in earlier lockdowns, but I'm not sure that's up to much now)


----------



## _Russ_ (Dec 16, 2021)

Nah, Wales did no more to enforce anything than England did (I.E. Ffuck all), though first time round lots adhered as it was actually stated as being the law, but soon as everyone noticed there wasnt any enforcement then the selfish cunt contingent just did what they liked and that is the current situation


----------



## andysays (Dec 16, 2021)

smmudge said:


> Soo do we know... is the quick spread of omicron down to how quickly someone exposed then becomes infectious, or just how many more people one person will pass it on to.. or bit of both?


I would guess that those two factors are connected, and that the quicker someone becomes infectious, the more people they're likely to pass it on to. particularly if asymptomatic.


----------



## StoneRoad (Dec 16, 2021)

andysays said:


> I would guess that those two factors are connected, and that the quicker someone becomes infectious, the more people they're likely to pass it on to. particularly if asymptomatic.


Which is why - I think - people should mask up and keep their distance ... at the very least.


----------



## Bahnhof Strasse (Dec 16, 2021)

France closing the boarders to British travellers in a futile attempt to stop it coming in. French and EU citizens are still allowed to enter.


----------



## StoneRoad (Dec 16, 2021)

Bahnhof Strasse said:


> France closing the boarders to British travellers in a futile attempt to stop it coming in. French and EU citizens are still allowed to enter.



I agree !


----------



## MrCurry (Dec 16, 2021)

Bahnhof Strasse said:


> France closing the boarders to British travellers in a futile attempt to stop it coming in. French and EU citizens are still allowed to enter.


That’ll work then   Probably more political than anything else.


----------



## 2hats (Dec 16, 2021)

Bahnhof Strasse said:


> France closing the boarders to British travellers in a futile attempt to stop it coming in.


Understandable given as how public schoolboys are well known to exacerbate this pandemic.


----------



## Bahnhof Strasse (Dec 16, 2021)

2hats said:


> Understandable given as how public schoolboys are well known to exacerbate this pandemic.




Meh, they're still allowed in, just had a call from a Radley College one who was worried that he wouldn't be allowed back next week. "You live in Monaco, it's fine."


----------



## Flavour (Dec 16, 2021)

it's futile but it's prob the right thing to do


----------



## wemakeyousoundb (Dec 16, 2021)

Still can't use it as an excuse to stay here for the birthday of our lord and saviour then. :/
e2a: actually I'll have to isolate for 2 days out of the 3 days I'm there...
ffs


----------



## cupid_stunt (Dec 16, 2021)

> There are 15 confirmed people in UK hospitals with the Omicron variant, but the actual number is likely to be “much bigger.”
> 
> Dr Susan Hopkins, chief medical adviser of the UK Health Security Agency, told the Commons Health and Social Care Committee:
> 
> ...











						Covid live: Italy reports highest daily cases since March; Canada’s Omicron cases ‘could overwhelm Ontario ICUs’
					

Italy reports 26,109 new cases, its highest daily number since 12 March; experts warn Ontario hospitals could be overwhelmed




					www.theguardian.com


----------



## Yossarian (Dec 16, 2021)

The pessimistic but reliable Dr. Eric Feigl-Ding is comparing headlines about omicron being mild to the Jan-March 2020 headlines about COVID being milder than the flu.


----------



## two sheds (Dec 17, 2021)

I read symptoms can come on between 2 and 14 days after exposure - means you can be walking round with it infecting people for quite a while


----------



## danny la rouge (Dec 17, 2021)

I heard it's got magnets on its tail, so's if you're made out of metal it can attach itself to you and instead of a mouth, it's got four arses!


----------



## Mation (Dec 17, 2021)

danny la rouge said:


> I heard it's got magnets on its tail, so's if you're made out of metal it can attach itself to you and instead of a mouth, it's got four arses!


Guessing you didn't intend that to come out sounding quite so mean!


----------



## Saunders (Dec 17, 2021)

Whoops accidental post


----------



## danny la rouge (Dec 17, 2021)

Mation said:


> Guessing you didn't intend that to come out sounding quite so mean!


It’s a Father Ted quote. I didn’t intend it to sound mean.


----------



## weltweit (Dec 17, 2021)

Covid-19: Omicron is causing more infections but fewer hospital admissions than delta, South African data show
					

Data from South Africa’s largest private health insurer suggest that omicron is spreading faster than any previous coronavirus variant and showing signs of immune escape, with both vaccinated and previously infected people more at risk than in previous waves.  More than 90% of newly sequenced...




					www.bmj.com


----------



## elbows (Dec 17, 2021)

The big questions about Omicron hospitalisation will have to be answered in the UK context, and there is likely to be quite a strong relationship between the emerging realities of that and what happens in terms of Omicron case numbers in people that are not young. Also chuck in some unknowns about vaccine protection against severe disease. And some unknowns about whether there is increased hospital risk for younger people too.


----------



## littlebabyjesus (Dec 17, 2021)

elbows said:


> The big questions about Omicron hospitalisation will have to be answered in the UK context, and there is likely to be quite a strong relationship between the emerging realities of that and what happens in terms of Omicron case numbers in people that are not young. Also chuck in some unknowns about vaccine protection against severe disease.


While this is true, the South Africa numbers are far from worthless. For starters, SA numbers for omicron can be compared with SA numbers for previous waves. The difference is startling thus far - case fatality rates falling from around 3% to around 0.5% within the same population (and a significant chunk of that 0.5% are delta infections). 

We've all been waiting to see if South Africa goes pear-shaped with omicron over the last three weeks. It still hasn't happened. Yes, SA has a very high number of people previously infected with other variants, but so does the UK, and the UK has far higher vaccination among the high-risk groups. SA's daily covid deaths are still only around 30 per day, which, with a population about the same size as the UK's, is way lower than the UK's rate at any point since July. There are reporting issues of course, but the excess death data released on Wednesday showed SA's excess deaths running a little up, but only a little. 

There is a strong pattern here that SA sees excess deaths go up before reported covid deaths in each wave, but each week that goes by without this happening significantly adds to the evidence pool suggesting that this wave is something very different. Add to that the reports from the ground about the different nature of infection, oxygen needs etc. 



https://www.samrc.ac.za/reports/report-weekly-deaths-south-africa


Something that I'm surprised hasn't been picked up on more widely is this study published in pre-print last week suggesting that omicron has become more infectious by nicking some DNA from a cold virus inside someone (probably an HIV-infected person) infected with both. That does provide a decent explanation both for the much higher infectiousness and the milder symptoms. It may be wrong, of course, but it makes sense as a mechanism by which it has become, as the study says, 'more human'. 

Omicron may have acquired a mutation from common cold virus, say researchers


----------



## elbows (Dec 17, 2021)

The size of South Africas population compared to the UK is far less relevant than their population pyramid compared to the UKs. This, along with differences in previous waves (including that they had a beta wave rather than an alpha wave, and the proportion of their population that seems to have had a prior covid infection) are some of the reasons why I cannot use South Africas situation as a really strong guide as to what will happen in the UK.

I do not exclude the possibility that some of the positive indicators from South Africa will have some impact on what happens in the UK, but I cannot rely on this at all at this stage. I can use some of that stuff in order to retain in my mind the possibility that the UKs Omicron wave may not be a complete catastrophe, but I cannot have sufficient confidence in that outcome that I could use it to heavily influence my impresssion of what measures need to be taken in the UK. Pandemic policies based on optimism and best case scenarios are sadly unsuitable, we have to act with the worst case possibilities in mind instead. Only once we have experienced a wave that demonstrates that the nature of the Covid threat has been transformed (or a prolonged absence of huge waves), could I begin to factor in such possibilities strongly when it comes to the future of this virus and how we must respond to it.

A population pyramid for South Africa, the shape of which is so incredibility different to what we are used to seeing for nations like our own:









						Demographics of South Africa - Wikipedia
					






					en.wikipedia.org


----------



## Supine (Dec 17, 2021)

littlebabyjesus said:


> While this is true, the South Africa numbers are far from worthless. For starters, SA numbers for omicron can be compared with SA numbers for previous waves. The difference is startling thus far - case fatality rates falling from around 3% to around 0.5% within the same population (and a significant chunk of that 0.5% are delta infections).
> 
> We've all been waiting to see if South Africa goes pear-shaped with omicron over the last three weeks. It still hasn't happened. Yes, SA has a very high number of people previously infected with other variants, but so does the UK, and the UK has far higher vaccination among the high-risk groups. SA's daily covid deaths are still only around 30 per day, which, with a population about the same size as the UK's, is way lower than the UK's rate at any point since July. There are reporting issues of course, but the excess death data released on Wednesday showed SA's excess deaths running a little up, but only a little.
> 
> ...



Do you have a link to the pre-print? An article that doesn’t specify what this supposed change is isn’t much use.


----------



## elbows (Dec 17, 2021)

This post covers that:

       #430     



> (nference, MA) A preprint of a comparative mutational analysis of omicron with other HCoV suggests it exhibits signs of recombination with a common cold coronavirus, possibly HCoV-229E (though there are other potential candidates, eg HCoV-OC43, HCoV-NL63).


----------



## littlebabyjesus (Dec 17, 2021)

Supine said:


> Do you have a link to the pre-print? An article that doesn’t specify what this supposed change is isn’t much use.


Here.

https://osf.io/f7txy/

It's by no means definitive proof that omicron has mutated into something much milder, but it is at least a plausible mechanism by which it may have done so.


----------



## elbows (Dec 17, 2021)

Also note an alternative possibility to the 'immunocompromised human host' possibility.

Rodents, more specifically mice.

       #443


----------



## elbows (Dec 17, 2021)

two sheds said:


> Omicron found to grow 70 times faster than Delta in bronchial tissue
> 
> 
> Study of tubes between windpipe and lungs could help explain Covid variant’s rapid transmission
> ...


Details from that are relevant to the recent discussion of severity, cold-like attributes, more effective transmission and NHS burden:



> The Omicron Covid variant has been found to multiply about 70 times quicker than the original and Delta versions of coronavirus in tissue samples taken from the bronchus, the main tubes from the windpipe to the lungs, in laboratory experiments that could help explain its rapid transmission.
> 
> The study, by a team from the University of Hong Kong, also found that the new variant grew 10 times slower in lung tissue, which the authors said could be an indicator of lower disease severity.





> Michael Chan Chi-wai, who led the work, said the result needed to be interpreted with caution because severe disease is determined not only by how quickly the virus replicates but also by a person’s immune response and, in particular, whether the immune system goes into overdrive, causing a so-called cytokine storm.
> 
> “It is also noted that by infecting many more people, a very infectious virus may cause more severe disease and death even though the virus itself may be less pathogenic,” he said. “Therefore, taken together with our recent studies showing that the Omicron variant can partially escape immunity from vaccines and past infection, the overall threat from the Omicron variant is likely to be very significant.”


That last point I quoted takes us back to the simple maths of severity vs transmissibility and why I cannot find a lot of reassurance at the moment. I can hope, but I cannot do much with that hope, and the shadow of the basic maths still looms large in my mind. A phenomenal reduction in severity could change the balance of that maths, but it probably needs to be massive to have the desired outcome.


----------



## littlebabyjesus (Dec 17, 2021)

elbows said:


> The size of South Africas population compared to the UK is far less relevant than their population pyramid compared to the UKs. This, along with differences in previous waves (including that they had a beta wave rather than an alpha wave, and the proportion of their population that seems to have had a prior covid infection) are some of the reasons why I cannot use South Africas situation as a really strong guide as to what will happen in the UK.
> 
> I do not exclude the possibility that some of the positive indicators from South Africa will have some impact on what happens in the UK, but I cannot rely on this at all at this stage. I can use some of that stuff in order to retain in my mind the possibility that the UKs Omicron wave may not be a complete catastrophe, but I cannot have sufficient confidence in that outcome that I could use it to heavily influence my impresssion of what measures need to be taken in the UK. Pandemic policies based on optimism and best case scenarios are sadly unsuitable, we have to act with the worst case possibilities in mind instead. Only once we have experienced a wave that demonstrates that the nature of the Covid threat has been transformed (or a prolonged absence of huge waves), could I begin to factor in such possibilities strongly when it comes to the future of this virus and how we must respond to it.
> 
> ...


Sure, which is why you have to compare SA with SA.

And the pattern of divergence is emerging.

Just from a rough look at worldometers, on the day the average daily case numbers hit 10,000 for delta, there was an average of 110 deaths reported per day. On the day, the average cases hit 20,000 for delta (its peak), there was an average of more than 400 reported deaths per day. The equivalent numbers for omicron are 24 and 25 (12 days ago and 4 days ago respectively).

Those are weekly averages for the seven days previous to those dates, so there was an average of 10,000 cases per day across the whole week in the week ending nearly two weeks ago in SA. That provides a decent lag for deaths to start appearing.


----------



## teuchter (Dec 17, 2021)

littlebabyjesus said:


> Just from a rough look at worldometers, on the day the average daily case numbers hit 10,000 for delta, there was an average of 110 deaths reported per day. On the day, the average cases hit 20,000 for delta (its peak), there was an average of more than 400 reported deaths per day. The equivalent numbers for omicron are 24 and 25 (12 days ago and 4 days ago respectively).


Still not entirely reassuring in the scenario where the case number reach over 10x their previous highs though... which I guess is why everyone is hoping that the peaks are shown to happen relatively early.


----------



## littlebabyjesus (Dec 17, 2021)

teuchter said:


> Still not entirely reassuring in the scenario where the case number reach over 10x their previous highs though... which I guess is why everyone is hoping that the peaks are shown to happen relatively early.


There are signs that Gauteng is peaking. Its active case number has been hovering around 80,000 for the last few days. Meanwhile other regions in SA are a bit behind Gauteng so still in the process of rapidly increasing, notably KwaZulu Natal.

I'm not sure a scenario with x10 cases is realistic.

The period in which growth is near-exponential (never exactly exponential - you don't get that in nature as you need unlimited resources) is scary cos you can't tell when it will level off. In Gauteng province, at least, that period does appear to be at an end.


----------



## elbows (Dec 17, 2021)

Chris Whitty warns against over-interpreting early Omicron data
					

The chief medical officer said even if the new variant is milder, its ability to spread faster means there could still be an issue.




					www.independent.co.uk
				






> England’s top medic has warned that early data from South Africa on the Omicron variant should be treated with caution as there is a danger people have over-interpreted it to mean there is no problem.
> 
> Professor Chris Whitty said what is lacking currently is “clear data on some of the really key questions”.
> 
> The chief medical officer said even if the new variant is milder, its ability to spread faster means there could still be an issue.





> He said it is also important to note that immunity in South Africa is “far higher” in the face of this wave, due to a prior Delta wave and the country’s vaccination programme, adding that that makes their lower hospitalisation rate so far “unsurprising”.
> 
> He stated that he remains concerned there will be a problem with Omicron, but the exact nature of it is currently unknown.
> 
> He said: “That doesn’t mean that there isn’t some degree of slightly milder disease, that is possible. But I just think there’s a danger people have over-interpreted this to say, ‘this is not a problem and what are we worrying about?’





> Dr Michael Head, senior research fellow in global health at the University of Southampton, said the analysis covered just three weeks of data and warned that it was important to “avoid inferring too much right now from any national scenario”.


----------



## elbows (Dec 17, 2021)

littlebabyjesus said:


> There are signs that Gauteng is peaking. Its active case number has been hovering around 80,000 for the last few days. Meanwhile other regions in SA are a bit behind Gauteng so still in the process of rapidly increasing, notably KwaZulu Natal.
> 
> I'm not sure a scenario with x10 cases is realistic.


They have data lag, had some IT problems some time ago which cased a backlog, and the extent to which that has now cleared is unknown to me. They also had a national holiday yesterday.

We may well anticipate a sharper, narrower peak due to the differences in transmissibility this time, but I dont want to overinterpret the current data from South Africa at all.


----------



## elbows (Dec 17, 2021)

Early estimate caveats apply to this analysis, but its something:









						First estimate of booster jab impact on Omicron
					

According to the modelling, the top-up shot could provide about 85% protection against severe illness.



					www.bbc.co.uk
				






> *UK researchers have analysed the likely impact that a Covid booster shot will have on Omicron and say it could provide around 85% protection against severe illness. *
> 
> The protection is a bit less than vaccines gave against earlier versions of Covid.
> 
> ...



