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Omicron variant

The home for all non-political Coronavirus (Covid-19) discussions on The Lemon Fool
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This is the home for all non-political Coronavirus (Covid-19) discussions on The Lemon Fool
dealtn
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Re: Omicron variant

#464234

Postby dealtn » December 8th, 2021, 1:24 pm

Hallucigenia wrote:
The time for action was last week.


Yes, but what action? It's fair to say the authorities haven't ignored it and done nothing either.

So in a world of high uncertainty, and not knowing what to do, and at the risk of doing the wrong thing, or going too far, how easy is it to judge (without the eventual hindsight) the actions of the authorities?

It's a presumption but surely they are taking advice from those with more specialist knowledge, acting in accordance with such, and appear to be in line with similar responses from other authorities across the world. Isn't that sufficient to judge they are making an appropriate response?

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Re: Omicron variant

#464239

Postby Lootman » December 8th, 2021, 1:32 pm

dealtn wrote:
Hallucigenia wrote:The time for action was last week.

Yes, but what action? It's fair to say the authorities haven't ignored it and done nothing either.

So in a world of high uncertainty, and not knowing what to do, and at the risk of doing the wrong thing, or going too far, how easy is it to judge (without the eventual hindsight) the actions of the authorities?

It's a presumption but surely they are taking advice from those with more specialist knowledge, acting in accordance with such, and appear to be in line with similar responses from other authorities across the world. Isn't that sufficient to judge they are making an appropriate response?

There is a school of thought which suggests that we should over-react every time a new variant appears just in case the new one is more infectious AND more deadly AND resistant to vaccines.

But it would be massively disruptive to globally shut everything down "just in case". And despite all the variants that have emerged since March 2020, the hospitalisations and deaths have consistently been lower since then, indicating that a more balanced approach has been justified. The development of vaccines and better treatments has made the situation tenable in a way that was not possible 20 months ago.

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Re: Omicron variant

#464242

Postby Julian » December 8th, 2021, 1:47 pm

Hallucigenia wrote:
servodude wrote:
Hallucigenia wrote:It's only been in existence for maybe 6-7 weeks so there will only be a handful in hospital in the UK yet.


I've been trying to do the back of a fag pack calcs on this
Given that it shows pretty easily in PCR tests... how many cases do you currently expect are about in the UK?
And how many, given vaccine coverage, would you expect to need to have before any reasonable judgement on the relative virulence could be made?
Basically, how much do you need out there to decided whether you need to take further action or not?!
-sd


Prof Alastair Grant has access to a non-public SPI-M datafeed that includes S-gene dropout data from the 40% of tests with S-gene primers. He says there's been 994 S-gene dropouts out of 256k tests in those labs since 20 November - ie 0.4% of the cumulative total since then, suggesting 2500 in total (although tests on travellers have probably been preferentially given to the S-gene labs?). S-gene dropouts were 2% of swabs on 4 November.

Obviously S-gene dropout is not a perfect indicator of omicron, not least because some members of the omicron lineage don't show S-gene dropout, but it's the best we have at the moment.

The really scary thing is that both the UK and SA seem to be showing a doubling time of 3 days or less, whereas the delta wave was showing a doubling time of 2 weeks. So in the time delta takes to go from 1 case to 2 cases, omicron will go from 1 case to 10+ cases, the current Rt seems to be around 3.5.

The time for action was last week.

It will be interesting to see how much of this is down to any increase in transmissibility and how much is down to immune escape.

I’ve seen 2 labs releasing data on neutralising antibody titres today (mentioned in this video with links in the video description - https://youtu.be/E6rk8w_NeJQ) and the results are all over the place, in particular the Sweden one seems very vague about what antibodies were being tested since I couldn’t see a description of the donor plasma beyond vague references to vaccinations but no specifics. The paper seems to have been taken down temporarily but from the twitter discussion also linked in the video description it appears that the SA lab titres used serum from doubly Pfizer vaccinated donors and showed a 41-fold reduction in antibody neutralisation vs antibody neutralisation of the Wuhan strain. From memory the reduction against Delta is just under 4 vs Wuhan (3.9 I think) so if these results hold up that would be about a 10-fold reduction vs Delta.

