B.1.1.529 Omicron variant

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jdc
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Re: B.1.1.529 Omicron variant

Post by jdc » Thu Dec 23, 2021 9:25 pm

Woodchopper wrote:
Thu Dec 23, 2021 7:29 pm
As for vaccines having primed people immune systems to work against other variants, that is likely.
The original strain mRNA vaccines generated B cells that could bind the original strain and three variants that followed, per the pre-Omicron paper below. And a booster with an mRNA vaccine enhanced this cross-reactivity, providing "potent neutralization of Omicron" per the post-Omicron paper even further below.

https://www.science.org/doi/10.1126/science.abm0829
mRNA vaccination also generated spike- and RBD-specific memory B cells, including memory B cells that cross-bound Alpha, Beta, and Delta RBDs, that were capable of rapidly producing functional antibodies after stimulation ... also generated a higher frequency of variant cross-binding memory B cells than mild SARS-CoV-2 infection alone, with >50% of RBD-specific memory B cells cross-binding all three VOCs at 6 months. These variant-binding memory B cells were more hypermutated than wild-type–only binding cells
https://www.medrxiv.org/content/10.1101 ... 21267755v1
Remarkably, neutralization of Omicron was undetectable in most vaccinated individuals. However, individuals boosted with mRNA vaccines exhibited potent neutralization of Omicron only 4-6-fold lower than wild type, suggesting that boosters enhance the cross-reactivity of neutralizing antibody responses.
Nice image here that shows the booster dose restoring neutralization against wild-type virus to previous levels and getting neutralization against Delta & Omicron to higher levels than ever. https://www.medrxiv.org/content/medrxiv ... .large.jpg

Image

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Mon Dec 27, 2021 8:50 am

Thanks for that jdc

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Mon Dec 27, 2021 8:51 am

More on Omicron causing less damage to the lungs: https://drive.google.com/file/d/1rhCazF ... fFckR/view

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Re: B.1.1.529 Omicron variant

Post by raven » Mon Dec 27, 2021 7:30 pm

New Omicron figures are out after the Christmas break:
https://assets.publishing.service.gov.u ... Dec_21.pdf

Almost 160,000 confirmed cases, 353,000 spike-failures. 407 hospitalisations and 39 deaths.

There's new figures for % unvaccinated hospitalised too, but I don't have time to look right now.

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Mon Dec 27, 2021 10:14 pm

Thread update on the NHS.
https://twitter.com/chrisceohopson/stat ... 90723?s=21

So far cases due to Omicron are manageable. People admitted with Covid (rather that for) are still an issue as they need to be isolated. Personnel being unavailable may be as big a problem as the number of very sick people. Still early days as infections haven’t yet ripped through the elderly population.

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Re: B.1.1.529 Omicron variant

Post by Grumble » Mon Dec 27, 2021 11:03 pm

Woodchopper wrote:
Mon Dec 27, 2021 10:14 pm
Thread update on the NHS.
https://twitter.com/chrisceohopson/stat ... 90723?s=21

So far cases due to Omicron are manageable. People admitted with Covid (rather that for) are still an issue as they need to be isolated. Personnel being unavailable may be as big a problem as the number of very sick people. Still early days as infections haven’t yet ripped through the elderly population.
Hopefully the boosters, which were well underway for older folk before omicron started, will prevent it being an issue
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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Tue Dec 28, 2021 4:10 am