'a bit less' is feeble language so I will dig into the details myself as soon as I have time,.


----------



## elbows (Dec 17, 2021)

Other stuff below, as I've not found the vaccine protection against severe disease stuff yet. These numbers have big, horrible implications.



> Controlling for vaccine status, age, sex, ethnicity, asymptomatic status, region and specimen date, Omicron was associated with a 5.40 (95% CI: 4.38-6.63) fold higher risk of reinfection compared with Delta. To put this into context, in the pre-Omicron era, the UK “SIREN” study of COVID infection in healthcare workers estimated that prior infection afforded 85% protection against a second COVID infection over 6 months. The reinfection risk estimated in the current study suggests this protection has  fallen to 19% (95%CI: 0-27%) against an Omicron infection.





> Depending on the estimates used for vaccine effectiveness against symptomatic infection from the Delta variant, this translates into vaccine effectiveness estimates against symptomatic Omicron infection of between 0% and 20% after two doses, and between 55% and 80% after a booster dose. Similar estimates were obtained using genotype data, albeit with greater uncertainty.
> 
> Prof Neil Ferguson from Imperial College London said: “This study provides further evidence of the very substantial extent to which Omicron can evade prior immunity given by both infection or vaccination. This level of immune evasion means that Omicron poses a major, imminent threat to public health.”











						Omicron largely evades immunity from past infection or two vaccine doses | Imperial News | Imperial College London
					

The Omicron variant largely evades immunity from past infection or two vaccine doses according to the latest Imperial modelling.




					www.imperial.ac.uk


----------



## elbows (Dec 17, 2021)

I didnt quote the bit about severity because its based on a very limited amount of data, but with that said here it is:



> The study finds no evidence of Omicron having lower severity than Delta, judged by either the proportion of people testing positive who report symptoms, or by the proportion of cases seeking hospital care after infection. However, hospitalisation data remains very limited at this time.


----------



## 2hats (Dec 17, 2021)

elbows said:


> Also note an alternative possibility to the 'immunocompromised human host' possibility.
> 
> Rodents, more specifically mice.
> 
> #443


Actually, it's the post just before that one that has the more compelling evidence.


----------



## elbows (Dec 17, 2021)

Thanks. 2hats have you by any chance found the Imperial document that deals with the vaccine protection against severe disease estimate?


----------



## elbows (Dec 17, 2021)

Ah here it is. Very preliminary.



> The researchers also find that this reduction in neutralising antibodies could impact vaccine efficacy against severe disease. In a worst-case scenario where the decay rate after a booster dose is the same as that observed after the first 2 doses, the study predicts that vaccine efficacy against severe disease (hospitalisation) may drop from 96.5% (95% CrI 96.1%–96.8%) against Delta to 80.1% (76.3%–83.02) against Omicron by 60 days after the primary vaccine course followed by a booster of the Pfizer-BioNTech vaccine if antibodies decay at the same rate following the booster as observed following the primary vaccine course. If this rate of decay is half that rate, the drop is estimated to be from 97.6% (95% CrI 97.4%-97.9%) against Delta to 85.9% (95% CrI 83.1%-88.3%) against Omicron. However, this could be further moderated by the increased longevity of T cell-mediated immunity.
> 
> The researchers say that whilst these numbers are currently associated with a high degree of uncertainty, they indicate that Omicron-variant specific vaccines and/or further boosters are likely to be needed to restore protection.





> The researchers note that we still do not know how severe the disease caused by the Omicron variant is compared to disease caused by previous variants.











						Boosters vital to mitigate impact of Omicron, but may lose some effectiveness | Imperial News | Imperial College London
					

Levels of neutralizing antibody to prevent Omicron infection reduced and vaccine efficacy against severe disease predicted to drop says new report.




					www.imperial.ac.uk


----------



## Griff (Dec 17, 2021)

Encouraging news from South Africa.

South Africa Hospitalisations Down


----------



## 2hats (Dec 17, 2021)

elbows said:


> Thanks. 2hats have you by any chance found the Imperial document that deals with the vaccine protection against severe disease estimate?


It's all part of report 49.


----------



## elbows (Dec 17, 2021)

Griff said:


> Encouraging news from South Africa.
> 
> South Africa Hospitalisations Down



But note this bit:



> Scientists have cautioned that other nations may have a different experience to South Africa as the country’s population is young compared with developed nations. Between 70% and 80% of citizens may also have had a prior Covid-19 infection, according to antibody surveys, meaning they could have some level of protection.


----------



## elbows (Dec 17, 2021)

At least their wastewater analysis offers some clues about their actual trend in cases in a particular area:



> A wastewater analysis carried out by the South African Medical Research Council for the week ended Dec. 10 showed a declining proportion of viral particles for two successive weeks at the plant that treats water draining from central Pretoria.


----------



## danny la rouge (Dec 17, 2021)

Have we done pronunciation yet?

I thought omicron (literally micro o) in Ancient Greek was “oh”.

Whereas omega (literally mega o) in Ancient Greek was “aw”.

So why has everyone seemingly settled on aw-micron instead of oh-micron?


----------



## elbows (Dec 17, 2021)

elbows said:


> Early estimate caveats apply to this analysis, but its something:
> 
> 
> 
> ...



Not sure if the following quote was originally part of the article as I was in a rush earlier and I believe they updated the article since then, but I'll certainly quote this bit now:



> Dr Clive Dix, former chair of the UK Vaccine Taskforce, said: "There is a huge amount of uncertainty in these modelled estimates and we can only be confident about the impact of boosters against Omicron when we have another month of real-world data on hospitalisation, ICU [intensive care] numbers and deaths.
> 
> "It remains the case that we still need to get vaccines current and future to the whole world."


----------



## Pickman's model (Dec 17, 2021)

elbows said:


> Not sure if the following quote was originally part of the article as I was in a rush earlier and I believe they updated the article since then, but I'll certainly quote this bit now:


let's just hope that we don't move on to pi or rho while they are deliberating


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## andysays (Dec 17, 2021)

danny la rouge said:


> Have we done pronunciation yet?
> 
> I thought omicron (literally micro o) in Ancient Greek was “oh”.
> 
> ...


There may be an issue with regional variations in pronunciation, but I've been pronouncing omicron like omnivore, and pronounce omega with more of a long "oh" sound.

ETA and I was unaware of the Greek letter omicron until very recently


----------



## danny la rouge (Dec 17, 2021)

andysays said:


> There may be an issue with regional variations in pronunciation, but I've been pronouncing omicron like omnivore, and pronounce omega with more of a long "oh" sound.


I was the opposite, but now I’m confused. I am not a scholar of Ancient Greek, though.


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## andysays (Dec 17, 2021)

danny la rouge said:


> I was the opposite, but now I’m confused. *I am not a scholar of Ancient Greek, though*.


Me neither (see edit above)


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## teuchter (Dec 17, 2021)

In case anyone hadn't noticed, we don't live in Ancient Greece.


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## cupid_stunt (Dec 17, 2021)

teuchter said:


> In case anyone hadn't noticed, we don't live in Ancient Greece.


----------



## xenon (Dec 17, 2021)

I understand the need for erring on the side of caution. Not over interpreting available data from SA.

But, typethinking:

Part of the explanation for relatively low hospitalisation figures, is because they've had so many cases of delta and prior beta, that this may afford some immunity.

Haven't we been having thousands of cases of delta for months, why would this not do the same?

Or is simply question of scale. SA has had delta so much worse because of lower vaccination rates?

What about the large number of imuno compromised HIV infected people in SA, has that been factored in?

As an aside, the anti vaccers will love the idea that boosters against omicron aren't as affective as infection.


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## xenon (Dec 17, 2021)

I've been pronouncing omicron as
Oh micron.


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## prunus (Dec 17, 2021)

xenon said:


> I've been pronouncing omicron as
> Oh micron.



I’ve always pronounced it as 

Om as in Tom
ic as in thick
ron as in a-do-ron-ron. 

Om-ic[k]-ron.

Although I know ohm-ic-ron would be more accurate.


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## elbows (Dec 17, 2021)

xenon said:


> I understand the need for erring on the side of caution. Not over interpreting available data from SA.
> 
> But, typethinking:
> 
> ...



As per a news item I quoted earlier, for South Africa it was said that between 70% and 80% of citizens may also have had a prior Covid-19 infection, according to antibody surveys, meaning they could have some level of protection.

I dont have a nice, tidy number for the UK or for England. Studies of things like blood donors here have tended to show antibodies from previous infections at rates in the 20 something percent range. There are limitations to such estimates and I dont really have a percentage estimate for prior infections here in mind, and its not something that the press or the authorities spend much time going on about here either. Especially since such antibodies wane over time.

One thing that seems clear is that the vastly different sie of older population in the UK compared to South Africa means that in theory that country could perhaps have 'afforded' to let that many infections happen there without totally destroying the healthcare system, and the UK could not do that.


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## two sheds (Dec 17, 2021)

'aw' is american (usually)
'oh' is british


there's a short bbc piece somewhere









						How do you say Omicron?
					

Omicron is the 13th variant of the Covid-19 virus to receive a Greek name but the pronunciation is up for debate.



					www.bbc.co.uk


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## two sheds (Dec 17, 2021)

unless you're Biden and some others when it's omnicrom


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## teuchter (Dec 17, 2021)

Remember the emphasis must go on the second syllable. If it sounds like an Irish surname then that's correct.


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## elbows (Dec 17, 2021)

Most of my remaining hopes in regarding a less than horrific Omicron situation outcome comes down to protection from things like T cells, stuff that is harder to measure and where we are only likely to discover the truth via what actually happens in practice with this wave.

I note that 2hats has recently pointed to something on that front: Covid Mutations


----------



## Supine (Dec 17, 2021)

Oh Mick Ron


----------



## elbows (Dec 17, 2021)

Following on from my previous response xenon I have had a quick go at counting the number of cases detected in England via official positive results from the start of June to the end of November, so covering the bulk of the Delta wave. Take these numbers with a pinch of salt for several reasons, not least that the testing system does not capture anything like the full picture, many people dont get a test. Many of Decembers cases were also Delta but I cant be getting into picking apart Delt from Omicron these days so I just stopped at the end of November instead.

I've broken these down into broad age groups to give some sense of where particular concerns may be right now. Figures are for England rather than the UK.

For people aged 0-19 I counted around 1.7 million.
For ages 20-39 I counted around 1.4 million.
For ages 40-59 the number I have is around 1.2 million.
For those aged 60 and above I see around 450,000 in the official figures.

Combine that sort of picture with vaccine uncertainties and the very different population demographics of South Africa, and if I were the UK authorities I would be concerned about the Omicron impact across age groups but in older people especially.


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## 2hats (Dec 17, 2021)

xenon said:


> Part of the explanation for relatively low hospitalisation figures, is because they've had so many cases of delta and prior beta, that this may afford some immunity.
> 
> Haven't we been having thousands of cases of delta for months, why would this not do the same?


SA: two consecutive waves, first of beta (highly immune evasive) then delta, in a younger population with much lower vaccination coverage.
UK: one recent wave (delta) in an older population with much higher vaccination coverage.

Immunity acquired by infection after vaccination is blunted (that's what vaccines do!) compared to immunity acquired by infection with no vaccination. Also consider: survivorship bias.

e2a:


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## Mation (Dec 17, 2021)

danny la rouge said:


> It’s a Father Ted quote. I didn’t intend it to sound mean.


Ah. My Father Ted knowledge is certainly wanting.

Thank you for just saying what it was about and what you meant/didn't mean, rather than launching into battle*. Massively helpful for us literal folk (or me, at least). 

*E2a: Not that you do, in case it sounded like that. But it's a thing that can happen with (other) people.


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## 2hats (Dec 17, 2021)

2hats said:


> It's all part of report 49.


More detailed analysis of the global impact on omicron of booster doses in report 48.


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## Spandex (Dec 17, 2021)

The people making the most noise about the figures in South Africa seem to be the same 'it's just flu' crew who've been talking down the seriousness of Covid since March 2020. That means anything they point at fails to reassure me.

Who knows if they're onto somthing? I have no idea what's going to happen in the UK in the next couple of weeks and nor does anyone else. We might be heading for disaster; or boosters/immunity/the nature of Omicron might mean we get away with it.

With tens of thousands of lives at risk pointing at early, inconclusive, figures from another continent and going 'it'll probably be okay' doesn't strike me as the best public health approach.


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## elbows (Dec 17, 2021)

Yeah I will be content to dance around to good news only with the benefit of hindsight.


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## elbows (Dec 17, 2021)

> AMSTERDAM, Dec 17 (Reuters) - The health experts advising the Netherlands' government on COVID-19 strategy have recommended the country go into a "strict" lockdown, Dutch media reported on Friday, just days after a partial lockdown was extended through January.
> 
> Broadcaster RTL Nieuws and newspaper NRC Handelsblad cited sources within the panel of experts, whose recommendations are not made public until after the government has taken a decision, that they have advised the closure of all but essential stores.











						Dutch health experts advise a full lockdown to slow Omicron -media
					

The health experts advising the Netherlands' government on COVID-19 strategy have recommended the country go into a "strict" lockdown, Dutch media reported on Friday, just days after a partial lockdown was extended through January.




					www.reuters.com


----------



## elbows (Dec 17, 2021)

SAGE minutes leaked to the BBC again for at least the third time in a row:









						Covid: Action needed to limit hospital admissions - Sage scientists
					

Scientists say admissions could reach 3,000 a day in England if more restrictions are not brought in soon.



					www.bbc.co.uk
				






> The document says there are "many uncertainties" about the future path of hospitalisations linked to Omicron.





> According to the leaked minutes, the Sage advisers say that without intervention measures beyond the Plan B rules currently in place, modelling indicates that hospital admissions could peak at "at least" 3,000 a day in England.





> The Sage minutes say: "If the aim is to reduce the levels of infection in the population and prevent hospitalisations reaching these levels, more stringent measures would need to be implemented very soon."
> 
> The record of the meeting goes on to say that measures equivalent to those in place after Step Two or Step One of the roadmap in England, if enacted early enough, "could substantially reduce the peak in hospital admissions and infections compared with Plan B alone".
> 
> Step One and Two of the roadmap for easing lockdown - which was in place in England in the Spring - banned indoor social contact and indoor hospitality. Step Three allowed six people, or two households, to meet indoors and indoor hospitality could reopen.





> "The timing of such measures is crucial," say the Sage minutes. "Delaying until 2022 would greatly reduce the effectiveness of such interventions and make it less likely that these would prevent considerable pressure on health and care settings."



Sounds like quite a bit of whats said in the minutes relates to the modelling we already talked about recently.


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## elbows (Dec 17, 2021)




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## elbows (Dec 17, 2021)




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## elbows (Dec 17, 2021)




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## xenon (Dec 17, 2021)

elbows said:


>




I've got a mate from Zimbabwe. This time last year, was how so many more cases were brought there and other countries around South Africa. As just that, workers going home for Christmas. He actually lost a life long mate who was in his 40s through it.


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## teuchter (Dec 18, 2021)

I don't really get how a portion of the population leaving would produce a peak. More like a ledge surely? Even if half of the entire population leaves...if the rate is a doubling every couple of days,  you've only delayed reaching a certain number by a couple of days haven't you?


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## _Russ_ (Dec 18, 2021)

The whole travel to see your family thing is for the UK a cultural import made easy by mass car ownership and cheap air travel, 40 years ago nobody did it, now its viewed as some sort of societal right.


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## cupid_stunt (Dec 18, 2021)

_Russ_ said:


> The whole travel to see your family thing is for the UK a cultural import made easy by mass car ownership and cheap air travel, 40 years ago nobody did it, now its viewed as some sort of societal right.



Bollocks, we always went to visit our grandparents over the Christmas period, over 40 years ago.


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## Supine (Dec 18, 2021)

My unvaxxed sis, BiL and three kids are leaving omicron head office to visit us next week for xmas. Not exactly happy about living in the same house as a bunch of londoners who are going out socialising this weekend.


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## zora (Dec 18, 2021)

Well, chances are extremely high that they will catch covid beforehand and have to cancel their travels, if that's any consolation...:/


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## two sheds (Dec 18, 2021)

zora said:


> Well, chances are extremely high that they will catch covid beforehand and have to cancel their travels, if that's any consolation...:/


whether they _will _cancel is another thing by the sound of it. I'd phone them and say 'sorry, but no'.