Of course that’s not the end of the story, I also heard one virologist mention that he’d just heard results from someone that T-cell epitopes appear to be mostly well conserved in Omicron so that sounds encouraging re T-cell responses and protection against severe disease but with that hit to antibody neutralisation I can easily imagine people double vaccinated 4 or 5 months ago with any of the vaccines the UK used now being a pretty easy target for Omicron to at least infect them even if it doesn’t then go on to cause severe disease. That might explain why we are seeing that high R number, similar to SA’s number, even though we are a much more vaccinated population.

The booster jab really does seem critical now because data there is showing that it gives a massive boost back up in antibody levels, hopefully sufficient to counteract whatever drops in convalescent and various vaccine induced antibody effects does end up being the accurate final data for Omicron vs Delta. People really do need to go out and get their boosters ASAP.

- Julian

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Re: Omicron variant

#464317

Postby XFool » December 8th, 2021, 6:08 pm

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

BBC News

Hospital admissions from the Omicron variant may reach at least 1,000 a day in England by the end of the year without extra restrictions being put in place, government advisers have said.

"The numbers are contained in leaked minutes of a meeting of the government's scientific advisers held on Tuesday and seen by the BBC."

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Re: Omicron variant

#464319

Postby monabri » December 8th, 2021, 6:20 pm

What about the effect of admissions due to delta?

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Re: Omicron variant

#464342

Postby Bouleversee » December 8th, 2021, 8:21 pm

Many thanks to all who responded to my questions. Very informative, though it's still not certain as to how soon an infection which hasn't produced any symptoms can be passed on, though as one of you said, it's unlikely to be within the time-frame I mentioned. However, having discovered that the guest mentioned had attended the Twickenham S. Africa match mentioned on here and furthermore had had a bad reaction to his subsequent booster jab (I gather that one should get a Covid test in that case but he didn't) and having had second thoughts about the small size of the restaurant and proximity of other tables, my son has decided he would prefer to have a dinner party at home and ensure that all guests had a negative LFT that day, which he couldn't as regards other diners in the restaurant. I feel very sorry for the restaurateur but as the new variant is spreading at a much faster rate than its predecessors, I think it does make sense for people to meet in locations where they can ensure adequate ventilation and spacing. I should add that I had nothing to do with the selection and booking of the restaurant table (I was merely paying the bill) and I think my son and sibling should have considered the possibility of a new variant or increase in cases of the Delta one come winter and all the implications. I'm not sure that the government's laissez faire approach, which they are now having to tighten up on, did anyone any favours. Having said that, with opposing views in the electorate, they can't win whatever they do.

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Re: Omicron variant

#464363

Postby servodude » December 8th, 2021, 9:29 pm

Julian wrote:
Hallucigenia wrote:
servodude wrote:
I've been trying to do the back of a fag pack calcs on this
Given that it shows pretty easily in PCR tests... how many cases do you currently expect are about in the UK?
And how many, given vaccine coverage, would you expect to need to have before any reasonable judgement on the relative virulence could be made?
Basically, how much do you need out there to decided whether you need to take further action or not?!
-sd


Prof Alastair Grant has access to a non-public SPI-M datafeed that includes S-gene dropout data from the 40% of tests with S-gene primers. He says there's been 994 S-gene dropouts out of 256k tests in those labs since 20 November - ie 0.4% of the cumulative total since then, suggesting 2500 in total (although tests on travellers have probably been preferentially given to the S-gene labs?). S-gene dropouts were 2% of swabs on 4 November.

Obviously S-gene dropout is not a perfect indicator of omicron, not least because some members of the omicron lineage don't show S-gene dropout, but it's the best we have at the moment.

The really scary thing is that both the UK and SA seem to be showing a doubling time of 3 days or less, whereas the delta wave was showing a doubling time of 2 weeks. So in the time delta takes to go from 1 case to 2 cases, omicron will go from 1 case to 10+ cases, the current Rt seems to be around 3.5.

