B.1.1.529 Omicron variant

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Re: B.1.1.529 Omicron variant

Post by shpalman » Tue Nov 30, 2021 9:42 am

having that swing is a necessary but not sufficient condition for it meaning a thing
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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Tue Nov 30, 2021 10:30 am


"Most of our daily increases at this stage are from Gauteng, at about 81%. There has been a tremendous increase in the past 10 to 14 days,” said Dr Michelle Groome, head of the division of public health surveillance and response at the NICD.

Dr Waasila Jassat, also of the NICD, said that unvaccinated patients suffered more severe symptoms than vaccinated ones, and were most likely to face hospitalisation if infected by the new Covid-19 variant. She reported that 87% of all admissions in Pretoria were unvaccinated patients.

“We have been tracking this across the country since February, and what we can say is there is a much higher chance of death among those who are unvaccinated,” Dr Jassat said.
https://www.iol.co.za/news/politics/the ... 3ea83cb250


Speaking at a news conference on Monday, Groome said Gauteng has seen a rapid and sustained increase in COVID-19 cases.

“For all intents and purposes, Gauteng is in the fourth wave. This will certainly spill over to other provinces,” said Groome.

She said Limpopo, North West, and Mpumalanga are currently experiencing an increase in cases.

[…]

The new infections are being driven by younger people but those who are dying are over the age of 65, said the NICD’s Dr. Wassila Jassat said

She added that a higher number of children under two were getting infected.

“We may need to look at paediatric bed preparedness”, she said

[…]

Groome said most patients being admitted to hospitals are unvaccinated.

“In Tshwane, 13% of hospital admissions are vaccinated people and 87% are unvaccinated people. There is a much higher risk of death among unvaccinated patients who get admitted than vaccinated patients,” she said.
https://health-e.org.za/2021/11/29/gaut ... urth-wave/

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Tue Nov 30, 2021 10:54 am


She said there has been no significant rise in the presence of S-gene target failure in the positive Covid cases being genomically sequenced in the UK. S-gene target failure is not proof of Omicron (other variants feature it), but given that it is now very rare, and that Omicron does feature it (or S-gene dropout, as it is sometimes called), it is a good indicator for Omicron. “We have seen no rise, no significant rise, from the normal 1 in 1,000 cases that we would normally have,” she said.
From The Guardian live blog.

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Re: B.1.1.529 Omicron variant

Post by shpalman » Tue Nov 30, 2021 11:29 am

Woodchopper wrote:
Tue Nov 30, 2021 10:54 am

She said there has been no significant rise in the presence of S-gene target failure in the positive Covid cases being genomically sequenced in the UK. S-gene target failure is not proof of Omicron (other variants feature it), but given that it is now very rare, and that Omicron does feature it (or S-gene dropout, as it is sometimes called), it is a good indicator for Omicron. “We have seen no rise, no significant rise, from the normal 1 in 1,000 cases that we would normally have,” she said.
From The Guardian live blog.
Also from the live blog
At yesterday’s Covid briefing, Scotland’s chief medical officer, Gregor Smith said that the first Omicron case in Scotland was tested 6 days ago. “The earliest indication we have at this moment in time - and I stress at this moment in time - is that the first positive PCR test in relation to this, a confirmed case, is the 23rd of November,” he said.

But he also explained that health officials were conducting a “loop back exercise” of going through previous PCR tests back to 16 November now that they know what to look for as an indication of the Omicron variant.

He said that one of the “quirks” of the new variant was the presence of a “S-gene dropout or negative on PCR testing”. This allowed specialises to identify a potential Omicron case before genomic sequencing...
But not before you're told that you have to look out for it, obviously.
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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Tue Nov 30, 2021 1:15 pm

Pretty graphs on Gauteng data from John Burn Murdoch: https://twitter.com/jburnmurdoch/status ... 82725?s=20

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Tue Nov 30, 2021 8:11 pm

Woodchopper wrote:
Sun Nov 28, 2021 4:15 pm
Hospital admissions are the metric that matters.

You can see the South Africa data here: https://www.nicd.ac.za/diseases-a-z-ind ... ov-report/

Hospital admissions in Gauteng province have gone from 135 in week 45 to 418 in week 47 (22-28 November).

Seems to be consistent with Omicron causing severe illness. Though of course we don’t yet know the ratio.

The data on hospital admissions for Gauteng is looking worse, presumably after more data has been reported.

Now it’s:

Week 45: 136
Week 46: 279
Week 47: 647

Cases continue to rise rapidly as well.