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## Pickman's model (Dec 18, 2021)

cupid_stunt said:


> Bollocks, we always went to visit our grandparents over the Christmas period, over 40 years ago.


It'll save you time if each time you see _Russ_ by a post you just skip past it


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## kabbes (Dec 18, 2021)

danny la rouge said:


> Have we done pronunciation yet?
> 
> I thought omicron (literally micro o) in Ancient Greek was “oh”.
> 
> ...


It’s because people have become confused between Ancient Greek and Modern Greek.  Like a lot of languages, Greek has undergone some serious vowel (and consonant) shifts in the last few thousand years.  The letters iota, omicron and upsilon used to be pronounced, respectively, like “eye”, “oh” and “eye” (again), equivalent to i, o and y in how we pronounce words like “micro” for the former two and “Pythagoras” in the last case.  But this isn’t the case any more.  Modern Greek doesn’t have these vowel sounds (well, the “eye” sound still exists and is rendered as αι but it is not how either ι or υ are pronounced any more).  As such, the letter ο or omicron is pounced “o’ mee cron“ with a short o.  (Similarly, pi is now pronounced “pee” and chi is pounced “chee”).

For the variants, I think they are trying to use Ancient Greek, and that’s what people are used to in terms of saying things like “delta” (which is now more like dhelta) and pi.  In that case, it should be oh-m-eye-cron.  But unlike delta and pi, people in the West aren’t used to hearing the Greek letter “omicron” so they have turned to hearing how the Greeks say it, which means they are picking up the modern pronunciation instead.


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## elbows (Dec 18, 2021)

teuchter said:


> I don't really get how a portion of the population leaving would produce a peak. More like a ledge surely? Even if half of the entire population leaves...if the rate is a doubling every couple of days,  you've only delayed reaching a certain number by a couple of days haven't you?



I'd need to know the place and the holiday well in order to judge. But certainly keep in mind the vast number of opportunities the virus needs in order to sustain doubling.

And then consider what happened here when the Euros ended and schools went on holiday. The established pattern of contacts changes overnight, and in the case of the UK this led to a peak that most commentators didnt seem to be expecting, despite Scotland having experienced the same thing. Then consider how potent this effect was when so many of the cases were driven by young age groups. Throw in large changes to workforce mixing patterns, and the possibility that the virus was already going to struggle to keep finding twice as many fresh victims to infect, and perhaps the possibility can seem more plausible to you. We can also add in how these sudden changes in behaviour can also affect testing, and publication of test data, although in this case there was also the wastewater analysis that I mentioned earlier. Obviously there is a difference between a peak and the permanent decline of a wave, again as seen in the UK when it came to Delta dragging on, so I dont read as much into peaks now as I did to peaks that were behaviour+lockdown induced, where we knew those brakes would be left on some months, pushing levels of infection all the way down in a sustained way. But even when that doesnt happen, sudden changes to viral momentum can take some time to come undone.


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## teuchter (Dec 18, 2021)

It seems plausible that it could bring an apparent "peak" forward somewhat, but less plausible that it could disguise a situation where otherwise a very rapid increase would have been sustained for some time.

It seems like most people are kind of agreed on what the doubling time is for the Omicron variant - much faster than previous ones - but much of the disagreement is around how long it can sustain that rapid growth. Of course, the answer to that might be quite different in different populations.


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## _Russ_ (Dec 18, 2021)

cupid_stunt said:


> Bollocks, we always went to visit our grandparents over the Christmas period, over 40 years ago.


You is not representative of the UK as a whole..thank fuck


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## cupid_stunt (Dec 18, 2021)

_Russ_ said:


> You is not representative of the UK as a whole..thank fuck



You fucking eejit.


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## Carvaged (Dec 18, 2021)

_Russ_ said:


> You is not representative of the UK as a whole..thank fuck



I found this interesting. I asked all the old people I know (a princely sample size of 5) and they claimed it was actually pretty normal for family dispersed all over the country to meet up for Christmas: even before mass car ownership, people were pretty happy to make use of trains and buses, of which there were a far higher and more convenient number and route density than today, of course.


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## cupid_stunt (Dec 18, 2021)

Carvaged said:


> I found this interesting. I asked all the old people I know (a princely sample size of 5) and they claimed it was actually pretty normal for family dispersed all over the country to meet up for Christmas: even before mass car ownership, people were pretty happy to make use of trains and buses, of which there were a far higher and more convenient number and route density than today, of course.



Of course it was, _Russ_ is just posting bollocks again.


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## teuchter (Dec 18, 2021)

Yeah, _Russ_ is talking nonsense. 40 years ago was already the 80s anyway.


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## teuchter (Dec 18, 2021)

Also, cupid_stunt is very much "average UK person".


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## two sheds (Dec 18, 2021)

Yeh I always went home for Christmas right from the 70s, even when I was living in the Netherlands - I went by train.


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## elbows (Dec 18, 2021)

teuchter said:


> It seems plausible that it could bring an apparent "peak" forward somewhat, but less plausible that it could disguise a situation where otherwise a very rapid increase would have been sustained for some time.
> 
> It seems like most people are kind of agreed on what the doubling time is for the Omicron variant - much faster than previous ones - but much of the disagreement is around how long it can sustain that rapid growth. Of course, the answer to that might be quite different in different populations.



At the heart of traditional modelling is the number of remaining susceptible people at each moment in time, so yes that is a huge factor.

In this case people were just warning about over-interpreting recent data. I dont think they made any specific claims about when a peak would happen if it were not for the holiday there. Looking at things in a simplistic way, if the climb up a peak is very steep, we might expect the peak to diminish rapidly and for the overall length of wave to be quite different to that seen with slower variants. Because the virus will burn through the suscpetible population more rapidly. Complications to this simplistic picture include as always the impact of people changing their behaviours when faced with such waves.


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## TopCat (Dec 18, 2021)

Mayor of London has just declared a "major incident" over covid. This triggers a few resources and allows some stuff to be dropped.


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## platinumsage (Dec 18, 2021)

Khan last did this on January the 8th 2021, two days after what was to turn out as the peak of patient admissions at 977/day. In this omicron wave the latest data is for 210 admission on the 15th. If Khan had declared a major incident at 210 admissions in the delta wave he'd have done it a whole month earlier on 7 Dec 2020 when admissions were exactly 210.


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## wemakeyousoundb (Dec 18, 2021)

platinumsage said:


> Khan last did this on January the 8th 2021, two days after what was to turn out as the peak of patient admissions at 977/day. In this omicron wave the latest data is for 210 admission on the 15th. If Khan had declared a major incident at 210 admissions in the delta wave he'd have done it a whole month earlier on 7 Dec 2020 when admissions were exactly 210.


then there is staff shortages in the ambulance service (100 ambulances down in London) and hospitals.


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## TopCat (Dec 18, 2021)

Speaking to emergency services people over the last two days has been a bit of an eyeopener. Loads and loads actually positive and sick. I doubt 500 police will be on duty throughout tomorrow.


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## elbows (Dec 18, 2021)

Yeah staff shortages are an even bigger issue this time, as expected with a variant this transmissible, this vaccine-evading and with such a low doubling time.

This was one of the non-hospital reasons for previous lockdowns, since by reducing all sorts of normal human activities massively, some non-covid pressure on emergency services is relieved a bit. The authorities actually acknowledged this the first time they had to start cancelling mass events in wave 1. Though part of the reason they acknowledged it back then was to downplay the extent to which they were u-turning on mass gatherings for covid transmission reasons, having previously claimed outdoor events werent a big transmission issue.


----------



## Monkeygrinder's Organ (Dec 18, 2021)

teuchter said:


> Also, cupid_stunt is very much "average UK person".



Yes, I heard cupid_stunt has one breast and one testicle.


----------



## teuchter (Dec 18, 2021)

Monkeygrinder's Organ said:


> Yes, I heard cupid_stunt has one breast and one testicle.


In fact not quite a whole one of either.


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## bimble (Dec 18, 2021)

I might be growing paranoid, living under this government for what seems like decades, but it seems possible that they'll change the rules on isolation, to make it significantly shorter, to address the staffing disaster that is happening. The numbers are incredible, not just the firefighters and hospital staff but everything else too the less visible stuff. 
Already we don't have to isolate at all if we are a vaccinated confirmed contact of covid positive people which tbh makes no medical sense really at all does it.


----------



## elbows (Dec 18, 2021)

Dutch Omicron lockdown confirmed. Back at the start of the pandemic their establishments instincts were quite similar to the UKs in terms of the 'herd immunity' approach.









						Covid: Dutch go into Christmas lockdown over Omicron wave
					

Non-essential shops, schools, bars, restaurants and other public venues will be closed until at least mid-January.



					www.bbc.co.uk


----------



## elbows (Dec 18, 2021)

bimble said:


> I might be growing paranoid, living under this government for what seems like decades, but it seems possible that they'll change the rules on isolation, to make it significantly shorter, to address the staffing disaster that is happening. The numbers are incredible, not just the firefighters and hospital staff but everything else too the less visible stuff.
> Already we don't have to isolate at all if we are a vaccinated confirmed contact of covid positive people which tbh makes no medical sense really at all does it.



I dont think thats growing paranoid, its more like seeing whats on the front page of the fucking Daily Mail today.

I wont have a complete meltdown if they reduce it to 7 days, since thats better than essential services having a complete meltdown. If it must be done it should be done at the same time as compensatory measures to reduce number of infections in other ways. Which is not what the fucking Mail have in mind.









						Newspaper headlines: Fresh Omicron fears and No 10 inquiry 'in disarray'
					

The focus of most front pages this morning is on the No 10 parties' inquiry chief Simon Case quitting his role.



					www.bbc.co.uk


----------



## elbows (Dec 18, 2021)

Sorry bimble I did my usual trick of sticking more thoughts into that post, after you'd already read it.


----------



## bimble (Dec 18, 2021)

thats ok elbows . I'm just sat here wondering whether i am reassured or not that my paranoid thoughts and the daily mail front page are the same thing.


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## bimble (Dec 18, 2021)

does this underlined bit make sense? Idk. 
seems to not make much sense (guardian just now) . how can it not help.


----------



## prunus (Dec 18, 2021)

I think it’s not that it won’t help at all, just that it won’t prevent hospitalisations rising through the early months of 2022.

Very roughly, if it takes 2 weeks from infection to hospitalisation, and 2 weeks from booster to extra protection, then vaccinations happening today don’t have an effect on hospitalisation rates for 4 weeks.


----------



## bimble (Dec 18, 2021)

i see.


----------



## Badgers (Dec 18, 2021)

France should be fine  









						Time-lapse of long Eurostar queue before travel ban
					

Travellers in St Pancras station, London, line up to get to France before it closes its borders to the UK.



					www.bbc.co.uk


----------



## Sasaferrato (Dec 18, 2021)

Carvaged said:


> I found this interesting. I asked all the old people I know (a princely sample size of 5) and they claimed it was actually pretty normal for family dispersed all over the country to meet up for Christmas: even before mass car ownership, people were pretty happy to make use of trains and buses, of which there were a far higher and more convenient number and route density than today, of course.



When we lived in the Outer Hebrides people came home for Christmas from all over.


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## weltweit (Dec 18, 2021)

Omicron = Moronic


----------



## 8ball (Dec 18, 2021)

Badgers said:


> France should be fine
> 
> 
> 
> ...



Yeah, that looks fine.


----------



## elbows (Dec 18, 2021)

Real numbers wont even need to come close to some of this modelling in order for very bad things to still happen:



> The government’s SPI-M-O group of scientists, which reports to the Scientific Advisory Group for Emergencies (Sage), also warned that, based on their modelling, hospitalisations could peak between 3,000 and 10,000 a day and deaths at between 600 and 6,000 a day.





> As well as the alarming scenarios above, Sage also modelled the impact of measures imposed under step 1 of the roadmap used last spring. If step 1 measures were imposed, the modelling suggested that infections could be limited to between 200,000 and a million a day. Hospitalisations could run at between 1,500 and 5,000 admissions a day and daily deaths would be 200 to 2,000.











						UK scientists: bring in curbs now or face up to 2m daily Covid infections as Omicron spreads
					

Deaths could hit 6,000 a day and delaying restrictions until New Year will cut effectiveness, say Sage experts




					www.theguardian.com


----------



## wemakeyousoundb (Dec 18, 2021)

weltweit said:


> Omicron = Moronic


PCR = PRC
makes you think


----------



## 8ball (Dec 18, 2021)

wemakeyousoundb said:


> PCR = PRC
> makes you think



LFT = TFL


----------



## Sasaferrato (Dec 18, 2021)

8ball said:


> LFT = TFL



Well, the vessels of your liver do resemble a tube map (sortish of vaguely) so liver function tests could be of use to the mappers at TFL.


----------



## kabbes (Dec 18, 2021)

Realistically, infections can't run at 2 million a day for very long.  In a week, you'd have infected 20% of the UK population.  After a month, there is literally nobody left to infect, but the bushfire would have burned out long before that point.  

Don't get me wrong, this is a disastrous scenario that would totally fuck things up, and the systems would collapse for as long as the badly ill infected people that need hospitalisation stay alive, which means that many people would unnecessarily die.    I'm just saying that you can't reduce it to the soundbite of "2 million infected a day."


----------



## 8ball (Dec 18, 2021)

Sasaferrato said:


> Well, the vessels of your liver do resemble a tube map (sortish of vaguely) so liver function tests could be of use to the mappers at TFL.



I was going with Lateral Flow Test.


----------



## elbows (Dec 18, 2021)

kabbes said:


> Realistically, infections can't run at 2 million a day for very long.  In a week, you'd have infected 20% of the UK population.  After a month, there is literally nobody left to infect, but the bushfire would have burned out long before that point.
> 
> Don't get me wrong, this is a disastrous scenario that would totally fuck things up, and the systems would collapse for as long as the badly ill infected people that need hospitalisation stay alive, which means that many people would unnecessarily die.    I'm just saying that you can't reduce it to the soundbite of "2 million infected a day."



You can talk about that as a peak value, especially if talking about the actual number of infections on a day rather than the number we manage to detect.

And yes we might expect a rapid variant like Omicron to burn through the population rather rapidly, at least if peoples behaviour doesnt change enough.


----------



## kabbes (Dec 18, 2021)

elbows said:


> You can talk about that as peak values, especially if talking about the actual number of infections on a day rather than the number we manage to detect.


You can, but then the headline, "up to 2m daily infections" is misleading.  "Daily" implies some kind of sustained rate, not a peak.


----------



## elbows (Dec 18, 2021)

No claim is built into the headline as to how long that would be sustained, and previous stuff months ago from the likes of Javid warning of 100,000 cases a day were not so very different, in terms of lacking detail of the wider context. Such figures are really an illustration of how rapidly exponential growth can lead to staggeringly huge numbers. Such nubers often fail to come to full fruition due to the massive disruption to contact mixing patterns that arise from things like self-isolation, large behavioural shifts and new restrictions. And there is no way our testing system will manage to formally record a huge chunk of them once they grow that big, but some very large Omicron numbers will probably show up via different sorts of case estimates, whatever happens next.


----------



## kabbes (Dec 18, 2021)

I guess my point is that things are fucked up enough as it is.  There is no need to create things unrealistically beyond fucked-up to talk about.  If the paper talks about the rate reaching "2m daily infections" and then it actually "only" reaches 1m daily infections (and that for "only" five days, say), you give the establishment an out to say, "well, it wasn't as bad as they said it might get."


----------



## Sasaferrato (Dec 18, 2021)

FFS! Is that really the best that can be predicted?  The high figures are ten times that of the low. Ten times.


----------



## kabbes (Dec 18, 2021)

Sasaferrato said:


> FFS! Is that really the best that can be predicted?  The high figures are ten times that of the low. Ten times.


Deaths are a proportion of a proportion of a range of predictions.  It doesn't take much variation in each element of that model to get to a 10x variation overall.  600-6,000 seems like a sensible range to me.  I'm pretty sure it doesn't even represent a proper 95% confidence interval, or anything -- just a range of reasonable best estimates.


----------



## 8ball (Dec 18, 2021)

Sasaferrato said:


> FFS! Is that really the best that can be predicted?  The high figures are ten times that of the low. Ten times.



Sometimes that’s the nature of the models.  Once you factor in variability in “lucky” (ie. unlucky) super-spreader events, then you can end up with very wide confidence intervals.