The time for action was last week.

It will be interesting to see how much of this is down to any increase in transmissibility and how much is down to immune escape.



I'm trying to think of a way to reconcile a return to a doubling time of 3 days (which would be around where wild covid was when this started) in a population that has good vaccine coverage without it involving a good degree of immune escape
I suppose the considerations compound - so 50% escape with a doubling of transmissibility could do it?

- sd

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Re: Omicron variant

#464389

Postby zico » December 8th, 2021, 11:21 pm

servodude wrote:
I'm trying to think of a way to reconcile a return to a doubling time of 3 days (which would be around where wild covid was when this started) in a population that has good vaccine coverage without it involving a good degree of immune escape
I suppose the considerations compound - so 50% escape with a doubling of transmissibility could do it?

- sd


Presumably a mixture of Omicron going through the several million of unvaccinated people like a dose of salts plus a mixture of waning double-vaxxed immunity plus a bit of immune escape.

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Re: Omicron variant

#464390

Postby Hallucigenia » December 8th, 2021, 11:25 pm

Alastair Grant has more good news :

6.4% of swabs from 6th December are SGTF [S-gene target failure]
This increase represents an R-value of 4.06 (CI 3.25, 5.06)
A doubling time of 2.5 days
Cases are spread widely, although many areas in and around London have relatively high numbers


servodude wrote:I'm trying to think of a way to reconcile a return to a doubling time of 3 days (which would be around where wild covid was when this started) in a population that has good vaccine coverage without it involving a good degree of immune escape
I suppose the considerations compound - so 50% escape with a doubling of transmissibility could do it?

You can graph this kind of thing, as Trevor Bedford has for different levels of immunity, omicron will lie somewhere on the dotted line of transmissibility vs escapiness. Current thinking seems to be that it lies towards the bottom-right - relatively less escapy, more transmissible - I guess because there seems to be not much difference in R between the 75% part/fully vaxed UK and the 30% part/fully vaxed SA.
Image

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Re: Omicron variant

#464393

Postby servodude » December 8th, 2021, 11:45 pm

Hallucigenia wrote:You can graph this kind of thing, as Trevor Bedford has for different levels of immunity, omicron will lie somewhere on the dotted line of transmissibility vs escapiness. Current thinking seems to be that it lies towards the bottom-right - relatively less escapy, more transmissible - I guess because there seems to be not much difference in R between the 75% part/fully vaxed UK and the 30% part/fully vaxed SA.


Thanks

Finding a/the twitter thread from Trevor Bedford with that graph (and having a quick scan though) I'm surprised that the thinking isn't reversed (perhaps it's changed during the week)

- sd

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Re: Omicron variant

#464399

Postby jfgw » December 9th, 2021, 12:13 am

Interesting graph.

The 85% population immunity seems high. It would require something between 100% of people with 85% immunity, and 85% of people with 100% immunity.


Julian F. G. W.

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Re: Omicron variant

#464401

Postby Julian » December 9th, 2021, 12:18 am

Pfizer-BioNTech has released some results that confirm some of my previous thoughts. The main point is on pretty much the first line….

Preliminary laboratory studies demonstrate that three doses of the Pfizer-BioNTech COVID-19 Vaccine neutralize the Omicron variant (B.1.1.529 lineage) while two doses show significantly reduced neutralization titers


Note that this is looking at antibodies. They also did do some T cell research, maybe this is what the virologist I heard was talking about when he said he had heard a talk yesterday on T-cell epitopes. Pfizer also say in the report…

As 80% of epitopes in the spike protein recognized by CD8+ T cells are not affected by the mutations in the Omicron variant, two doses may still induce protection against severe disease


Full release here - https://www.pfizer.com/news/press-relea ... on-variant

Really quite encouraging. It’s also worth pointing out that the antibody levels seen after a Pfizer boost were really quite similar regardless of whether the previous 2 doses had been AZ or Pfizer so I don’t think that those of us who had AZ originally need to get too hung up on the fact that this is data for Pfizer+Pfizer+Pfizer; from what I’ve read these findings should translate pretty well to us AZ folks being boosted with Pfizer.