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Tue Nov 30, 2021 9:12 pm

COVID: First signs that vaccine protects against Omicron – health minister
https://www.jpost.com/health-and-wellne ... day-687392

I think we need to wait for some better data.

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Re: B.1.1.529 Omicron variant

Post by jimbob » Tue Nov 30, 2021 10:45 pm

jimbob wrote:
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.
And there's more information continuing this
Have you considered stupidity as an explanation

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Wed Dec 01, 2021 8:49 am

Recommended thread which pulls together a lot of what has been posted here: https://twitter.com/K_G_Andersen/status ... 21442?s=20

Notably, it speculates that evolution of Omicron may have been human -> animal -> human (something which would explain Omi's long disappearance and sudden emergence as a highly contagious strain). IMHO Africa would be a likely place to find such a route as there are a lot of families living off subsistence farming who live very close to animals.

The thread doesn't rule out an immunocompromised individual, but suggests that as Omi's evolution dropped out of sight for over a year that seems to be too long for such a highly contagious variant to remain in a human host without infecting other people and causing an earlier outbreak. They would presumably have passed on intermediate versions of Omi to others that would have spread and been detected at some point.

IMHO, if evolution in animal hosts has happened it's very bad news. We can still hope to contain Covid through mass vaccination and boosters etc of the human population. But if it's evolving and mutating among the animal population then we can predict new variants indefinitely (and like influenza, some may be much more serious than others).

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Re: B.1.1.529 Omicron variant

Post by lpm » Wed Dec 01, 2021 9:20 am

I don't see why it couldn't have been constrained in a single individual. An entire household catches Covid. One of them never shakes it off and is ill for a year. Housebound and without medical care.

Doesn't spread to family members who have prior immunity and by chance doesn't spread to occasional visitors. Until eventually it does.

Seems far more plausible that going via an animal host. Even in Britain there are ill people cared for in family homes who never leave the house and never get NHS treatment.
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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Wed Dec 01, 2021 9:36 am

lpm wrote:
Wed Dec 01, 2021 9:20 am
I don't see why it couldn't have been constrained in a single individual. An entire household catches Covid. One of them never shakes it off and is ill for a year. Housebound and without medical care.

Doesn't spread to family members who have prior immunity and by chance doesn't spread to occasional visitors. Until eventually it does.

Seems far more plausible that going via an animal host. Even in Britain there are ill people cared for in family homes who never leave the house and never get NHS treatment.
Possibly, but only if a) the individual was particularly isolated and the household didn't, for example, get visitors; and b) the carers' immunity prevented them from being infected despite waning immunity and being in close contact for long periods.

Anyway, the author of the thread didn't rule out an immunocompromised individual.

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Re: B.1.1.529 Omicron variant

Post by lpm » Wed Dec 01, 2021 10:05 am

Sure, the author continually stresses the lack of information. But didn't both Beta and Delta have these long divergences as well - common ancestor, single line for two or three months, then rapid divergence again? OK, 15 months is far longer than two or three, but the same underlying method?

Or maybe I'm too much of an amateur looking at charts with too much missing.
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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Wed Dec 01, 2021 10:08 am

lpm wrote:
Wed Dec 01, 2021 10:05 am
Sure, the author continually stresses the lack of information. But didn't both Beta and Delta have these long divergences as well - common ancestor, single line for two or three months, then rapid divergence again? OK, 15 months is far longer than two or three, but the same underlying method?

Or maybe I'm too much of an amateur looking at charts with too much missing.
I don't think anyone really knows at the moment. But its interesting to speculate.

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Wed Dec 01, 2021 11:29 am

The impact of the Omicron variant on the UK is "highly uncertain" but may require a "very stringent response", government advisers have said.

The BBC has seen leaked minutes of a meeting of the Scientific Advisory Group for Emergencies held on Monday.

Officials should prepare now for a "potentially significant" wave of infections while data on the variant is collected and analysed, they say.

[...]

The minutes, which have not yet been published but have been seen by the BBC, say that it is "highly likely" that Omicron can escape immunity caused by previous infection or vaccination "to some extent".

The existing Delta variant is already more resistant to vaccines than the original version of the virus found in Wuhan.

The advisers say that there is not currently any evidence of widespread community transmission of Omicron in the UK, as there has been in parts of South Africa. They say the impact on a country like the UK remains uncertain as it is different in terms of age structure, the numbers previously infected with coronavirus and the level of vaccination coverage.

The scientists believe that booster jabs are likely to provide protection against severe disease, hospitalisation and death from most variants in the short term.

But they note: "Any significant reduction in protection against infection could still result in a very large wave of infections. This would in turn lead to a potentially high number of hospitalisations even with protection against severe disease being less affected."