Not to mention the fact that the starting conditions are very uncertain, and we are guessing about at what point we are at in an exponential growth phase.


----------



## elbows (Dec 18, 2021)

Note for example this bit from the SAGE minutes the Guardian mentioned earlier:





__





						SAGE 99 minutes: Coronavirus (COVID-19) response, 16 December 2021
					






					www.gov.uk
				






> In England it is almost certain that there are now hundreds of thousands of new Omicron infections per day. Levels of Omicron infection are currently highest in London. Reported numbers of confirmed and suspected Omicron infections will only be a small proportion of the actual number. This is because there are lags between people becoming infected, being tested, and getting test results (data lags matter most when growth is very fast); not all tests allow the variant to be identified; and not everyone who is infected is tested.


----------



## elbows (Dec 18, 2021)

Various modelling documents are also available int he December 16th section. I havent had time to read them just yet.





__





						SAGE meetings, December 2021
					

Minutes and papers from the Scientific Advisory Group for Emergencies (SAGE) meetings held in December 2021.




					www.gov.uk


----------



## elbows (Dec 18, 2021)

From those minutes:



> 13. Behavioural factors are likely to significantly affect the timing and scale of the peak. Behaviour remains a source of major uncertainty in modelling. Some data indicate that people have been adopting safer behaviours in recent days including increased use of face coverings (up to around 95% self-reported usage) and reductions in contacts. These changes will take some time to lead to any slowing of growth in infections, and longer to affect hospitalisations, and so whilst potentially significant, are unlikely on their own be sufficient to avert the large wave of hospitalisations.
> 
> 14. Enabling people to make safer behavioural choices will remain important, particularly over the festive period where they may feel obligations or pressures to participate in some higher-risk activities or events in addition to the ones they do want to prioritise.


----------



## kabbes (Dec 18, 2021)

I produced a model once that suggested a number would probably be between 0 and 100 million with a median of about 500k.  I couldn't be sure it wouldn't be more than 100 million, but at least I knew it wasn't possible to be less than 0.


----------



## elbows (Dec 18, 2021)

8ball said:


> Sometimes that’s the nature of the models.  Once you factor in variability in “lucky” (ie. unlucky) super-spreader events, then you can end up with very wide confidence intervals.
> 
> Not to mention the fact that the starting conditions are very uncertain, and we are guessing about at what point we are at in an exponential growth phase.



Significant unknowns include peoples behaviour, severity of Omicron, and remaining protection against severe Omicron illness by vaccines.


----------



## 8ball (Dec 18, 2021)

elbows said:


> Significant unknowns include peoples behaviour, severity of Omicron, and remaining protection against severe Omicron illness by vaccines.



Indeed.  Just about all the input parameters are guesswork.  One order of magnitude seems fairly tight tbf.


----------



## elbows (Dec 18, 2021)

kabbes said:


> I produced a model once that suggested a number would probably be between 0 and 100 million with a median of about 500k.  I couldn't be sure it wouldn't be more than 100 million, but at least I knew it wasn't possible to be less than 0.



Due to a lack of functioning time machines, imperfect modelling remains a critical tool for making policy decisions. Even a wide range is much better than leaving it to peoples imagination, especially when some of them seem to lack an imagination or have deluded quantities of optimism.


----------



## Badgers (Dec 18, 2021)

TopCat said:


> Speaking to emergency services people over the last two days has been a bit of an eyeopener. Loads and loads actually positive and sick. I doubt 500 police will be on duty throughout tomorrow.


Those 500 will be busy


----------



## Badgers (Dec 18, 2021)




----------



## elbows (Dec 18, 2021)

Some of my comments about the impact of behaviour are reflected in SAGE modelling group documents from December 15th:





__





						SPI-M-O: Consensus statement on COVID-19, 15 December 2021
					






					www.gov.uk
				






> 16. Behaviour change (spontaneous, recommended or mandated) could significantly affect the peak of infections and hospitalisations. Current modelling assumes no change in behaviours beyond those previously seen upon imposition of equivalent measures in the past. Non-mandated behaviour change, however, has the potential to make a big difference in either direction. If cases increase to high levels very rapidly, there may be a spontaneous precautionary reduction in mixing patterns, thus slowing transmission. The festive period, however, may see changes in mixing between households and generations, joining up networks, that could lead to increased transmission.
> 
> 17. Hospital admissions have been between 500 and 1,000 per day in England since mid-July 2021, likely due to spontaneous behaviour changes. It is possible that similar behavioural changes could result in a long, extended period of high hospitalisations, rather than a single sharp peak.


----------



## Sasaferrato (Dec 18, 2021)

8ball said:


> Sometimes that’s the nature of the models.  Once you factor in variability in “lucky” (ie. unlucky) super-spreader events, then you can end up with very wide confidence intervals.
> 
> Not to mention the fact that the starting conditions are very uncertain, and we are guessing about at what point we are at in an exponential growth phase.



Och, I know. Ignore me, I'm fed up and crabbit tonight.

I've been (along with hordes of others) been pretty much isolating for nearly two years now. I just want it to stop.


----------



## 8ball (Dec 18, 2021)

Sasaferrato said:


> Och, I know. Ignore me, I'm fed up and crabbit tonight.
> 
> I've been (along with hordes of others) been pretty much isolating for nearly two years now. I just want it to stop.



Yep.  It feels like a decade.


----------



## elbows (Dec 18, 2021)

Other stuff from that modelling document:



> 20. In June to July 2021, the ‘pingdemic’ and significant behaviour change coincided with (and may have caused) a sharp reversal of epidemic growth; at the time, the R value for England was slightly above 1 (approximately 1.2 to 1.4 over this period, with a growth rate of approximately +3% to +6% per day). It is unlikely that such an ‘intervention’ would have such a significant impact now due to the significant growth of Omicron (estimated percentage growth rate of around 50% per day [footnote 5] ). If, however, many people were isolating as a result of being a COVID-19 case or potential contact of one, then this reduction in network transmission would reduce Omicron cases.





> 22. Even a marked reduction in any aspect of severity is unlikely to offset the impact of a larger susceptible pool (a consequence of immune escape) or increased transmissibility without further measures, as is implied by Omicron’s evident growth advantage. The severity of a disease, however, is multi-layered and includes: whether people require hospital treatment if infected (infection hospitalisation risk (IHR)); how long they spend in hospital when they get there (length of stay); and whether they need to be transferred, for example, to intensive care. Omicron may appear to have lower severity as a result of protection due to prior infection or vaccination – this apparent decreased severity may not correspond to an intrinsically lower severity of this variant. This may also be affected by the demographics of individuals infected with Omicron and their immune status. Pressure on health and care settings, particularly hospital bed occupancy, will depend on all aspects of severity and how these interact. It may be that a changed average length of stay affects how hospitals are able to manage their admissions.





> 23. Previous epidemic waves have seen the hospital fatality risk increase, together with substantial changes in length of stay. The coming wave of admissions and increased pressure in hospitals is likely to see similar observations, although these will be modified by changes in treatment options and clinical requirements of patients.
> 
> 24. There are early indications for shorter lengths of stay in South Africa, however, it is unknown whether such observations would be seen in the UK, given differences in population demographics, COVID-19 epidemic timing and variant composition to date, vaccination types and programmes, health care systems, and so on. It is too early to make an assessment of what the UK’s average length of stay would be for hospitalisations due to Omicron infection.





> 28. There remains considerable uncertainty whilst the full range of biological parameters of the Omicron variant remain poorly described. Information about Omicron’s transmissibility and immune escape compared to Delta will be significantly improved over the next 2 weeks, although disentangling the difference between these 2 may take longer.
> 
> 29. Other uncertainties also remain, such as how Omicron infections will move through and affect different age groups, how differently Omicron may evade natural and vaccine-acquired immunity and how this may hold for booster vaccinations, and the relative scale of reduction in vaccine effectiveness between infection and severe disease. Current analyses assume Omicron has the same generation time as Delta, but this remains unknown.


----------



## elbows (Dec 18, 2021)

kabbes said:


> I guess my point is that things are fucked up enough as it is.  There is no need to create things unrealistically beyond fucked-up to talk about.  If the paper talks about the rate reaching "2m daily infections" and then it actually "only" reaches 1m daily infections (and that for "only" five days, say), you give the establishment an out to say, "well, it wasn't as bad as they said it might get."



Pandemic shitheads will always find some dubious way to make their points, we've seen that plenty in the past. I do not believe in falsely sugarcoating worst case estimates in at attempt to pander to such bullshitters. They will just make shit up and return to make the same false claims again and again, no matter how deadly their errors of judgement were in the past. No matter how ridiculous their past utterances were before we were swamped by death in previous waves, plenty of them still have the nerve to repeat the exercise despite the evidence of how wrong they were. Brass necks and brass eyes.

I would have been useless in this pandemic if I were too afraid of leaving myself open to the accusation that I had cried wolf. Better to err on that side of things rather than reckless optimism and wishful thinking. Unknowns about Omicron and a messy picture of immunity make the crying wolf risk greater this time, but I still dont consider that a reason to change my approach this time.


----------



## elbows (Dec 20, 2021)

Since I often moan about a lack of published covid wastewater analysis for England, I should point out that Omicron detection via those means is covered by pages 32-34 of the variant technical report of December 17th. However the info it provides is now rather out of data and uninteresting and irrelevant compared to other sources. They say that such data will be published monthly in experiemental form from 2022.



			https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1042046/Technical_Briefing_32.pdf


----------



## MrCurry (Dec 21, 2021)

Do we have any better info now on characteristic symptoms of omicron cases, or are they maybe as varied as delta and undifferentiated from other variants? 

MiL has come down with vomiting overnight, following heartburn and painful tummy yesterday evening, and while it could be anything, I’m wondering if it maybe fits omicron?  She hasn’t eaten anything different from others who are unaffected.


----------



## platinumsage (Dec 21, 2021)

MrCurry said:


> Do we have any better info now on characteristic symptoms of omicron cases, or are they maybe as varied as delta and undifferentiated from other variants?
> 
> MiL has come down with vomiting overnight, following heartburn and painful tummy yesterday evening, and while it could be anything, I’m wondering if it maybe fits omicron?  She hasn’t eaten anything different from others who are unaffected.



Certainly not typical symptoms of omicron or any other variant. That doesn't mean it isn't, as some people experience unusual symptoms, but I'd be looking for other causes first.


----------



## LDC (Dec 21, 2021)

MrCurry said:


> Do we have any better info now on characteristic symptoms of omicron cases, or are they maybe as varied as delta and undifferentiated from other variants?
> 
> MiL has come down with vomiting overnight, following heartburn and painful tummy yesterday evening, and while it could be anything, I’m wondering if it maybe fits omicron?  She hasn’t eaten anything different from others who are unaffected.



You're trying to make symptoms that clearly fit something else fit covid. I'd rule out the something else first.


----------



## 8ball (Dec 21, 2021)

But do a test anyway.

Just FYI - there has been a bit of norovirus about.


----------



## nagapie (Dec 21, 2021)

MrCurry said:


> Do we have any better info now on characteristic symptoms of omicron cases, or are they maybe as varied as delta and undifferentiated from other variants?
> 
> MiL has come down with vomiting overnight, following heartburn and painful tummy yesterday evening, and while it could be anything, I’m wondering if it maybe fits omicron?  She hasn’t eaten anything different from others who are unaffected.



Lots of friends in London reporting tummy aches and vomiting actually. More among their positive children but not only.


----------



## weltweit (Dec 21, 2021)

WHO urges cancelling some holiday events over Omicron fears
					

"An event cancelled is better than a life cancelled," warns the World Health Organization's head.



					www.bbc.co.uk
				






> *The World Health Organization has urged people to cancel some of their holiday plans to protect public health, as the Omicron variant spreads globally. *


----------



## elbows (Dec 21, 2021)

4th dose for older and more vulnerable Israelis to fight the Omicron wave (because their previous vaccines were given longer ago):









						Israeli PM announces fourth Covid jab for over-60s to tackle Omicron
					

Booster will also be available to medical teams and immunodeficient people four months after third dose




					www.theguardian.com


----------



## magneze (Dec 21, 2021)

Just saw that. Is this what we're onto next? Ffs 😞


----------



## 8ball (Dec 22, 2021)

magneze said:


> Just saw that. Is this what we're onto next? Ffs 😞



Our next one is likely to be an Omicron-specific vaccine, and if we get lucky there might be a “universal Covid” vaccine not too far behind it.


----------



## gentlegreen (Dec 22, 2021)

I've only ticked-off two of the four techs - I hope we at least get to try the protein one


----------



## elbows (Dec 22, 2021)

bimble said:


> I might be growing paranoid, living under this government for what seems like decades, but it seems possible that they'll change the rules on isolation, to make it significantly shorter, to address the staffing disaster that is happening. The numbers are incredible, not just the firefighters and hospital staff but everything else too the less visible stuff.
> Already we don't have to isolate at all if we are a vaccinated confirmed contact of covid positive people which tbh makes no medical sense really at all does it.



It didnt take long to come true. I've nothing to add really since I already shared my thoughts when you brought the possibility up.









						Covid: Self-isolation cut from 10 days to seven with negative tests
					

The new rules in England mean some people could end their self-isolation in time for Christmas.



					www.bbc.co.uk


----------



## elbows (Dec 22, 2021)

It doesnt sound like the awaited early analysis of Omicron severity and vaccine protection is going to add much to the picture beyond what we might already have expected:









						London Playbook: SCOOP: Omicron milder in UK — New Year’s fireworks — Liz vs. No. 10
					

What's driving the day in Westminster. Politics and policymaking in the UK capital.




					www.politico.eu
				






> The best news in the early data is that Britons who fall sick with Omicron are less likely to become severely ill than those who caught Delta. More people are likely to have a mild illness with less serious symptoms — probably in part due to Britain’s large number of vaccinated and previously infected people, and possibly because Omicron may be intrinsically milder.





> The less good news is that while Omicron seems milder overall, the UKHSA has found it is not necessarily mild enough to avoid large numbers of hospitalizations. The experts have found evidence that for those who do become severely ill, there is still a high chance of hospitalization and death. The UKHSA has also confirmed that transmissibility of Omicron is very high, meaning that even though it is milder, infections could rocket to the point large numbers still end up in hospital — essentially negating the reduction in severity.





> Playbook is told the UKHSA is also expected to conclude that while two doses of a vaccine are not enough to offer strong protection, a booster dose does significantly reduce the chance of both symptomatic infection and ending up in hospital.


----------



## littlebabyjesus (Dec 22, 2021)

Study published yesterday that appears to be being referenced in various places in the news at the moment.

Early assessment of the clinical severity of the SARS-CoV-2 Omicron variant in South Africa

Findings:

80% reduced risk of hospitalisation per infection with omicron compared to delta. (adjusted odds ratio (aOR) 0.2, 95% confidence interval (CI) 0.1-0.3)

Significantly reduced risk of severe disease compared to previous delta infections (aOR 0.3, 95% CI 0.2-0.6) but not compared to concurrent delta infections (aOR 0.7, 95% CI 0.3-1.4). They did find a possible small reduced risk (at 0.7), but don't consider it statistically secure due to wide confidence intervals, which seem to have been set at 'double' and 'half' the given figure, which is probably a bit of a guesstimate - the old problem 'what are the error bars on my error bars?'


----------



## elbows (Dec 22, 2021)

The usual story then, same sort of stuff as Whitty mentioned recently, ie the last sentence from this bit of the abstract of that study:



> Early analyses suggest a reduced risk of hospitalisation among SGTF-infected individuals when compared to non-SGTF infected individuals in the same time period, and a reduced risk of severe disease when compared to earlier Delta-infected individuals. Some of this reduction is likely a result of high population immunity.



I think its been pretty clear from the start of Omicron that it does not lead us 'all the way back to square one' in this pandemic. But beyond that, I mostly have to wait for the full UK picture of how much its eroded our protection to emerge. The number of infections we allow in this country will certainly provide huge amounts of data in time.


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## Supine (Dec 22, 2021)

A bit of UKHSA leakage


----------



## elbows (Dec 22, 2021)

This is why I hate the ignore function, I already mentioned that but my pandemic rants are not to Supines taste and so they probably didnt see my post on the subject.