- Julian

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Re: Omicron variant

#464432

Postby 1nvest » December 9th, 2021, 8:45 am

jfgw wrote:Interesting graph.

The 85% population immunity seems high. It would require something between 100% of people with 85% immunity, and 85% of people with 100% immunity.

Julian F. G. W.

My then 89 year old mother had Covid back in January, other than a positive test we'd never even had known (she contracted it whilst in hospital following a fall) as the symptoms were very mild. My mid 20's unvaccinated son contracted Covid in July, had a 'cold' like experience for a week or so.

Since April the daily figures have been of the order of out of the average 1700 people that die each day around 50 average had a positive Covid test in the prior 28 days, less than 3%. I suspect if you modified that to how many had had a 'cold' in the past month the number would likely be similar.

If everyone stays in bed for a day (lockdown) then perhaps that days number of deaths might halve (850), but the next day (no lockdown) the figure would tend to be above average (2550).

In Sweden where they've not really applied lockdowns/imprisonments, proportionately they've had fewer deaths than the UK. On that measure lockdowns have induced deaths that might otherwise have been avoided. I can only speak from personal experience where the only Covid related death I am familiar with is a early 20's girl who committed suicide largely as a consequence of lockdowns.

Much of Covid management would seem to be a consequence of political agendas (divert attention/introduce greater 'open prison' controls), and the agendas of pharmaceuticals who are on course to make $$$ trillions. The vaccines are themselves not risk free and have apparently caused often heart related deaths in otherwise fit/relatively young individuals.

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Re: Omicron variant

#464453

Postby servodude » December 9th, 2021, 10:24 am

1nvest wrote:
jfgw wrote:Interesting graph.

The 85% population immunity seems high. It would require something between 100% of people with 85% immunity, and 85% of people with 100% immunity.

Julian F. G. W.

My then 89 year old mother had Covid back in January, other than a positive test we'd never even had known (she contracted it whilst in hospital following a fall) as the symptoms were very mild. My mid 20's unvaccinated son contracted Covid in July, had a 'cold' like experience for a week or so.

Since April the daily figures have been of the order of out of the average 1700 people that die each day around 50 average had a positive Covid test in the prior 28 days, less than 3%. I suspect if you modified that to how many had had a 'cold' in the past month the number would likely be similar.

If everyone stays in bed for a day (lockdown) then perhaps that days number of deaths might halve (850), but the next day (no lockdown) the figure would tend to be above average (2550).

In Sweden where they've not really applied lockdowns/imprisonments, proportionately they've had fewer deaths than the UK. On that measure lockdowns have induced deaths that might otherwise have been avoided. I can only speak from personal experience where the only Covid related death I am familiar with is a early 20's girl who committed suicide largely as a consequence of lockdowns.

Much of Covid management would seem to be a consequence of political agendas (divert attention/introduce greater 'open prison' controls), and the agendas of pharmaceuticals who are on course to make $$$ trillions. The vaccines are themselves not risk free and have apparently caused often heart related deaths in otherwise fit/relatively young individuals.


I've highlighted a word using bold

Think about it

Come back and explain.

Or don't...

Moderator Message:
Less than polite bit removed. - Chris



Peace
-sd

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Re: Omicron variant

#464468

Postby Hallucigenia » December 9th, 2021, 11:12 am

servodude wrote:Finding a/the twitter thread from Trevor Bedford with that graph (and having a quick scan though) I'm surprised that the thinking isn't reversed


Don't forget that even the right end of that chart still has immune escape of 30%.

AIUI the general thinking seems to be that although the theory and neutralisation assays are Bad for antibodies, the rest of the immune system is far less broken by omicron and works well enough that overall it's not too bad. And I guess you can do something with the epidemiology in SA vs UK to get an idea of where on the chart omicron lies.

One other thought - what if it's breaking (to some extent) the immunity from other sources, like "being young"? You might get all sorts of effects in the data if omicron gives many more symptoms in children for a given prevalence, particularly in places that don't have heavy surveillance testing of kids.