The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters

The emergence of SARS-CoV-2 variants of concern (VoCs) has exacerbated the COVID-19 pandemic. End of November 2021, a new SARS-CoV-2 variant namely the omicron (B.1.1.529) emerged. Since this omicron variant is heavily mutated in the spike protein, WHO classified this variant as the 5th variant of concern (VoC). We previously demonstrated that the other SARS-CoV-2 VoCs replicate efficiently in Syrian hamsters, alike also the ancestral strains. We here wanted to explore the infectivity of the omicron variant in comparison to the ancestral D614G strain. Strikingly, in hamsters that had been infected with the omicron variant, a 3 log10 lower viral RNA load was detected in the lungs as compared to animals infected with D614G and no infectious virus was detectable in this organ. Moreover, histopathological examination of the lungs from omicron-infecetd hamsters revealed no signs of peri-bronchial inflammation or bronchopneumonia. Further experiments are needed to determine whether the omicron VoC replicates possibly more efficiently in the upper respiratory tract of hamsters than in their lungs.
https://www.biorxiv.org/content/10.1101 ... 4.474086v1

tl;dr unlike previous variants Omicron didn’t infect the hamsters’ lungs (buy may have infected their upper respiratory tract). This suggests that it’s intrinsically milder.

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Tue Dec 28, 2021 12:53 pm


Omicron infection enhances neutralizing immunity against the Delta variant
https://secureservercdn.net/50.62.198.7 ... -Sigal.pdf

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Re: B.1.1.529 Omicron variant

Post by bjn » Tue Dec 28, 2021 12:59 pm

Would infecting the upper respiratory tract give Omi a competitive advantage which simultaneously makes it less virulent? I have no idea what I'm talking about, but if infecting sites in the nose/throat rather than deep in the lungs, is that not easier for aerosol born viral particles to reach and so lodge and infect? Also if in nose/throat would you not sneeze/breath out more viral particles than if infected deep in the lungs?

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Re: B.1.1.529 Omicron variant

Post by Trinucleus » Tue Dec 28, 2021 6:17 pm

bjn wrote:
Tue Dec 28, 2021 12:59 pm
Would infecting the upper respiratory tract give Omi a competitive advantage which simultaneously makes it less virulent? I have no idea what I'm talking about, but if infecting sites in the nose/throat rather than deep in the lungs, is that not easier for aerosol born viral particles to reach and so lodge and infect? Also if in nose/throat would you not sneeze/breath out more viral particles than if infected deep in the lungs?
I'm no expert either, but that sounds very logical.

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Re: B.1.1.529 Omicron variant

Post by jdc » Tue Dec 28, 2021 6:53 pm

Trinucleus wrote:
Tue Dec 28, 2021 6:17 pm
bjn wrote:
Tue Dec 28, 2021 12:59 pm
Would infecting the upper respiratory tract give Omi a competitive advantage which simultaneously makes it less virulent? I have no idea what I'm talking about, but if infecting sites in the nose/throat rather than deep in the lungs, is that not easier for aerosol born viral particles to reach and so lodge and infect? Also if in nose/throat would you not sneeze/breath out more viral particles than if infected deep in the lungs?
I'm no expert either, but that sounds very logical.
The original strain and variants all infect the bronchus, but Omicron does so much more effectively -
Omicron variant replicates faster than the original SARS-CoV-2 virus and Delta variant in the human bronchus. At 24 hours after infection, the Omicron variant replicated around 70 times higher than the Delta variant and the original SARS-CoV-2 virus.
And the apparent trade-off is that it's worse at infecting lungs -
In contrast, the Omicron variant replicated less efficiently (more than 10 times lower) in the human lung tissue than the original SARS-CoV-2 virus, which may suggest lower severity of disease.
https://www.med.hku.hk/en/news/press/20 ... -infection

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Re: B.1.1.529 Omicron variant

Post by bjn » Tue Dec 28, 2021 7:31 pm

That all fits in with my hypothesis.

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Re: B.1.1.529 Omicron variant

Post by jimbob » Wed Dec 29, 2021 8:20 pm

Not sure how much milder it is.