----------



## littlebabyjesus (Dec 22, 2021)

Supine said:


> A bit of UKHSA leakage



One other piece of potentially good news not included there is that London appears to be following a Gauteng-like curve. Cases shot up rapidly but look like they may have peaked rapidly as well, as happened in Gauteng. Tentatively, London may have hit a peak around the middle of last week. That's led to increased hospitalisations this week, but those may be nearing or at their peak now as well. 

So when they say that hospitalisations may shoot up, there is also some reason to suspect that they won't, that we will continue to follow a path that is comparable to that in South Africa. 

This is Gauteng's omicron curve so far:



And this is London's (grey bars are incomplete, but none of the grey bars is likely to exceed the peak bar that represents last Wednesday):



One obvious difference is that London didn't start from near-zero like Gauteng, but Gauteng peaked within a few days of omicron really exploding, and London may be doing the same thing.


----------



## magneze (Dec 22, 2021)

🤞🤞


----------



## Sasaferrato (Dec 22, 2021)

8ball said:


> But do a test anyway.
> 
> Just FYI - there has been a bit of norovirus about.



Fuck. The year that keeps on giving.


----------



## ska invita (Dec 22, 2021)

littlebabyjesus said:


> One other piece of potentially good news not included there is that London appears to be following a Gauteng-like curve. Cases shot up rapidly but look like they may have peaked rapidly as well, as happened in Gauteng. Tentatively, London may have hit a peak around the middle of last week.


All social engagements got binned for me two weeks ago as trying to get over the line so as to see people at xmas without being positive....needs factoring in, rather than Omi has run out of people to infect. Anecdotally true for lots of people.


----------



## klang (Dec 22, 2021)

Yes, I know quite a few people who have been laying low the last couple of weeks.


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## elbows (Dec 22, 2021)

littlebabyjesus said:


> One other piece of potentially good news not included there is that London appears to be following a Gauteng-like curve. Cases shot up rapidly but look like they may have peaked rapidly as well, as happened in Gauteng. Tentatively, London may have hit a peak around the middle of last week. That's led to increased hospitalisations this week, but those may be nearing or at their peak now as well.
> 
> So when they say that hospitalisations may shoot up, there is also some reason to suspect that they won't, that we will continue to follow a path that is comparable to that in South Africa.


As of yesterdays published data, hospital admissions figures only went up to Sunday, so that needs to be taken into account when estimating timescales of hospital peaks in the data.

Also a path similar to that seen in South Africa will involve hospitalisations shooting up. I havent done much with South Africas data because the format befuddles me at times, have you attempted any exercises to see what a comparable number might be here if the hospitalisations trajectory and peak proportions turn out to be similar?

You know that I consider your instincts and analysis of the first few UK waves were far wide of the mark. However with every passing wave and with every expansion of the vaccine programme, in theory the reality should become closer to your expectations than it was at the start. Mostly because of the evolving immunity picture, which gradually brings reality closer to what you incorrectly hoped was the case after the first wave. Uncertainties about the extent to which Omicron can evade prior immunity of various forms, most crucially protection against severe disease, continues to make it very hard for me to judge the chances of you being right this time. We are at least at the phase of the pandemic where I wont just automatically shit all over your views with a high degree of confidence at this particular moment.


----------



## littlebabyjesus (Dec 22, 2021)

ska invita said:


> All social engagements got binned for me two weeks ago as trying to get over the line so as to see people at xmas without being positive....needs factoring in, rather than Omi has run out of people to infect. Anecdotally true for lots of people.


Yep. True of a lot of people. Wandering through London the last couple of days, it has been deserted. Pubs still open but empty. 

Whatever the reason for it, the rapid rise does appear to have halted, although we do still need this week's numbers to be sure of that. By far the biggest rises in infection in London came in the 20-40 age group, though, which is the age group least likely to drastically alter its behaviour.


----------



## elbows (Dec 22, 2021)

When todays data comes out I will provide some graphs for the London region showing cases by age. Especially as the timing can vary in different groups, the hospitalisation prospects vary by age group, and one of the large differences between us and South Africa is the number of people in older age groups.

In the delta wave the different rates and timing between age groups meant that we could not rely on the previous simple approach of expecting hospitalisation peaks to follow x days after peak in overall case numbers. Because the July peak was sponsored by younger people, and things actually got worse in older age groups later on, which was also reflected in subsequent hospitalisation peaks much later. So I have to apply lessons from data in that wave to our current view of the Omicron wave.

Our attempts to tell simple stories via hospitalisation data are also going to be complicated by hospital infections which will affect the headline numbers.


----------



## l'Otters (Dec 22, 2021)

elbows said:


> This is why I hate the ignore function, I already mentioned that but my pandemic rants are not to Supines taste and so they probably didnt see my post on the subject.


Fwiw I find getting both/all versions offered here of how info is framed useful - often takes a few different methods of explaining the same thing for something to go in. (for me anyway.)


----------



## Monkeygrinder's Organ (Dec 22, 2021)

littlebabyjesus said:


> Yep. True of a lot of people. Wandering through London the last couple of days, it has been deserted. Pubs still open but empty.
> 
> Whatever the reason for it, the rapid rise does appear to have halted, although we do still need this week's numbers to be sure of that. By far the biggest rises in infection in London came in the 20-40 age group, though, which is the age group least likely to drastically alter its behaviour.



I think the particular timing of it - ie that getting it now means Christmas in isolation - probably has a big additional effect in terms of behaviour to what would normally be the case


----------



## gentlegreen (Dec 22, 2021)

.


----------



## elbows (Dec 22, 2021)

littlebabyjesus said:


> That's led to increased hospitalisations this week, but those may be nearing or at their peak now as well.


I forgot to explicitly check whether that means you really think the London daily hospital admissions figures will not exceed levels similar to the amount shown in yesterdays published data?

Even if we get a relatively happy scenario that doesnt sound plausible to me.

(Recent figures which now include an additional days worth since your comments, which I'm sticking on the UK thread because there was a story that government are going to make some decisions based on whether the figure exceeds 400 by the end of the week        #44,796       )


----------



## magneze (Dec 22, 2021)

Monkeygrinder's Organ said:


> I think the particular timing of it - ie that getting it now means Christmas in isolation - probably has a big additional effect in terms of behaviour to what would normally be the case


I think we're almost too close now. Getting it now - you might not test positive until after Christmas.


----------



## teuchter (Dec 22, 2021)

Do we have a clue from south Africa what the length of the cases--admissions lag might be for Omicron might be, and is it likely to be shorter than we have been used to so far?


----------



## littlebabyjesus (Dec 22, 2021)

elbows said:


> I forgot to explicitly check whether that means you really think the London daily hospital admissions figures will not exceed levels similar to the amount shown in yesterdays published data?
> 
> Even if we get a relatively happy scenario that doesnt sound plausible to me.
> 
> (Recent figures which now include an additional days worth since your comments, which I'm sticking on the UK thread because there was a story that government are going to make some decisions based on whether the figure exceeds 400 by the end of the week        #44,796       )


If cases really did peak (or at least plateau) last week, we are likely to see a peak (or plateau) in hospital admissions this week if previous patterns are anything to go by. Nothing is certain of course, but that would also follow roughly what happened in South Africa. Monday was 300, exactly a week after the first day that new cases went over 20,000. Will that storm past 400 this week? Perhaps. Or perhaps it will sneak past 400, or it will level out around that level. Will we see much shorter stays in hospital like South Africa? Dunno, but as with all this stuff, I don't see a compelling reason why not. 

400 is a pretty arbitrary number to choose, though, especially if the numbers show it probably won't go much higher than that. Also, I don't know how many of those 300 on Monday tested positive on admission for something else. In South Africa, a high proportion of patients on covid wards a couple of weeks ago were people being treated for something separate, with either mild symptoms or no symptoms. 

But I was actually quite clear I think in what I said - that if cases peaked last week then admissions were likely to peak this week. I didn't give a day, and I didn't give a specific level. I'm watching with interest to see what happens this week following the record high level of cases last week.


----------



## zahir (Dec 22, 2021)

A new record today.









						UK Covid live: research into Omicron severity in England finds ‘moderate reduction’ in hospitalisation risk compared with Delta – as it happened
					

Latest updates: researchers at Imperial College London stress that reduction in severity must be balanced with larger risk of infection




					www.theguardian.com


----------



## elbows (Dec 22, 2021)

littlebabyjesus said:


> If cases really did peak (or at least plateau) last week, we are likely to see a peak (or plateau) in hospital admissions this week if previous patterns are anything to go by. Nothing is certain of course, but that would also follow roughly what happened in South Africa. Monday was 300, exactly a week after the first day that new cases went over 20,000. Will that storm past 400 this week? Perhaps. Or perhaps it will sneak past 400, or it will level out around that level. Will we see much shorter stays in hospital like South Africa? Dunno, but as with all this stuff, I don't see a compelling reason why not.
> 
> 400 is a pretty arbitrary number to choose, though, especially if the numbers show it probably won't go much higher than that. Also, I don't know how many of those 300 on Monday tested positive on admission for something else. In South Africa, a high proportion of patients on covid wards a couple of weeks ago were people being treated for something separate, with either mild symptoms or no symptoms.
> 
> But I was actually quite clear I think in what I said - that if cases peaked last week then admissions were likely to peak this week. I didn't give a day, and I didn't give a specific level. I'm watching with interest to see what happens this week following the record high level of cases last week.


Thanks for the answer.

I too heard about the proportion of cases in South Africa thing some time back, but I fear it wasnt accurate. I'm pretty sure I saw someone visualising such data from South Africa more recently which showed the proportion of those cases that were in hospital for 'non-covid' reasons had actually remained quite consistent with the past, and still quite a low proportion (perhaps around 10%). But I dont know if I'll be able to find what I saw. I'll try and will post it here if I find it.

I have reasons to doubt that London admissions will remain at recent sort of levels, my brain still tells me to prepare for large jumps. But another part of my brain is pumping much more uncertainty into the mix than I had with the first few waves. This uncertainty was also the case for me with the Delta wave, but this Omicron wave features larger case numbers so my brain is a bit of a mess right now, a big tug of war between fearing a very bad wave and retaining some hope that worst fears wont come close to being met.


----------



## teuchter (Dec 22, 2021)

zahir said:


> A new record today.
> 
> 
> 
> ...


It will be very surprising if we don't see "new records" most days for the next couple of weeks - it's what is predicted and it's going to get a bit boring if it keeps being presented as news.


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## elbows (Dec 22, 2021)

And no I dont know why the government picked 400 as a measures threshold, if that story in the news is even true.


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## elbows (Dec 22, 2021)

teuchter said:


> It will be very surprising if we don't see "new records" most days for the next couple of weeks - it's what is predicted and it's going to get a bit boring if it keeps being presented as news.


The modelling cover a large number of scenarios and they always point out that it is not a prediction.


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## elbows (Dec 22, 2021)

This points in the same direction as other early studies:









						Omicron wave appears milder, but concern remains
					

The risk of needing hospital treatment could be 30 - 70% lower with Omicron than other variants.



					www.bbc.co.uk
				




I havent done the maths on case numbers to guesstimate what the implications still are. And I'll really have to wait till more people in older age groups catch it and have time to show up in hospital numbers before I get too carried away.


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## weltweit (Dec 22, 2021)

If it is milder then how lucky were we? Imagine if it had been as infectious as it is and more deadly than Delta, we would be up shit creek.


----------



## elbows (Dec 22, 2021)

Can still be up shit creek via transmissibility alone.

Because if it only generates a third of the hospitalisations of other variants, but you have three times more cases, you get the same number of hospitalisations.

I had a quick go at using the ridilously oversimplified maths to apply that to Londons peak in cases (so far) & hospitalisations already seen this time compared to peak delta wave figures for that region. I think it already fails to work that simply, but maybe I did the maths wrong. But I wouldnt expect it to work out that simply because of age-dependant hospitalisation rates. Would have to drill down into cases by age to even do the simple maths version more correctly.


----------



## bluescreen (Dec 22, 2021)

Do the data distinguish between people hospitalised because of Covid and those admitted for other reasons who on routine testing are shown to happen to have it as well? Eg, admitted for broken leg?


----------



## kabbes (Dec 22, 2021)

elbows said:


> Can still be up shit creek via transmissibility alone.
> 
> Because if it only generates a third of the hospitalisations of other variants, but you have three times more cases, you get the same number of hospitalisations.
> 
> I had a quick go at using the ridilously oversimplified maths to apply that to Londons peak in cases (so far) & hospitalisations already seen this time compared to peak delta wave figures for that region. I think it already fails to work that simply, but maybe I did the maths wrong. But I wouldnt expect it to work out that simply because of age-dependant hospitalisation rates. Would have to drill down into cases by age to even do the simple maths version more correctly.


I suspect there is a complication that arises due to the fact that cases are not so simply multiplied.  If the transmissibility is x100 then you don't have cases x100, because that would be more than 100% of the population.  On the other hand, if transmissibility is x1.01, it's probably reasonable to assume cases x1.01 as well.  Somewhere between those extremes, you have omicron.  Maybe 5 times as transmissible as delta but what that translates to as a multiple of cases depends on how much delta there would have been in the population anyway, and what peak prevalence can theoretically be based on the epidemiological dynamics.


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## elbows (Dec 22, 2021)

bluescreen said:


> Do the data distinguish between people hospitalised because of Covid and those admitted for other reasons who on routine testing are shown to happen to have it as well? Eg, admitted for broken leg?


No and I often go on about that, official daily data is for 'hospitalisations/diagnoses'. and includes people who went in for other reasons and thsoe who caught it in hospital.

There is seperate data about reason for hospitalisation that can be used to get a rough idea about that though. It doesnt come out daily but I will talk about it and its implications at the next opportunity.

Also we cant just remove all those 'other reasons' cases from the picture because unfortunately a fair chunk of the death burden in previous waves was caused by those sorts of cases - people that were already rather sick or frail for whom covid on top was fatal. There have been a really large number of hospital-acquired infections during this pandemic with quite major consequences . Vaccines should have reduced the consequences but not down to negligible levels.


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## elbows (Dec 22, 2021)

kabbes said:


> I suspect there is a complication that arises due to the fact that cases are not so simply multiplied.  If the transmissibility is x100 then you don't have cases x100, because that would be more than 100% of the population.  On the other hand, if transmissibility is x1.01, it's probably reasonable to assume cases x1.01 as well.  Somewhere between those extremes, you have omicron.  Maybe 5 times as transmissible as delta but what that translates to as a multiple of cases depends on how much delta there would have been in the population anyway, and what peak prevalence can theoretically be based on the epidemiological dynamics.


I didnt do any such maths to the case numbers. I took the actual recorded case numbers, and checked how many more times that amount has already been reached in London at its highest Omicron point seen in the data so far, comapred to the Delta wave peak case numbers. Then I took peak hospital rates from Delta wave for London and multiplied them by the same factor. Then I divided them to account for the decrease mentioned in the aforementioned study. Number came out significantly lower than a number already seen in the London hospital data in this Omicron wave.

Reasons why I would not have expected this crude attempt to match the actual figures at all includes the need to take into account age of cases, hospital infections, and those who went to hospital for other reasons but were already infected before admission as discussed in previous post. I only did this exercise briefly, and without discussing the actual figures, mostly so I could then warn others not to base their expectations on this simplified method or how many hospital admissions there were at peak in London in the delta wave.

Other problems would include the difference between the detected number of positive cases and the actual case numbers. Reasons for that including attitudes to testing, availability of testing, and the fact the published case numbers dont count reinfections (although they do in Wales).


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## kabbes (Dec 22, 2021)

elbows said:


> I didnt do any maths to the case numbers. I took the actual recorded case numbers, and checked how many more times that amount has already been reached in London at its highest Omicron point seen in the data so far. Then I took peak hospital rates from Delta wave for London and multiplied them by the same factor. Then I divided them to account for the decrease mentioned in the aforementioned study. Number came out significantly lower than a number already seen in the London hospital data in this Omicron wave.
> 
> Reasons why I would not have expected this crude attempt to match the actual figures at all includes the need to take into account age of cases, hospital infections, and those who went to hospital for other reasons but were already infected before admission as discussed in previous post. I only did this exercise briefly, mostly so I could then warn others not to base their expectations on this simplified method or how many hospital admissions there were at peak in London in the delta wave.


The ratio for delta at its peak was lower than the current ratio for omicron?  I suspect you are seeing some relative of the effect I was talking about, then.  I think you probably need the integrals of the total cases and total hospitalisations, otherwise it will be affected by how close you are to the inflection point.

