B.1.1.529 Omicron variant

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Martin Y
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Re: B.1.1.529 Omicron variant

Post by Martin Y » Mon Nov 29, 2021 1:15 pm

lpm wrote:
Mon Nov 29, 2021 10:14 am
Wait, wait, I've just learned something from Facebook, omicron is fake, everyone stand down.

The New World Order gave us a clue right in it's name: omicron is an anagram of moronic.
Since it knows so much about the omicron virus, has Facebook told us what happens when we get to the omega virus?

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Re: B.1.1.529 Omicron variant

Post by jimbob » Mon Nov 29, 2021 1:50 pm

shpalman wrote:
Mon Nov 29, 2021 1:14 pm
Take it up with the WHO then.
I admit there isn't sufficient information for complete certainty, but it's already very likely and looking increasingly so, just comparing news of its spreading against a background of Delta.
Have you considered stupidity as an explanation

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Re: B.1.1.529 Omicron variant

Post by shpalman » Mon Nov 29, 2021 2:31 pm

Essex Omicron case linked, indirectly, to person who arrived from South Africa two weeks ago

So it's had at least two weeks to spread around Essex (which is at about 1000 cases per day at the moment, meaning a case rate of 500/100,000/week).
... the case was two steps removed from the South African arrival, said Dr Mike Gogarty, Essex county council’s director of public health. “This case contracted the case from somebody else who contracted it from one of her family who had been recently to Africa.”

He said the person with the confirmed case was tested on 20 November, but that genomic sequencing only confirmed it as Omicron at the weekend.
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Re: B.1.1.529 Omicron variant

Post by Bird on a Fire » Mon Nov 29, 2021 2:41 pm

The fact that it's probably been here undetected for quite a while would seem to have implications for estimating rate of spread.
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Re: B.1.1.529 Omicron variant

Post by shpalman » Mon Nov 29, 2021 2:52 pm

There can't have been that much of it about or else UKHSA should have noticed.

Variants of concern or under investigation: data up to 24 November 2021

(Note that VUI-21OCT-01 is "Delta plus")
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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Mon Nov 29, 2021 3:07 pm

Bird on a Fire, Shpalman

All true, but I wonder what's the threshold for them noticing something that they aren't looking for? At about 40 000 positive tests per day and perhaps a few times times as many not detected there is a lot of room for Omicron cases to remain unnoticed.

I assume that at the moment they are looking at all the data which shows s gene dropout on PCR tests.

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Mon Nov 29, 2021 3:18 pm

Thread which looks at Omicron’s increased prevalence in Gauteng and compared explanations of transmission with increased immune escape.
Basically theoretical until there’s better data.
https://twitter.com/c_althaus/status/14 ... 97478?s=21

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Re: B.1.1.529 Omicron variant

Post by shpalman » Mon Nov 29, 2021 3:19 pm

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Re: B.1.1.529 Omicron variant

Post by shpalman » Mon Nov 29, 2021 4:04 pm

Two more Omicron cases found in England
The total number of confirmed cases in England is now five.

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.
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Re: B.1.1.529 Omicron variant

Post by shpalman » Mon Nov 29, 2021 5:46 pm

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Re: B.1.1.529 Omicron variant

Post by shpalman » Mon Nov 29, 2021 5:47 pm

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Mon Nov 29, 2021 6:06 pm

Woodchopper wrote:
Mon Nov 29, 2021 3:18 pm
Thread which looks at Omicron’s increased prevalence in Gauteng and compared explanations of transmission with increased immune escape.
Basically theoretical until there’s better data.
https://twitter.com/c_althaus/status/14 ... 97478?s=21
Thread on a similar subject from the excellent Trevor Bedford
https://twitter.com/trvrb/status/146536 ... 85506?s=21

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Re: B.1.1.529 Omicron variant

Post by lpm » Mon Nov 29, 2021 6:40 pm

Woodchopper wrote:
Mon Nov 29, 2021 6:06 pm
Thread on a similar subject from the excellent Trevor Bedford
https://twitter.com/trvrb/status/146536 ... 85506?s=21
Interesting again.