Image

Cases scale LHS Admissions scale RHS 1/10 of cases scale
Have you considered stupidity as an explanation

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Thu Dec 30, 2021 6:03 am


SARS-CoV-2 spike T cell responses induced upon vaccination or infection remain robust against Omicron

Abstract

The SARS-CoV-2 Omicron variant has multiple Spike (S) protein mutations that contribute to escape from the neutralizing antibody responses, and reducing vaccine protection from infection. The extent to which other components of the adaptive response such as T cells may still target Omicron and contribute to protection from severe outcomes is unknown. We assessed the ability of T cells to react with Omicron spike in participants who were vaccinated with Ad26.CoV2.S or BNT162b2, and in unvaccinated convalescent COVID-19 patients (n = 70). We found that 70-80% of the CD4 and CD8 T cell response to spike was maintained across study groups. Moreover, the magnitude of Omicron cross-reactive T cells was similar to that of the Beta and Delta variants, despite Omicron harbouring considerably more mutations. Additionally, in Omicron-infected hospitalized patients (n = 19), there were comparable T cell responses to ancestral spike, nucleocapsid and membrane proteins to those found in patients hospitalized in previous waves dominated by the ancestral, Beta or Delta variants (n = 49). These results demonstrate that despite Omicron's extensive mutations and reduced susceptibility to neutralizing antibodies, the majority of T cell response, induced by vaccination or natural infection, cross-recognises the variant. Well-preserved T cell immunity to Omicron is likely to contribute to protection from severe COVID-19, supporting early clinical observations from South Africa.
https://www.medrxiv.org/content/10.1101 ... 21268380v1

Summary thread: https://twitter.com/virusmonologues/sta ... 21536?s=21

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Re: B.1.1.529 Omicron variant

Post by lpm » Thu Dec 30, 2021 11:36 am

Good news:

1. Voluntary lockdown seems quite extensive and has bought us time
2. Booster rollout has gone well and beaten expectations even if not meeting Boris fantasy target
3. Latest info seems to suggest average length of hospital stay is half Jan 2021 length - better treatments, milder variant

Bad news:

1. Statistics very muddled. Infections on Christmas Eve, Day and Boxing Day will show symptoms Tues/Weds/Thurs this week, showing up in test data at the end of this week
2. We're past the point of no return and January will be whatever it'll be. No point in govt lockdown as it will no longer bring any benefits

Irrelevant news:

1. Testing shortages means very little, no matter how important it seems to individuals
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Re: B.1.1.529 Omicron variant

Post by lpm » Thu Dec 30, 2021 11:37 am

⭐ Awarded gold star 4 November 2021

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Re: B.1.1.529 Omicron variant

Post by shpalman » Thu Dec 30, 2021 12:22 pm

The numbers actually in hospital in England have obviously started going up over the past few days. Numbers in MV beds haven't, though. Yet.
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Re: B.1.1.529 Omicron variant

Post by Bird on a Fire » Thu Dec 30, 2021 1:01 pm

Yes, good news.

Omicron may turn out to be a covid we can largely live with, once the antivaxxer problem is sorted one way or another.
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Re: B.1.1.529 Omicron variant

Post by Sciolus » Thu Dec 30, 2021 6:41 pm

I'm a bit brain-dead this evening (also their link to the Sage data is broken), but surely that's utter b.llsh.t? How can you say the average stay has gone from 12 weeks to 5 weeks when omicron has only been around for a month and hospitalising people for a fortnight at most? Are they only looking at average stays of people who have been discharged, not people who are still in hospital (which for older people with omicron will be almost all of them)?

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Re: B.1.1.529 Omicron variant

Post by shpalman » Thu Dec 30, 2021 6:43 pm

Sciolus wrote:
Thu Dec 30, 2021 6:41 pm
I'm a bit brain-dead this evening (also their link to the Sage data is broken), but surely that's utter b.llsh.t? How can you say the average stay has gone from 12 weeks to 5 weeks when omicron has only been around for a month and hospitalising people for a fortnight at most? Are they only looking at average stays of people who have been discharged, not people who are still in hospital (which for older people with omicron will be almost all of them)?
It's days, not weeks.
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Re: B.1.1.529 Omicron variant

Post by Sciolus » Thu Dec 30, 2021 6:47 pm

I said I was brain-dead...