Mind you, it's been a long time since I needed to think about calculus things, so I could be well off.


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## elbows (Dec 22, 2021)

I dont do that sort of maths in the pandemic, I was not trying to replicate what a proper study would do, and if I wanted to do it properly I'd need to wait for a whole lot more Omicron hospitalisation data and then do it with much hindsight. I just focussed on peaks and levels seen so far so I could advise others not to go down this simplistic path in an attempt to guide their expectations of what is to come, its not a reliable guide.


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## kabbes (Dec 22, 2021)

Well I certainly agree with you there!


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## elbows (Dec 22, 2021)

Its not something I'd even have brought up if it were not for the fact that some people think they've seen a peak in cases in London already. For some of those inclined to do that premature peak hunting (I have in past waves but am not doing so this time) there is then the temptation to use that to set their expectations of when the London region will see a peak in hospitalisations. And they might use estimates of Omicron severity and peak case numbers in this wave compared to the Delta wave to check whether their expectations of peak hospital numbers seem to fit that sort of range. I'd advise not to do that while hospital numbers are still in their explosive phase, especially given how sharp the explosion in case numbers was.


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## elbows (Dec 22, 2021)

That might also be why the government have picked 400 as a threshold for London hospitalisations in data available by the end of this week, in order to guide their decision-making (if that story is even true). Because if we add the couple of days data reporting lag to the expected lag between cases and hospitalisations, they are probably thinking that the explosive growth in daily hospitalisations would have that number sailing well past 400 by the end of the week, lining up with the explosion in positive cases already seen last week. But if something else was happening that enabled the optimists or wishful thinkers hopes to remain fully intact, ie no 'exponential explosion with very short doubling times' in the next few days hospital admissions data, then they can continue to justify to themselves the lack of additional restrictions.


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## elbows (Dec 22, 2021)

And the following is why I'm not keen on the talk about a cases peak in London, at least not when used to make claims about a hospitalisation peak.

Here are the daily positive cases by specimen date for the London region by age group. Note that falls in certain younger groups, where overall numbers got very high, have resulted in the overall totals doing what they've done recently. Note the rather different trend in other age groups. And note that since this is positive cases by specimen date, several more recent days data in incomplete and will grow in future.




I'm also tagging teuchter here because they have been going on about a peak in cases.


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## two sheds (Dec 23, 2021)

Not so promising - although not yet peer reviewed:









						Omicron infections appear no less severe than Delta; COVID-19 lowers sperm count, motility
					

The following is a summary of some recent studies on COVID-19. They include research that warrants further study to corroborate the findings and that has yet to be certified by peer review.




					www.reuters.com
				






> Dec 20 (Reuters) - The following is a summary of some recent studies on COVID-19. They include research that warrants further study to corroborate the findings and that has yet to be certified by peer review.
> 
> Omicron infections no less severe based on early UK data
> 
> ...



Coronavirus goes for the goolies  



> Sperm quality is impaired for months for some people after recovery from COVID-19, researchers have found.
> 
> ...
> 
> The semen itself was not infectious, the researchers found. But among 35 men who provided samples within a month after recovery from symptomatic infection, reductions in sperm motility were evident in 60% and sperm counts were reduced in 37%.


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## Steel Icarus (Dec 23, 2021)

two sheds said:


> Coronavirus goes for the goolies


Personally this is of zero worry to me.


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## two sheds (Dec 23, 2021)

S☼I said:


> Personally this is of zero worry to me.


hehe me neither - would count as an advantage


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## bluescreen (Dec 23, 2021)

S☼I said:


> Personally this is of zero worry to me.


Funnily enough, I suspect the alleged anti-sperm properties of Omicron might be the persuasive factor for some - not all - vaccine-hesitant people to finally surrender their arms to the noxious needle.


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## Epona (Dec 23, 2021)

littlebabyjesus said:


> Yep. True of a lot of people. Wandering through London the last couple of days, it has been deserted. Pubs still open but empty.
> 
> Whatever the reason for it, the rapid rise does appear to have halted, although we do still need this week's numbers to be sure of that. By far the biggest rises in infection in London came in the 20-40 age group, though, which is the age group least likely to drastically alter its behaviour.



For sure, in normal times with OH having a week off work we'd have been in the pub a couple of times, out shopping in Stratford (pre-Xmas window shopping and perhaps buying a couple of gifts), maybe meeting up with friends, he might have had a work Xmas party to go to - nope, I want to see my parents on Xmas day so we are having some quality sofa + telly time and being really careful if we need to shop.


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## MrCurry (Dec 23, 2021)

bluescreen said:


> Funnily enough, I suspect the alleged anti-sperm properties of Omicron might be the persuasive factor for some - not all - vaccine-hesitant people to finally surrender their arms to the noxious needle.


I wonder if this guy is feeling quite as smug as when he had the Tshirt printed…


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## elbows (Dec 23, 2021)

oops double post, see the next post instead.


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## elbows (Dec 23, 2021)

In regards the whole thing about hospitalisations where the people are being treated primarily for covid rather than it being incidental:



Also I may as well quote the blurb about this stuff from the NHS data site:





__





						Statistics » COVID-19 Hospital Activity
					

Health and high quality care for all,  <br />now and for future generations




					www.england.nhs.uk
				






> The majority of inpatients with Covid-19 are admitted as a result of the infection. A subset of those who contract Covid in the community and are asymptomatic, or exhibited relatively mild symptoms that on their own are unlikely to warrant admission to hospital, will then be admitted to hospital to be treated for something else and be identified through routine testing. However these patients still require their treatment in areas that are segregated from patients without Covid, and the presence of Covid can be a significant co-morbidity in many cases. Equally, while the admission may be due to another primary condition, in many instances this may have been as a result of contracting Covid in the community. For example research has shown that people with Covid are more likely to have a stroke (Stroke Association); in these cases people would be admitted for the stroke, classified as ‘with’ Covid despite having had a stroke as a result of having Covid.





> The headline published numbers in publications to date have been “inpatients with confirmed Covid” without differentiating between those in hospital “for” Covid and those in hospital “with” Covid. Recognising the combination of high community infections rates, with the reduced likelihood of admission for those who contract Covid in the community and are fully vaccinated, the Covid SitRep was enhanced in June 2021 to add a requirement for providers to distinguish between those being primarily treated ‘for’ Covid and those ‘with’ Covid but for whom the primary reason for being in hospital was non-Covid related. In practice this distinction is not always clear at the point of admission when the patient’s record has not been fully clinically coded. In light of this, trusts have been asked to provide this “for” and “with” split on a ‘best endeavours’ basis.



By the way I think this distinction is only available for the data that covers people in hospital, as opposed to daily admission figures.


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## Supine (Dec 23, 2021)




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## Mr.Bishie (Dec 23, 2021)

Supine you need to take elbows off ignore cos posting the same stuff 3 hours later is a fuckin ball ache.


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## elbows (Dec 23, 2021)

London admissions published today look to have been around 300 again so it seems like I'm not going to see a new dramatic increase before the Christmas data break that would allow me to add much more to what I already said in recent days. It would be really nice if I end up being able to keep saying that once hospital data publishing for England resumes next Tuesday. Well there is still tomorrows data to come, but I'm hoping it doesnt show anything that requires me to comment.

I'll probably still look at todays cases by age for the London region this evening, but posting graphs of those every single day would be rather too tedious even for me. Maybe if some new trend stands out today I will draw attention to it later, but I'm looking forward to this mini-break from staring at too much data.


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## teuchter (Dec 23, 2021)

elbows said:


> I'll probably still look at todays cases by age for the London region this evening, but posting graphs of those every single day would be rather too tedious even for me.


They are certainly interesting to see every few days at least though.


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## elbows (Dec 23, 2021)

teuchter said:


> They are certainly interesting to see every few days at least though.


I'm glad to hear that because I never got round to using a database & software to process that data, I have to do a load of manual copying and pasting in a spreadsheet and its rather tedious, especially as to get all the very latest data per age group I have to process both male and female cases and then combine them. I suspect other people do graphs of this sort of data on twitter or their own websites, but sometimes I dont like the way they group ages together or use rolling averages if I feel the need to see each days specific figure instead.

If I was full of energy then I'd probably try to do the per age group equivalent of the 'yellow todays daily published figures contribution to cases by specimen date' that you took an interest in with overall London numbers recently, but I'm not setup to make those graphs and I'm also knackered. Instead I might just try to describe what I've seen, or maybe I will pick a few age groups in particular and just post yesterdays and todays graph for those side by side. Depends what stories if any are in todays London data, I've no clue yet until I do the tedious processing.


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## Supine (Dec 23, 2021)

Mr.Bishie said:


> Supine you need to take elbows off ignore cos posting the same stuff 3 hours later is a fuckin ball ache.



I can’t see it posted on this thread by anyone else ignored or otherwise and i posted it here because it relates to the discussion with teuchter about hospital case rates falling (or not). 

You’re having a laugh if you think it’s possible to read all threads before posting a link!


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## zahir (Dec 23, 2021)

Supine said:


> I can’t see it posted on this thread by anyone else ignored or otherwise and i posted it here because it relates to the discussion with teuchter about hospital case rates falling (or not).
> 
> You’re having a laugh if you think it’s possible to read all threads before posting a link!



The post before yours.


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## teuchter (Dec 23, 2021)

Supine said:


> the discussion with teuchter about hospital case rates falling (or not).


Not that anyone probably cares, but to be clear, I've not tried to suggest that hospital rates are falling, just that it seems plausible that London reported cases have peaked or are at least levelling off somewhat. They certainly don't look to be rising at rapid exponential rates anymore.


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## cupid_stunt (Dec 23, 2021)

Supine said:


> I can’t see it posted on this thread by anyone else ignored or otherwise and i posted it here because it relates to the discussion with teuchter about hospital case rates falling (or not).
> 
> You’re having a laugh if you think it’s possible to read all threads before posting a link!



It's in the post just above yours.


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## Supine (Dec 23, 2021)

zahir said:


> The post before yours.



Oh yeah. I’ll just stop posting on the thread


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## elbows (Dec 23, 2021)

Its good to see the latest estimates on severity, the UKHSA ones that the press have been anticipating for some days.









						Omicron up to 70% less likely to need hospital care
					

However, a major report showed the protection from catching Covid started to wane 10 weeks after the booster.



					www.bbc.co.uk
				




I just hope the headlines dont mess up the mood music to the extent that behaviours swing back too much in a direction that then goes on to make this wave much more horrible than it has to be. But then as I've been saying on the main UK thread, I also dont know whether, even if we avoid the sort of rapid hospitalisation rises that force government to act, we will also avoid the sort of continuous grinding pressure that can also force authorities to bring in new restrictions.


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## 2hats (Dec 23, 2021)

UKHSA Technical Briefing 33 now published.

Highlights the apparent onset of waning of third-dose booster efficacy to symptomatic infection after around 5-9 weeks post third dose, based on estimates from a test-negative case control design constructed from epidemiological data (vaccination rates in PCR-positive cases were compared to vaccination rates in those who tested negative during the period 27 Nov till 17 Dec).

(Insert standard warnings about sample size and behavioural biases. e2a: Control arm might have more prior infection immunity than supposed so overbiasing the reduction in vaccine efficacy.)

The report also highlights how many cases are now reinfections - a significant fraction and that is likely an undercount.


These factors could become important as omicron reaches into older/vulnerable cohorts (currently infections in under-50s dominate).

Thread.


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## Supine (Dec 23, 2021)

2hats said:


> UKHSA Technical Briefing 33 now published.
> 
> Highlights the apparent onset of waning of third-dose booster efficacy to symptomatic infection after around 5-9 weeks post third dose, based on estimates from a test-negative case control design constructed from epidemiological data (vaccination rates in PCR-positive cases were compared to vaccination rates in those who tested negative during the period 27 Nov till 17 Dec).
> View attachment 302572
> ...



I’m not sure at what point the expectation came about that vaccines would stop infections. I had always presumed they would stop deaths and limit hospitalisation and that would be good enough. I guess people want the max even if it means people in other countries are still dieing from having no first or second shots.


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## teuchter (Dec 23, 2021)

2hats said:


> Thread.



She says it's not slowing down yet, but those graphs do suggest that it is slowing in London & SE and other regions too. Obviously it could look different again in a few more days.


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## Supine (Dec 24, 2021)

teuchter said:


> She says it's not slowing down yet, but those graphs do suggest that it is slowing in London & SE and other regions too. Obviously it could look different again in a few more days.




How are you seeing that as slowing down? Is it something you want to see?


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## teuchter (Dec 24, 2021)

Supine said:


> How are you seeing that as slowing down? Is it something you want to see?


Of course it's something I want to see. But it's visible in the shape at the end of the graph(s) where the gradient flattens, and they only plot the numbers up to the 17th, and we have, elsewhere, numbers for the days after that which are entirely consistent with a slowing down, at least for London. I don't get why this seems such a controversial observation.


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## kabbes (Dec 24, 2021)

As long as the graph slopes up at all, the rate of growth is increasing. It’s a graph of the number per day, which IS the rate of growth.  Plus it’s a log scale, on her graphs, which makes any slowdown look faster than it is. They might show that the rate of growth of the rate of growth is slowing, but the rate of growth itself is still increasing.  It’s hard to tell even whether the rate of growth of the rate of growth is slowing, though, due to the scale.


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## _Russ_ (Dec 24, 2021)

kabbes said:


> Plus it’s a log scale, on her graphs, which makes any slowdown look faster than it is.


.....ummm


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## teuchter (Dec 24, 2021)

kabbes said:


> As long as the graph slopes up at all, the rate of growth is increasing. It’s a graph of the number per day, which IS the rate of growth.  Plus it’s a log scale, on her graphs, which makes any slowdown look faster than it is. They might show that the rate of growth of the rate of growth is slowing, but the rate of growth itself is still increasing.  It’s hard to tell even whether the rate of growth of the rate of growth is slowing, though, due to the scale.


The tweet I was responding to, talks about the doubling time, in answer to the question "is it slowing down". She says "still about 2 day doubling", with the implication that it would be slowing down if the doubling time was becoming longer.

So, the rate of growth of the rate of growth is what we're talking about isn't it? In this context, slowing down to me means that we start to see a trend in the line, whether it's plotted on a log or a linear scale, that if it continues, it will curve around towards a peak, and then start going downwards. Yes, it has to be going downwards for the rate of growth itself to be decreasing, but that's not what we are initially interested in seeing - first you want to see signs that it's no longer shooting skywards in exponential fashion, then you want to see a peak appear and then of course you want to see a decline.

However...in any case when I looked more closely at those graphs last night, I realised that I don't think they are plotting absolute numbers of omicron cases, I think they are plotting proportion of all cases that are omicron cases, so they aren't actually showing what I initially though they were.


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## teuchter (Dec 24, 2021)

Here's someone who seems to have had a similar response to me, anyway


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## elbows (Dec 24, 2021)

Better to read the whole thread but here is the key bit:


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## kabbes (Dec 24, 2021)

teuchter said:


> The tweet I was responding to, talks about the doubling time, in answer to the question "is it slowing down". She says "still about 2 day doubling", with the implication that it would be slowing down if the doubling time was becoming longer.
> 
> So, the rate of growth of the rate of growth is what we're talking about isn't it? In this context, slowing down to me means that we start to see a trend in the line, whether it's plotted on a log or a linear scale, that if it continues, it will curve around towards a peak, and then start going downwards. Yes, it has to be going downwards for the rate of growth itself to be decreasing, but that's not what we are initially interested in seeing - first you want to see signs that it's no longer shooting skywards in exponential fashion, then you want to see a peak appear and then of course you want to see a decline.
> 
> However...in any case when I looked more closely at those graphs last night, I realised that I don't think they are plotting absolute numbers of omicron cases, I think they are plotting proportion of all cases that are omicron cases, so they aren't actually showing what I initially though they were.


If the rate of growth is growing, that means more people are infected today than were yesterday, which means that the infection is still gathering pace.  Yes, the first thing we have to look for is a slow down in the rate of growth of this rate of growth, but whilst a slowdown in acceleration is better than the opposite, it still places us in a highly vulnerable phase.  Even once you pass the fastest point of an S-curve, you still have a potentially unlimited upper limit in principle.