As humans we don't get hit by "natural" R0 any longer. That planet of 2019 no longer exists. We now live on this partially vaccinated, partially recovered, partially fully vulnerable planet.

If Omi's got less natural speed than Delta, but makes up for it in immunity evasion, then that's OK news? Everyone's going to get Covid over the coming years and decades. Better if the dominant variant is one that depends on immunity evasion, not raw speed, because it will be steadily defeated when people get immunity to that variant, either via infection or via tweaked vaccine boosters.

Are Ancestral, Alpha, Beta etc now effectively extinct? On the WWF Endangered Species list? If we get Omi to drive out Delta, we free ourselves from the fastest variant. We instead get a variant that's good at infecting vaccinated/recovered humans but they're the humans who are far less likely to be hospitalised/die. Omi wouldn't be as good as Delta, however, at hitting the unvaccinated vulnerable because it hasn't got the pace, and those are the ones consuming our healthcare resources.

I suppose Omi could mutate again, though, taking on Delta's speed in some future variant.
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Re: B.1.1.529 Omicron variant

Post by Bird on a Fire » Mon Nov 29, 2021 8:29 pm

lpm wrote:
Mon Nov 29, 2021 6:40 pm
Woodchopper wrote:
Mon Nov 29, 2021 6:06 pm
Thread on a similar subject from the excellent Trevor Bedford
https://twitter.com/trvrb/status/146536 ... 85506?s=21
Interesting again.

As humans we don't get hit by "natural" R0 any longer. That planet of 2019 no longer exists. We now live on this partially vaccinated, partially recovered, partially fully vulnerable planet.

If Omi's got less natural speed than Delta, but makes up for it in immunity evasion, then that's OK news? Everyone's going to get Covid over the coming years and decades. Better if the dominant variant is one that depends on immunity evasion, not raw speed, because it will be steadily defeated when people get immunity to that variant, either via infection or via tweaked vaccine boosters.

Are Ancestral, Alpha, Beta etc now effectively extinct? On the WWF Endangered Species list? If we get Omi to drive out Delta, we free ourselves from the fastest variant. We instead get a variant that's good at infecting vaccinated/recovered humans but they're the humans who are far less likely to be hospitalised/die. Omi wouldn't be as good as Delta, however, at hitting the unvaccinated vulnerable because it hasn't got the pace, and those are the ones consuming our healthcare resources.

I suppose Omi could mutate again, though, taking on Delta's speed in some future variant.
Maybe the antivaxxers are accidentally onto something.

The best form of covid, as you astutely set out, would be highly infectious but cause minimal damage, to get to the immune system before a nastier variant. In other words, a contagious vaccine.

We could wait for mother nature to come up with it Herself (maybe). But it would be faster to engineer it. Anyone heard of a virology institute, located in a region with a high natural diversity of related coronaviruses?
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Re: B.1.1.529 Omicron variant

Post by Bird on a Fire » Mon Nov 29, 2021 8:31 pm

There is another theory which states that this has already happened.
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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Mon Nov 29, 2021 11:06 pm

Thread on how Genetic diversity within Omicron suggests that sequenced examples have a common ancestor that existed about 2-3 months ago.
https://twitter.com/corneliusroemer/sta ... 87969?s=21

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Mon Nov 29, 2021 11:18 pm


JCVI advice on the UK vaccine response to the Omicron variant

[…]

JCVI advises the following immediate measures within the COVID-19 vaccine programmes:

Booster vaccination eligibility should be expanded to include all adults aged 18 years to 39 years.
Booster vaccination should now be offered in order of descending age groups, with priority given to the vaccination of older adults and those in a COVID-19 at-risk group. Booster vaccination should not be given within 3 months of completion of the primary course.
Severely immunosuppressed individuals who have completed their primary course (3 doses) should be offered a booster dose with a minimum of 3 months between the third primary and booster dose. Those who have not yet received their third dose may be given the third dose now to avoid further delay. A further booster dose can be given in 3 months, in line with the clinical advice on optimal timing.
Both the Moderna (50 microgram) and Pfizer-BioNTech (30 microgram) vaccines should be used with equal preference in the COVID-19 booster programme. Both vaccines have been shown to substantially increase antibody levels when offered as a booster dose.
In addition, JCVI advises the following secondary measure, subject to appropriate consideration by deployment teams regarding feasibility.