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Re: Omicron variant

#464477

Postby zico » December 9th, 2021, 11:46 am

Encouraging signs from South Africa that Omicron exponential growth may just be restricted to younger ages (and hence unvaccinated). This would be important here it would mean vaccinated cohorts have better protection, and if (big 'if') that is the case, Omicron would be doing us a huge favour by spreading to most of the morons (sorry, unvaccinated) and giving them potential immunity to other Covid variants - in effect, they'd be getting vaccinated, but in a much more random way, with much greater risks of harm to themselves.

Still very early days, and all scenarios definitely still on the table.

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Re: Omicron variant

#464484

Postby servodude » December 9th, 2021, 11:59 am

csearle wrote:a very polite moderation note after I reported my own post


Thanks Chris
- smoothly done
- and very much appreciated

Back to my very best behaviour
- sd

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Re: Omicron variant

#464488

Postby servodude » December 9th, 2021, 12:05 pm

zico wrote:Encouraging signs from South Africa that Omicron exponential growth may just be restricted to younger ages (and hence unvaccinated). This would be important here it would mean vaccinated cohorts have better protection, and if (big 'if') that is the case, Omicron would be doing us a huge favour by spreading to most of the morons (sorry, unvaccinated) and giving them potential immunity to other Covid variants - in effect, they'd be getting vaccinated, but in a much more random way, with much greater risks of harm to themselves.

Still very early days, and all scenarios definitely still on the table.


we all know that omicron == moronic
and that delta omicron == media control

so beacause of anagrams and stuff I fully expect some morons controlled by media to post moronic stuff about such things as the vaccines often causing heart problems

ah shite....
I'm off to bed

sorry
-sd

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Re: Omicron variant

#464497

Postby servodude » December 9th, 2021, 12:30 pm

Hallucigenia wrote:
servodude wrote:Finding a/the twitter thread from Trevor Bedford with that graph (and having a quick scan though) I'm surprised that the thinking isn't reversed


Don't forget that even the right end of that chart still has immune escape of 30%.

AIUI the general thinking seems to be that although the theory and neutralisation assays are Bad for antibodies, the rest of the immune system is far less broken by omicron and works well enough that overall it's not too bad. And I guess you can do something with the epidemiology in SA vs UK to get an idea of where on the chart omicron lies.

One other thought - what if it's breaking (to some extent) the immunity from other sources, like "being young"? You might get all sorts of effects in the data if omicron gives many more symptoms in children for a given prevalence, particularly in places that don't have heavy surveillance testing of kids.


Thanks
and you're totally right.... in that I was looking at that chart in the in the context of the axes given and not in the bigger picture

zoom in on any knuckle on a bode plot (or similar) and it will look the same - it's the "where" it is that gives it context

i "know" that there's enough noise in all the measurements that plotting the asymptotes is fraught with risk
- e.g. the first wave in the UK could have seen 10% to 50% infected ( there were claims round these parts of 80+ but i think they were politically motivated)

but "everyone" is vaccinated now
- so how do we work out - or when do we decide - that THIS (as a "new" variant) really matters?

I'll be the first to acknowledge that not every place can adopt an antipodean "up drawbridge" approach
- and I'll confess my main concern is the planned family trip tp Tasmania in a fortnight (I've lost both my parents-in-law in the past 16-months,and supported my better half through too many periods of hotel quaratine such that any personal covid concern has since become mostly societal and professional [we're still selling NIV machines.... yay! and you might need one FOREVER if you had really bad covid!])
- so we're (as western societies) about as ready for a resurge in this F***NG thing as we will be so...

...what do we do?

I guess there's no right (or wrong) answers
- and I'm interested in what and why people currently believe what they do
- (I say that ... although if you think getting rid of "the foreign folk" will help YOU ARE WRONG! and a bit misanthropic)

- sd

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Re: Omicron variant

#464515

Postby redsturgeon » December 9th, 2021, 1:45 pm

We have had three positive tests returned in the past two days, all show S-gene dropout.

John


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