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## elbows (Dec 24, 2021)

Explosive growth in Londons hospital admissions continues, but to avoid duplication I am mostly talking about this ont he main UK thread now        #44,875


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## Indeliblelink (Dec 25, 2021)

Something about the fusogenicity of the spike protein being related to it's pathogenicity.



Omicron - more transmissible but less infectious. In hamsters anyway.


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## 2hats (Dec 25, 2021)

Indeliblelink said:


> Something about the fusogenicity of the spike protein being related to it's pathogenicity.


Ravi Gupta identified this a few days ago. See the 'Nerdy amounts of detail' thread, post #145.


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## 8ball (Dec 26, 2021)

Indeliblelink said:


> Something about the fusogenicity of the spike protein being related to it's pathogenicity.



Fusogenicity is srs bsnss.


----------



## 8ball (Dec 26, 2021)

2hats said:


> Ravi Gupta identified this a few days ago. See the 'Nerdy amounts of detail' thread, post #145.



Am interested in your virology knowledge.  Always thought you were a spaceman.
Obviously, your insight is welcome.

And Merr Xmas obv.

(I just dip into this thread from time to time )


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## 2hats (Dec 26, 2021)

8ball said:


> Always thought you were a spaceman.


Have variously worked in both space- and biomedical-related disciplines over the years.


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## iona (Dec 26, 2021)

2hats said:


> Have variously worked in both space- and biomedical-related disciplines over the years.


Pfft. Knows about space and viruses and disappearing planes and nuclear stuff and weather and bats? You're clearly an evil supervillain posting from your secret lair underneath a volcano somewhere


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## Badgers (Dec 26, 2021)

iona said:


> Pfft. Knows about space and viruses and disappearing planes and nuclear stuff and weather and bats? You're clearly an evil supervillain posting from your secret lair underneath a volcano somewhere


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## 2hats (Dec 26, 2021)

iona said:


> Pfft. Knows about space and viruses and disappearing planes and nuclear stuff and weather and bats? You're clearly an evil supervillain posting from your secret lair underneath a volcano somewhere


I do have a cat on my lap right now.


----------



## Badgers (Dec 26, 2021)

2hats said:


> I do have a cat on my lap right now.


White? Fluffy?


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## 2hats (Dec 26, 2021)

Speaking of tropism shifts, you _might_ want to consider continuing (or resuming) swabbing tonsils as well as nose for LFTs...



			
				Google Translation said:
			
		

> Middle stick only in nose. With the others I put the stick in the back of my throat first.






Indeed...








						Saliva swabs are the preferred sample for Omicron detection
					

The Omicron variant is characterised by more than 50 distinct mutations, the majority of which are located in the spike protein. The implications of these mutations for disease transmission, tissue tropism and diagnostic testing are still to be determined. We evaluated the relative performance...




					www.medrxiv.org
				




PS The cats are neither white nor fluffy.


----------



## zahir (Dec 31, 2021)

Thread from Deepti Gurdasani


----------



## littlebabyjesus (Dec 31, 2021)

One of the unknowns about omicron was whether or not it would drive out delta, potentially a big benefit to places like the UK that were running very high delta. There was encouraging news the other day about how delta and omicron infections both provide cross-protection against the other, and the data from the UK is also encouraging in that regard. 

Latest testing figures suggest that it may already be driving delta right down. Nearly 95% of cases are coming up omicron now. With total cases at around 200k a day, that translates to 10,000 delta cases per day, down from 50,000 a month ago. That's a big fall. 

Essentially, in this graph, green is probable delta and purple is probable omicron. 



https://assets.publishing.service.g...44331/20211230_OS__Omicron_Daily_Overview.pdf


----------



## ska invita (Dec 31, 2021)

littlebabyjesus said:


> One of the unknowns about omicron was whether or not it would drive out delta, potentially a big benefit to places like the UK that were running very high delta. There was encouraging news the other day about how delta and omicron infections both provide cross-protection against the other, and the data from the UK is also encouraging in that regard.
> 
> Latest testing figures suggest that it may already be driving delta right down. Nearly 95% of cases are coming up omicron now. With total cases at around 200k a day, that translates to 10,000 delta cases per day, down from 50,000 a month ago. That's a big fall.
> 
> ...


Liked reading this with the fireworks


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## BigMoaner (Jan 1, 2022)

do the variants always get weaker?


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## weltweit (Jan 1, 2022)

BigMoaner said:


> do the variants always get weaker?


I don't think necessarily they have to no.


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## BigMoaner (Jan 1, 2022)

weltweit said:


> I don't think necessarily they have to no.


sorry bad english from me - i mean do they always have progressively less severe symptoms? the delta was slightly less worse than the original, and then omnicron etc.


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## 2hats (Jan 1, 2022)

BigMoaner said:


> do the variants always get weaker?


If there is selection pressure to do so.


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## l'Otters (Jan 1, 2022)

BigMoaner said:


> do the variants always get weaker?


I've seen a lot of people argue this is the case, and a whole load of people (who should know better imo) taking reports of omicron being "milder" as confirmation of this "rule", and evidence that we're on the home stretch with covid now.


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## weltweit (Jan 1, 2022)

The virus isn't intelligent, variants are produced almost at random and if they work, or infect a good number of hosts, then they can gain traction. 

I think we have been lucky in this case that Omicron seems to be less lethal than Delta. 

I am not an expert but my understanding is that it could be possible a new variant may arise that is both infectious and more deadly.


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## 2hats (Jan 1, 2022)

BigMoaner said:


> sorry bad english from me - i mean do they always have progressively less severe symptoms? the delta was slightly less worse than the original, and then omnicron etc.


You can't make direct comparisons between variants from different timepoints when your population's immunity profile is changing over time.


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## Supine (Jan 1, 2022)

2hats said:


> If there is selection pressure to do so.



So no. Sometimes yes, sometimes no. It changes with conditions on the ground.


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## elbows (Jan 2, 2022)

BigMoaner said:


> sorry bad english from me - i mean do they always have progressively less severe symptoms? the delta was slightly less worse than the original, and then omnicron etc.


Studies tended to conclude that Delta came with a notable increase in hospitalisation risk compared to earlier versions of the virus, not a reduced risk.

Such studies may be imperfect and they do have to adjust for certain things, which these days very much includes vaccination history of the people whose outcomes they use as data for the study. And we end up with estimates rather than completely rigid facts. But I think such signals for Delta were strong enough that its reasonable to conclude it was both more transmissible and more likely to result in hospitalisation, and quite a lot more likely at that. The only reason that the increased disease severity is not obvious when looking in a simple way at the UK Delta wave is the high level of vaccination in the UK.


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## 8ball (Jan 2, 2022)

BigMoaner said:


> do the variants always get weaker?



Kind of.  Until 3 weeks before the end of season special.


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## _Russ_ (Jan 6, 2022)

Chinese study on Omicron Origins

Omicron might have come from a mouse, but what kind of mouse?


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## BigMoaner (Jan 6, 2022)

_Russ_ said:


> Chinese study on Omicron Origins
> 
> Omicron might have come from a mouse, but what kind of mouse?


a very naughty one?


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## IC3D (Jan 6, 2022)

There are more known unknowns that we know about than we know about the unknowns of which we don't know. Someone once said.


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## _Russ_ (Jan 6, 2022)

Are you sure?


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## weltweit (Jan 6, 2022)

Covid: Deadly Omicron should not be called mild, warns WHO
					

The WHO cautions that just like previous variants, Omicron is hospitalising and killing people.



					www.bbc.co.uk


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## elbows (Jan 6, 2022)

weltweit said:


> Covid: Deadly Omicron should not be called mild, warns WHO
> 
> 
> The WHO cautions that just like previous variants, Omicron is hospitalising and killing people.
> ...


Speaking of the word mild and perceptions, here is some context I would like to have seen far more prominently:

Instead we've had plenty of conflation between the intrinsic severity of Omicron and the effect of vaccines and boosters.


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## gentlegreen (Jan 6, 2022)

It is though perhaps 30 percent less likely to kill those who opt for "natural immunity" over an effective vaccine ...


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## littlebabyjesus (Jan 6, 2022)

elbows said:


> Speaking of the word mild and perceptions, here is some context I would like to have seen far more prominently:
> 
> Instead we've had plenty of conflation between the intrinsic severity of Omicron and the effect of vaccines and boosters.



One important caveat to that is something that the report itself notes - that it doesn't consider the relative severity of the hospitalised cases. As we're seeing, it appears far fewer people are ending up in icu or on ventilators with omicron, and if you're attempting comparisons with previous strains, that's an important thing to factor in.


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## elbows (Jan 6, 2022)

Yes I totally agree that the caveats are mounting, things are much messier and harder to unpick these days due in great part due to complicated immunity picture. But yes, some more specifics about the clinical details of Omicron will also firm up a bit over the next period.

Plus you know me and hospital data, I'm prone to draw attention to a chunk of it actually being people who were in hospital for other reasons and then caught it there, and in the vaccine era those infections should lead to a different balance of outcomes than it did in the early waves.

Without having to do proper scientific analysis, we'll be able to do things like comparing what happens in the USA this month to what happens in the UK this month, because their immunity wall is missing a lot of booster vaccine doses compared to ours, and I think their previous vaccine coverage was also less well aligned to hugely cover as great a portion of the most vulnerable (older) population than ours has been.


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## elbows (Jan 6, 2022)

Found a tweet on that theme which somewhat sets that scene, but there is a further complication with attempting that comparison because the USA was at a different stage of Delta wave compared to us when Omicron arrived. And unpicking that wont be so easy.

Seems safe to assume that 'what stage of the pandemic it feels like we are at right now' is not going to be the same in the USA compared to the UK.


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## Miss-Shelf (Jan 7, 2022)

Anecdata about severity 
I've just been chatting with the person I caught original Wuhan covid from (spring 2020) 
She works in care homes for a national chain of homes 
In  Spring, 2020 residents (in homes that had covid ) were succumbing and dying rapidly 
Wuth omicron it is in nearly every home in the chain and very few people are dying from it


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## elbows (Jan 7, 2022)

Thats not a pure Omicron anecdote though, vaccines are quite a part of that picture.


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## teuchter (Jan 7, 2022)

elbows said:


> Found a tweet on that theme which somewhat sets that scene, but there is a further complication with attempting that comparison because the USA was at a different stage of Delta wave compared to us when Omicron arrived. And unpicking that wont be so easy.
> 
> Seems safe to assume that 'what stage of the pandemic it feels like we are at right now' is not going to be the same in the USA compared to the UK.



I'm a bit surprised by how small the red bits are in the last charts, in the England one. I thought the UK was about 70% vaccinated. Do those graphs indicate that nearly all of the 30% or so unvaccinated have already had the infection?


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## Miss-Shelf (Jan 7, 2022)

elbows said:


> Thats not a pure Omicron anecdote though, vaccines are quite a part of that picture.


Very true


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## elbows (Jan 7, 2022)

teuchter said:


> I'm a bit surprised by how small the red bits are in the last charts, in the England one. I thought the UK was about 70% vaccinated. Do those graphs indicate that nearly all of the 30% or so unvaccinated have already had the infection?


% of UK vaccinated depends on how many doses and whether all ages are included or only people over a certain age.

For example at the moment the UK dashboard vaccine stats now use population figures for everyone 12 and older. It used to be higher ages only but they changed it as they opened up vaccination to some younger ages.

Right now for population aged 12 and up the dashboard has UK figures of 90.2% for first dose, 82.7% for second dose, 60.6% for boosters. These figures will obviously drop if we included all younger children in the population figures, and those sorts of total population percentages are what some people prefer to use on twitter etc.

The other thing to keep in mind is that the chart in the tweet will not be 100% accurate, its almost certainly based on the data we get from blood donors, and they arent completely representative of the whole population. When they analyse those samples they have 2 different antibody tests, one that shows antibodies caused by vaccination and infection (Roche S), and one that only shows antibodies caused by infection (Roche N).

See pages 41 to 47 of this report for loads of details, charts etc:



			https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1045073/Vaccine_surveillance_report_week_1_2022.pdf
		


Here is some of the text from that which is relevant. The blood donors are aged 17 and over.



> Roche S seropositivity in blood donors has plateaued and is now over 96% across all age groups.
> 
> Seropositivity estimates for S antibody in blood donors are likely to be higher than would be expected in the general population and this probably reflects the fact that donors are more likely to be vaccinated. Seropositivity estimates for N antibody will underestimate the proportion of the population previously infected due to (i) blood donors are potentially less likely to be exposed to natural infection than age matched individuals in the general population (ii) waning of the N antibody response over time and (iii) recent observations from UKHSA surveillance data that N antibody levels are lower in individuals who acquire infection following 2 doses of vaccination. These lower N antibody responses in individuals with breakthrough infections (post-vaccination) compared to primary infection likely reflect the shorter and milder infections in these patients. Patients with breakthrough infections do have significant increases in S antibody levels consistent with boosting of their antibody levels.



One of the reasons this data indicates so much of the gap being plugged is that their data for people with antibodies caused by infection demonstrates that younger people, who are less liekly to be vaccinated, have had the highest levels of infection, especially once the Delta wave happened. But thats also considered to have been true right from the start of the pandemic, younger people were in harms way for all manner of reasons including having more social contacts, and a rather large proportion of the older population successfully hid from the virus in the first few waves. Although I suppose younger people are also more likely to generate higher antibody levels which show up for longer. Anyway here is one of the charts about that from the same report:



Previously when this subject came up I disagreed with littlebabyjesus about the extent of assumptions we could make in regards how many unvaccinated people had not yet been infected either. Thats partly down to the limitations of the blood donor data as already discussed, I prefer to leave a bit more wiggle room in my assumptions about this. But given the scale of the Omicron wave, reality will already have moved to become closer now to what littlebabyjesus assumed about this weeks ago.

We might be able to further refine our sense of how many unvaccinated, previously uninfected people remain in the population by keeping an eye on data about the vaccine status of people who have been hospitalised or died over a recent period. Such data, which tends to cover a 4 week period, is a bit laggy and wont be covering a 'mostly Omicron' period yet, but I will fish the latest version of it out anyway at some point on Friday. Actually its in the same report I already mentioned, a few pages earlier. Although if we use it for that purpose, we'll be making an assumption that this is those peoples first infection, which isnt necessarily the case. And there are plenty of deaths of vaccinated people in it which demonstrate that the immunity wall has its limits, especially as people get older. It doesnt currently offer info about whether they had a booster either.


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## elbows (Jan 7, 2022)

On a highly related subject, I am sorry I've been so rude to people with certain views in the pandemic so far, but I really hope that the current situation helps a few more people understand why I get so frustrated about those views....

Even assuming the current intensive care numbers and deaths dont shoot up a lot from their relatively stable levels in this wave, we've still had enough hospitalisations to cause real problems to the system. And this is under circumstances where we've got a variant that is less severe than Delta, and a really large prior infection & vaccination wall. So I'm bound to declare that even when we are beyond the acute initial phases of the pandemic, when the virus was still new to our bodies, this virus is still looking like a shit to manage. The original version of herd immunity that some tried to sell us now looks especially stupid, not least because immunity from infection and transmission has proven elusive. We are going to need some combination of things settling down on the new variant front, even less severe disease consequences, more treatments that can be given at home early to reduce the chances of hospitalisation, vaccines that can do more to prevent infection and transmission, and perhaps some other stuff I'm forgetting to mention right now, along with an overall population immunity picture that is less conducive to large waves being able to happen, in order to at least avoid putting hideous pressure on our hospitals and those who work in them. On paper the rather large Omicron wave should get us closer to that situation, but given how tricky things have been despite much progress on many fronts I'm unwilling to express a huge amount of confidence about that at this moment.

Anyway the point is that even if we make it to the stage where its much more feasible to cope with the virus in future, how difficult things have still been in this wave, even with much less really severe disease potential, hopefully shines light on just how big the threat was in the past, the extent to which non-pharmaceutical measures were essential to even begin to stand a chance of coping in those early waves. Lets just hope that living with 'endemic' covid is several degrees less of a nightmare than the Omicron wave has been for hospitals. I still dont rule out the possibility that living with covid long term may require permanent changes to the nature and capacity of healthcare systems, especially surge capacity. Especially if flu bounces back and demonstrates an ability to have waves that can coincide with covid waves, which is something I'm not at all clear on at this point, I guess nobody is too sure about that until we see it happen, or not happen for a prolonged period.