All children and young people aged 12 to 15 years should be offered a second dose (30 micrograms) of the Pfizer-BioNTech COVID-19 vaccine at a minimum of 12 weeks from the first dose. The interval between vaccines may be reduced to at least 8 weeks between doses if the emerging epidemiological data supports this (and those aged 16 to 17 may also be offered their second dose with an interval of at least 8 weeks).

The overall intention of the measures advised above is to accelerate the deployment of COVID-19 vaccines before the peak of any impending Omicron wave. There is currently no data to indicate that Omicron infection is associated with a change in the pattern of susceptibility to serious COVID-19 (hospitalisation and death). Persons of older age, or who are in COVID-19 at-risk groups are likely to remain at higher risk from serious COVID-19; therefore, vaccination should be prioritised accordingly.

Continued efforts should be made to offer COVID-19 vaccination (first, second and booster doses) to adults who have yet to receive any COVID-19 vaccinations.
https://www.gov.uk/government/publicati ... on-variant

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Re: B.1.1.529 Omicron variant

Post by raven » Mon Nov 29, 2021 11:20 pm

Woodchopper wrote:
Mon Nov 29, 2021 3:07 pm
Bird on a Fire, Shpalman

All true, but I wonder what's the threshold for them noticing something that they aren't looking for? At about 40 000 positive tests per day and perhaps a few times times as many not detected there is a lot of room for Omicron cases to remain unnoticed.

I assume that at the moment they are looking at all the data which shows s gene dropout on PCR tests.
Hm, optimistically, if it's not actually more transmissable than Delta, maybe somewhat comparable, and the UK has high rates of Delta does that sort of protect us as the two variants are competing for the same hosts? And then places like South Africa, and perhaps the rest of Europe, where rates of covid are low/lower would have less 'protection', so they'd maybe see more dramatic rises in case numbers....?

Or, on the pessimistic side, it just hasn't hit us yet.

I'd best go read Trevor Bedford. He'll be better than my uneducated guesses.

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Re: B.1.1.529 Omicron variant

Post by RoMo » Tue Nov 30, 2021 6:07 am

Woodchopper wrote:
Mon Nov 29, 2021 3:07 pm
I assume that at the moment they are looking at all the data which shows s gene dropout on PCR tests.
It would be interesting to know out of the pillar 1 & 2 testing platforms which ones have the S gene as a target. Certainly for ours, out of our three platforms for covid, only one of them has (and that is the platform that hardly ever gets used as it takes longer).

It's also currently taking weeks to get sequencing/genotyping data back.

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Tue Nov 30, 2021 6:29 am


The chief executive of Moderna has predicted that existing vaccines will be much less effective at tackling Omicron than earlier strains of Covid-19 and warned it would take months before pharmaceutical companies can manufacture new variant-specific jabs at scale.

Stéphane Bancel said the high number of Omicron mutations on the spike protein, which the virus uses to infect human cells, and the rapid spread of the variant in South Africa, suggested the current crop of vaccines may need to be modified next year.

“There is no world, I think, where [the effectiveness] is the same level . . . we had with Delta,” Bancel told the Financial Times in an interview at the company’s headquarters in Cambridge, Massachusetts.

He added: “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’.”

The Moderna chief executive’s comments come as other public health experts and politicians have tried to strike a more upbeat tone about the ability of existing vaccines to confer protection against Omicron.