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Re: B.1.1.529 Omicron variant

Post by shpalman » Thu Dec 30, 2021 9:09 pm

jimbob wrote:
Wed Dec 29, 2021 8:20 pm
Not sure how much milder it is.

Image

Cases scale LHS Admissions scale RHS 1/10 of cases scale
Now that the full UK hospitalization data has caught up a bit, it seems to me that numbers admitted to hospital are 2% of the daily cases after a 10-day lag, which is what it was before.

Given that the highest case rates are around the 20-25 age group (in England at least, I assume the other nations are the same) the lag of course is made up not just of the time it takes for someone to deteriorate enough to need to go to hospital, but also the time it takes for the infection to get from the young person to someone more likely to end up in hospital. I think this has been the case for most of the summer too, except not every peak made it out from the young people into the older people.

Neither deaths nor MV beds occupation appear to be going up yet, so something really has changed there.
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Re: B.1.1.529 Omicron variant

Post by jimbob » Thu Dec 30, 2021 10:53 pm

shpalman wrote:
Thu Dec 30, 2021 9:09 pm
jimbob wrote:
Wed Dec 29, 2021 8:20 pm
Not sure how much milder it is.

Image

Cases scale LHS Admissions scale RHS 1/10 of cases scale
Now that the full UK hospitalization data has caught up a bit, it seems to me that numbers admitted to hospital are 2% of the daily cases after a 10-day lag, which is what it was before.

Given that the highest case rates are around the 20-25 age group (in England at least, I assume the other nations are the same) the lag of course is made up not just of the time it takes for someone to deteriorate enough to need to go to hospital, but also the time it takes for the infection to get from the young person to someone more likely to end up in hospital. I think this has been the case for most of the summer too, except not every peak made it out from the young people into the older people.

Neither deaths nor MV beds occupation appear to be going up yet, so something really has changed there.

the number of people who struggle to read that graph, and indeed say it's misleading because I am using two scales is something.

I think it's too early to say. We' only saw hospital admissions start to rise on the 18th December. So it's a bit more of a lag for MV beds.
Have you considered stupidity as an explanation

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Re: B.1.1.529 Omicron variant

Post by shpalman » Fri Dec 31, 2021 7:31 am

South Africa reckons the fourth wave has passed thanks to... not selling alcohol after midnight and limiting gatherings to only 1000 people?

They're still wearing masks though.
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Re: B.1.1.529 Omicron variant

Post by shpalman » Fri Dec 31, 2021 11:49 am

jimbob wrote:
Thu Dec 30, 2021 10:53 pm
the number of people who struggle to read that graph, and indeed say it's misleading because I am using two scales is something.

I think it's too early to say. We' only saw hospital admissions start to rise on the 18th December. So it's a bit more of a lag for MV beds.
Well, I don't like how the two traces touch. Despite the different colours, it seems like they cross over.

To make my estimate I used my own spreadsheet. Zooming in on just the latest increase in admissions per day, I could maybe make a more precise estimate of a 7-day lag between case reports and admissions (instead of 10 days) and a 1.8% factor instead of 2%, as if that's meaningful.

I've been working with a 3-week lag between case reports and death reports, and a 0.4% CFR. I should probably revise the CFR down to 0.25%, but it's only just 3 weeks since cases started going nuts, so we'll probably have to wait another week or so to see what happens to deaths now because of Omicron (and for the stats to fully catch up after the Christmas and New Year's holidays). (In my previous post I thought deaths would already be going up if they were going to, but looking more closely, I see we still need to wait.)

Numbers in hospital are 17% of the reported cases per day, with a 15-day lag, but then that percentage itself also depends on the case rate (i.e. it combines information about both the severity and the speed of the spread). This is also true of the numbers in MV beds, which are about 1.8% of the reported cases per day and also here I've been assuming a 21-day lag so we don't know if that's going to go up yet.

Here's my graph but looking at it makes no sense if you haven't read all the above text.
covid-omicron-factors.png
covid-omicron-factors.png (42 KiB) Viewed 195 times
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