With that in mind I actually sort of hope that the immunity wall the data mentioned earlier implied wasnt actually as strong as implied, but is once this wave is done. Because that would mean I could tone down my thoughts on how hard endemic covid might be to live with compared to the Omicron wave experience.


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## elbows (Jan 7, 2022)

Oh and if that last post of mine turns out to be too gloomy in regards future endemic covid, its probably because of an aspect of Omicron which is very well known but somehow doesnt seem to have been fully incorporated into the way people talk about the Omicron variant - it an escape mutant. Even the UK government took Omicron seriously because of that, because it makes the existing wall of immunity less relevant, and its just a question of how less relevant. On this occasion we are lucky that the level of escape is nowhere close to sending us all the way back to square one, and that boosters using the existing vaccines have been able to restrengthen the wall.


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## elbows (Jan 7, 2022)

Early UK analysis of vaccine effectiveness in those aged 65 and over against Omicron, with emphasis on the booster 3rd jabs and any waning after those:



			https://khub.net/documents/135939561/338928724/Effectiveness+of+3+doses+of+COVID-19+vaccines+against+symptomatic+COVID-19+and+hospitalisation+in+adults+aged+65+years+and+older.pdf/ab8f3558-1e16-465c-4b92-56334b6a832a
		




> VE against symptomatic disease for cases aged 65 years or older is shown in Figure 1 for those who received a primary course of the ChAdOx1-S (AstraZeneca) (Figure 1a) and BNT162b2 (Pfizer) (Figure 1b) vaccine. In all periods, effectiveness was lower for Omicron compared to Delta. There was minimal or no effect against mild disease with the Omicron variant from 20 weeks after the second dose of either a ChAdOx1-S or BNT162b2 primary course. Among those who had received 2 doses of ChAdOx1-S, at 2 to 4 weeks after a booster dose (either BNT162b2 or mRNA-1273 (Moderna)), VE ranged from around 62% to 65%, dropping to 48% and 56% at 5-9 weeks for the BNT162b2 and mRNA-1273 booster, respectively. For the BNT162b2 booster, VE dropped further to 32% at 10+ weeks. Among those who had received 2 doses of BNT162b2 followed by a BNT162b2 booster, VE was 65% at 2 to 4 weeks post the booster, dropping to 49% at 5 to 9 weeks and 31% at 10+ weeks. For those who had received 2 doses of BNT162b2 followed by a mRNA-1273 booster, VE was 70% at 2 to 4 weeks post the booster, dropping to 57% at 5 to 9 weeks.





> There were 98 hospitalisations after 3 doses included in the analysis. Results for hospitalisations for cases aged 65 years or older are shown in Table 1. At 2 to 9 weeks post the third dose, receiving 3 doses of a vaccine was associated with an 89% reduced risk of hospitalisation among symptomatic cases with the Omicron variant. This dropped slightly but remained high at an 85% reduced risk of hospitalisation at 10+ weeks post receipt the third dose. This dropped slightly but remained high at an 85% reduced risk of hospitalisation at 10+ weeks post receipt of the third dose. When combined with VE against symptomatic disease this was equivalent to VE against hospitalisation of 94% 2 to 9 weeks after the booster dose and 89% at 10 weeks post the booster dose in those aged 65 years or older.





> These estimates suggest that VE against symptomatic disease with the Omicron variant is significantly lower than compared to the Delta variant and wanes rapidly in those aged 65 years or older. Nevertheless, protection against hospitalisation is much greater than that against symptomatic disease, in particular after a booster dose, where estimated VE against hospitalisation is around 90 to 95%.
> 
> These results should be interpreted with caution due to the low numbers and the possible biases related to differences in vaccine coverage and exposure to Omicron in different population groups.



Also covered by this news story:









						Covid: No need for a fourth jab yet, say UK advisers
					

The booster third dose continues to give high protection to people 65 and over, data suggests.



					www.bbc.co.uk


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## zahir (Jan 10, 2022)

__





						Active epidemiological investigation on SARS-CoV-2 infection caused by Omicron variant (Pango lineage B.1.1.529) in Japan: preliminary report on infectious period
					





					www.niid.go.jp


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## littlebabyjesus (Jan 10, 2022)

So what do we do? Extend isolation to 10 days? Those findings appear to suggest that would be the right thing to do if you were trying seriously to stop the spread.

Or do you accept that you can't stop the spread, that the costs of trying to do so are too high and you'd fail anyway? Move away from blanket isolation orders and towards something more nuanced and sustainable. 

The question is going to be moot soon enough anyway, given that we're probably at or just past peak already.


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## 8ball (Jan 10, 2022)

How about 7?


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## ska invita (Jan 10, 2022)

Everyone i know who has had it wouldnt be able to work after 5 days anyway


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## littlebabyjesus (Jan 10, 2022)

ska invita said:


> Everyone i know who has had it wouldnt be able to work after 5 days anyway


Omicron or delta?

Delta, sure. Everyone I know who had it (well everyone who had it symptomatically) was knocked sideways for at least a few days.

But omicron (sample size only 3 admittedly), all three said the vaccine was worse.

Govt has stopped reporting omicron proportions now as it reached 95% of all cases by 30 December. Presumably it's even higher than that now. Delta is nearly history, hopefully. 

https://assets.publishing.service.g...044522/20211231_OS_Daily_Omicron_Overview.pdf


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## elbows (Jan 10, 2022)

littlebabyjesus said:


> So what do we do? Extend isolation to 10 days? Those findings appear to suggest that would be the right thing to do if you were trying seriously to stop the spread.
> 
> Or do you accept that you can't stop the spread, that the costs of trying to do so are too high and you'd fail anyway? Move away from blanket isolation orders and towards something more nuanced and sustainable.
> 
> The question is going to be moot soon enough anyway, given that we're probably at or just past peak already.


I expect the authorities look at the widespread behavioural changes that were required to cope with this wave, and graphs like this one for Manchester University NHS Foundation Trust, and conclude that they didnt actually have an enormous amount of wiggle room.

They will move somewhat closer to what you want to see after this wave, not before it or during it. And they wont be sure as to exactly what they can get away with next winter, or what to expect on the future variants front.




			https://coronavirus.data.gov.uk/details/healthcare?areaType=nhsTrust&areaName=Manchester%20University%20NHS%20Foundation%20Trust


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## elbows (Jan 10, 2022)

To clarify, when I say not during it, I mean not during the initial upward phase of it. I cant really guess exactly how long they will wait beyond this point before making more changes to the rules. But its reasonable to epect that they will start talking about changes quite some time before actually making any of the largest ones.


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## elbows (Jan 10, 2022)

Plus they already cut it from 10 day to 7 for asymptomatic cases, that was clearly as far as they were prepared to push on that at the time. Now they will probably seek to push a bit more, but maybe still only for asymptomatic cases.

The story was similar with the previous wave - they resisted pressure to do more about the 'pingdemic', despite very loud noises from the right wing press,  because they were actually quite reliant on the pingdemic to do a chunk of the heavy lifting in that wave. So they fiddled around rather than demolishing the entire system. Eventually we will reach a point where they are prepared to go so much further, because they think they can make the numbers add up.


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## elbows (Jan 10, 2022)

I see in the news today that they've explicitly tied any changes to self-isolation periods to receiving new advice from the UKHSA. This gives them the usual scientific cover and buys them some time in terms of political pressure, and they also likely have some influence over that timing anyway.

In my book, and possibly theirs, they should wait till they have a better idea about what level cases look like are going to drop down to before doing this stuff, but they might get impatient if that evolution of that picture is slow.


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## Combustible (Jan 12, 2022)

There's a preprint on the relative outcomes of Delta and Omicron infections, showing considerably lower rates of hospitalizations, ICU admissions and mortality rates for omicron infections, regardless of vaccination status and known history of infections.









						Clinical outcomes among patients infected with Omicron (B.1.1.529) SARS-CoV-2 variant in southern California
					

Background The Omicron (B.1.1.529) variant of SARS-CoV-2 has rapidly achieved global dissemination, accounting for most infections in the United States by December 2021. Risk of severe outcomes associated with Omicron infections, as compared to earlier SARS-CoV-2 variants, remains unclear...




					www.medrxiv.org
				






> Among cases first tested in outpatient settings, the adjusted hazard ratios for any subsequent hospital admission and symptomatic hospital admission associated with Omicron variant infection were 0.48 (0.36-0.64) and 0.47 (0.35-0.62), respectively. Rates of ICU admission and mortality after an outpatient positive test were 0.26 (0.10-0.73) and 0.09 (0.01-0.75) fold as high among cases with Omicron variant infection as compared to cases with Delta variant infection. Zero cases with Omicron variant infection received mechanical ventilation, as compared to 11 cases with Delta variant infections throughout the period of follow-up (two-sided p<0.001). Median duration of hospital stay was 3.4 (2.8-4.1) days shorter for hospitalized cases with Omicron variant infections as compared to hospitalized patients with Delta variant infections, reflecting a 69.6% (64.0-74.5%) reduction in hospital length of stay. Conclusions: During a period with mixed Delta and Omicron variant circulation, SARS-CoV-2 infections with presumed Omicron variant infection were associated with substantially reduced risk of severe clinical endpoints and shorter durations of hospital stay.


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## zahir (Jan 12, 2022)




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## elbows (Jan 13, 2022)

Well I was wrong about how much they may delay the decision to reduce the self-isolation period to 5 days.

I havent looked into the detail yet, but Javid announced the change in the commons a little while ago.


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## elbows (Jan 24, 2022)

An additional immune escape method of Omicron is discussed here:


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## 2hats (Jan 25, 2022)

See also BA.2 v BA.1.

Meanwhile... (Kyoto) a new study of the environmental stability of a number of SARS-CoV-2 VOC, including omicron (hello fomites).

This study suggests that the omicron/B.1.1.529/BA.1 variant also has the highest environmental stability among VOCs, which _might_ be a contributory factor to omicron replacing the delta variant and spreading rapidly. 

On plastic surfaces, average survival times of original Wuhan strain, alpha, beta, gamma and delta variants were around 56, 191, 157, 59 and 144 hours, respectively, compared to 194 hours for omicron. On skin corresponding average virus survival times were around 9, 20, 19, 11, 17 and 21 hours.

All VOCs were completely inactivated by 15 second exposure to 35% ethyl alcohol based sanitiser.
DOI: 10.1101/2022.01.18.476607.


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## zahir (Feb 4, 2022)

"Omicron is mild" - a thread


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## elbows (Feb 4, 2022)

Yes, although to really demonstrate the point in a way that many reasonable people can get on board with, we'll just have to wait and see what happens when the effect of boosters start to wane. Until/unless that happens,  we'll be stuck with something that is equivalent to being bored by endless arguments about detail between the likes of me and littlebabyjesus

I've had to move with the current times because too many people were already moving on here before the Omicron wave even revealed its full potential. And I'm not that interested in fighting a losing battle for many months in a row, its too futile, especially when people are worn out and need a break. But I'll continue to move with the times which might mean leaning further towards 'its all over' but will also mean that if things deteriorate in future, I will renew my traditional pandemic stance. So no sense of permanence should be assumed when it comes to my current stance.


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## elbows (Feb 4, 2022)

And I still think Israel offers something for 'both sides' to watch at the moment.

For the current picture there probably offers clues about the raw potential that Omicron still has, and may also turn out to offer clues about booster waning. But it also offer clues about how far the authorities will feel the need to go in these sorts of circumstances - if the level of things like intensive care numbers end up being similar to previous waves, but without anything like the same number of restrictions on our lives, then we might assume this is a state of affairs that authorities in very many countries will be quite content with. Unfortunately this sort of thing may also demonstrate something I've often mentioned since the start of the pandemic, that its the hospital figures that force governments to act more than the number of deaths, although ultimately there are still some limits to the amount of death they will ask us to ensure too, but those limits are probably rather high. This point about deaths may not be obvious in countries like the UK which fucked things up so badly with the first few waves that we already had ridiculous amounts of death, but in countries that previously controlled things to a greater extent, the new approach may well stick out more in their latest death figures.


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## littlebabyjesus (Feb 4, 2022)

Israel is mirroring many other places in seeing excess death numbers falling as omicron deaths increase. It is a curious but marked phenomenon. 



Graphs and maps from EUROMOMO


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## zahir (Feb 4, 2022)

It looks like this is within the acceptable number of deaths.


> Children are not meant to die, so when people say the risk of a child dying of Covid-19 is very small, then yes, it absolutely should be. Unfortunately, we’ve been letting Covid spread quite freely in the UK, especially through schools. Children are now dying of Covid regularly, at a rate of about 2 or 3 per week. In fact, we’ve lost at least 133 children to Covid in the UK so far. My child probably won’t die of Covid, and yours probably won’t either, but in the next few days, someone’s child will.





> The rapid spread of Omicron has lead to an unprecedented acceleration in children being admitted to hospital, at more than double the rate of previous waves. Similar patterns were seen in South Africa and New York, but it is still too early to say whether this increase in hospitalisation will translate into increased child mortality rates. The rates of Long Covid from Omicron are also still unknown.











						Our children are sitting ducks *Corrected Article with FullFact link* – BJGP Life
					






					bjgplife.com


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## elbows (Feb 4, 2022)

littlebabyjesus said:


> Israel is mirroring many other places in seeing excess death numbers falling as omicron deaths increase. It is a curious but marked phenomenon.
> 
> View attachment 308709
> 
> Graphs and maps from EUROMOMO


I've already tried to explain why I dont find it very curious at this time of year.

The bar for what counts as an excess death changes throughout the year, and tends to be much higher in January, due to the normal seasonal pattern of flu, cold weather etc deaths. When these other forms of death are lower than normal, it creates more room for Covid deaths to occur without ending up counting as excess deaths.

I can demonstrate that point for England and Wales reasonably easily due to the large amount of regular death data that is published here. I find it much harder to achieve this for a lot of other countries, including Israel. For example if I could find weekly all cause death figures for Israel then we would be able to see the picture without the effect of the winter excess death bar being higher that I just described.

The site you got that graph from compounds this issue further by only publishing z-scores, a measurement that is even more convoluted but that I am not fit to attempt to explain properly.

Because I cannot find the raw data for Israel, I cannot say exactly to what extent the stuff I just described is responsible for the phenomenon you mention, but it would be surprising if it wasnt a big factor. But I will acknowledge several other potential factors too:

Data lag. The spike in Israels deaths are a very recent phenomenon, I dont know if those have filtered into the excess death figures yet.

Although I am not a fan of stretching the phenomenon of 'incidental deaths' too far for particular agendas, I am quite happy to acknowledge that such things are still some part of the mix. And they are expected to be a larger part of the mix during huge Omicron waves, due to the often much larger number of infections countries are experiencing from Omicron, the high levels of protection from vaccination, and some of the intrinsic properties of Omicron. Establishing exact causes of death is not a precise science, but where attempts are made to analyse this, for example in ONS reports for England and Wales, in the Omicron wave they are tending to say that 70-something percent of deaths where Covid was involved had Covid directly listed as the primary underlying cause of death. In other words, although I hate to describe things in these terms, some of those deaths may well have happened at this time of year even in the absence of an Omicron wave. I wont translate this directly to a 1-to-1 mapping, eg I wont claim that up to 30% of those deaths would certainly have happened anyway, but I will try to be fair by recognising that its some part of the picture we currently see. I tend to treat such estimates as an upper bar for 'incidental deaths', with the real figure for deaths that would have happened anyway being somewhere in the region of higher than 0% and less than 30%.

edit - to be more precise, the most recent ONS figures were:



> Of the 1,484 deaths involving COVID-19, 72.9% (1,082 deaths) had this recorded as the underlying cause of death in Week 3 compared with 77.4% in Week 2.


from Deaths registered weekly in England and Wales, provisional - Office for National Statistics

With that detail in mind we might also conclude that the proportion of 'incidental' deaths has continued to increase during the Omicron wave, as has also been the case with hospitalisations. This is another reason far more countries are taking a more relaxed approach now.


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## elbows (Mar 24, 2022)

I'm just linking to this post from Yossarian about the Hong Kong situation so that it is easier to find in future in the event that some are still tempted to talk shit about how 'mild' Omicron is, since that attempt to distort history seems quite likely to rear its head in future.









						COVID-19 in America
					

https://apnews.com/article/biden-government-free-n95-masks-program-2b4a59953281ca16028244ab9a5b1d6e




					www.urban75.net


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