[…]

On Monday, Scott Gottlieb, a director of Pfizer and former commissioner of the US Food and Drug Administration, told CNBC: “There’s a reasonable degree of confidence in vaccine circles that [with] at least three doses . . . the patient is going to have fairly good protection against this variant.”

However, Bancel said scientists were worried because 32 of the 50 mutations in the Omicron variant are on the spike protein, which the current vaccines focus on to boost the human body’s immune system to combat Covid-19.

Most experts thought such a highly mutated variant would not emerge for another one or two years, Bancel added.

[…]

Bancel said data giving an indication of how the existing vaccines perform against the Omicron variant, and whether it causes severe disease, should become available within two weeks.

But he said it would take several months before an Omicron-specific vaccine could be produced at scale, and suggested there might be a case for giving more potent boosters to the elderly or people with compromised immune systems in the meantime.

“[Moderna] and Pfizer cannot get a billion doses next week. The maths doesn’t work. But could we get the billion doses out by the summer? Sure,” said Bancel, who predicted Moderna could make a total of 2bn-3bn doses in 2022.

But he said it would be risky to shift Moderna’s entire production capacity to an Omicron-targeted jab at a time when other variants are still in circulation.

Bancel also hit out at critics who have accused vaccine makers of not doing enough to support jab rollouts in developing countries such as South Africa, where only a quarter of the population is fully inoculated, according to Johns Hopkins University.

“This was mostly a policy decision by the rich countries. In the US, we were told we had no choice but to give 60 per cent of our output to the US government. That was not a Moderna decision, that was a US government decision,” he said.

Bancel also said there was a surplus of jabs earmarked for Africa and that 70m Moderna vaccines were sitting in warehouses because Covax — an international body tasked with inoculating low income nations — or individual governments had not taken delivery of them.

He said: “We are running out of space. It’s because either they don’t have customs documents, or they don’t have fridge space, or because the ability to get doses in arms is a challenge.”
https://www.ft.com/content/27def1b9-b9c ... e432e0838f

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Tue Nov 30, 2021 7:37 am

lpm wrote:
Sun Nov 28, 2021 1:11 pm
It could be that all 13 are connected and are actually 1 case multiplied out, e.g. a football squad.

But if it is 13 separates out of 600 then it hints that Omi is milder and more asymptomatic - the case/hospitalisation/death data in South Africa doesn't show the upward spikes that this sort of proportion should imply.
It wasn’t a football team:
The Dutch sequences were all from travellers from South Africa.
The observed diversity indicates this was not just one single group but that travellers had picked up Omicron a number of times independently from the community, presumably in South Africa.
https://twitter.com/corneliusroemer/sta ... 34496?s=21

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Re: B.1.1.529 Omicron variant

Post by jimbob » Tue Nov 30, 2021 8:31 am

I wonder if you lot can help, I swear I saw an article about using (mouse?) models to look at different mutations a few days ago with reference to Omicron. But I can't find anything remotely similar.

Have you come across this.
Have you considered stupidity as an explanation

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Re: B.1.1.529 Omicron variant

Post by shpalman » Tue Nov 30, 2021 8:50 am

“I’d rather over-react than under-react”
to Omicron says junior health minister who hasn't ever reacted to 30-50,000 cases per day of Delta.
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Re: B.1.1.529 Omicron variant

Post by shpalman » Tue Nov 30, 2021 8:52 am

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Re: B.1.1.529 Omicron variant

Post by shpalman » Tue Nov 30, 2021 9:40 am

Woodchopper wrote:
Tue Nov 30, 2021 6:29 am

The chief executive of Moderna has predicted that existing vaccines will be much less effective at tackling Omicron than earlier strains of Covid-19 and warned it would take months before pharmaceutical companies can manufacture new variant-specific jabs at scale...
https://www.ft.com/content/27def1b9-b9c ... e432e0838f
That feels a bit like saying it's going to be hard so that people are more impressed with you when you manage it.
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Scott: Certainly, sir. How else can I keep my reputation as a miracle worker?
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