Although the size of any future wave remains "highly uncertain", the scientists say it may be of a scale that requires "very stringent response measures" to avoid unsustainable pressure on the NHS.

The minutes make it clear that it is too early to know how ill the Omicron variant will make those infected or how that might vary by age. They say the first indications of the likely impact on vaccines should come from laboratory studies over the coming weeks.

But the advisers note: "It is important to be prepared for a potentially very significant wave of infections with associated hospitalisations now, ahead of data being available."

They say that the earlier measures to reduce transmission are introduced, the stronger they are and the wider their geographical coverage, the more effective they will be.

"The situation could develop quickly over the coming weeks and decision makers may need to act while there is a high level of uncertainty including the potential need for stringent response measures," they say.

In the minutes, scientists also say that pre-departure Covid testing for travellers returning to the UK would be "valuable" and the government's current policy of a single PCR test within two days of arrival will "identify significantly fewer cases" than an additional test on either day five or day eight.
https://www.bbc.com/news/health-59484322

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Re: B.1.1.529 Omicron variant

Post by shpalman » Wed Dec 01, 2021 11:50 am

Well at least they're finally doing their jobs instead of playing it down like the WHO and the South African doctor or whoever decided they had a couple of extra weeks right at the beginning or that it wasn't worth bothering with doing anything in particular about Delta over the summer.

I look forward to the results of testing everyone in the entire UK by PCR two days after this announcement and then on days 5 and 8 because I'm sure you'll find a lot more cases that way than by testing incoming travellers.
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Re: B.1.1.529 Omicron variant

Post by shpalman » Wed Dec 01, 2021 12:52 pm

(or worrying about whether the public would accept new rules, which nonsense led to the absurd idea of delaying the first lockdown so that it wouldn't need to be too long.)
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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Wed Dec 01, 2021 1:27 pm

There's been a suspected Omicron outbreak in Oslo. Someone travelled from South Africa to Norway (following all the rules), and later went to a work function involving 100 people. I assume it was a Christmas party, so probably lots of dancing, singing and talking loudly over the noise. The traveler later tested himself and got a positive result, and it looks like 30-40 others were infected (either that evening or through secondary contact over the following days).

Link in Norwegian but Google Translate is your friend:
https://www.vg.no/nyheter/innenriks/i/R ... nvarianten

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Re: B.1.1.529 Omicron variant

Post by Bird on a Fire » Wed Dec 01, 2021 2:49 pm

I'm supposed to be going to a conference tomorrow. Vaccine passport and recent test are both required, masks throughout and assigned, distanced seating etc etc.

Fingers crossed I guess.
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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Wed Dec 01, 2021 2:56 pm

Bird on a Fire wrote:
Wed Dec 01, 2021 2:49 pm
I'm supposed to be going to a conference tomorrow. Vaccine passport and recent test are both required, masks throughout and assigned, distanced seating etc etc.

Fingers crossed I guess.
You probably won't be infected. As far as I know you're young, healthy and vaccinated so if you are ill it will likely be mild or even asymptomatic. You should though be concerned about any vulnerable people you might meet later. To reduce risks to others you could get some rapid tests and check yourself every morning.

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Re: B.1.1.529 Omicron variant

Post by shpalman » Wed Dec 01, 2021 4:41 pm

Reuters has compiled a breakdown of where Omicron cases have been detected, and how many, by region:

Africa
Botswana 19
Ghana (unspecified number)
Mozambique 2
Nigeria 2
South Africa about 100 (reported on 26 Nov)

Americas
Brazil 3
Canada 7

Asia
Japan 2
South Korea 5

Europe
Austria 1
Denmark 5
Germany 4
Ireland 1
Italy 1
Netherlands 14
Norway 2
Portugal 13
Spain 2
Sweden 3
United Kingdom 22

Middle east
Saudi Arabia 1
from live blog

That "Italy 1" refers to one index case, obviously, because then he infected his family but they're all fine because they're all vaccinated.
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Re: B.1.1.529 Omicron variant

Post by lpm » Wed Dec 01, 2021 4:56 pm

Yes! The UK takes an early lead in the race! The EU is nowhere in comparison. We really are good at this.
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Re: B.1.1.529 Omicron variant

Post by shpalman » Wed Dec 01, 2021 5:35 pm

lpm wrote:
Wed Dec 01, 2021 4:56 pm
Yes! The UK takes an early lead in the race! The EU is nowhere in comparison. We really are good at this.
It's because of all that sequencing you do when you get around to it.
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Re: B.1.1.529 Omicron variant

Post by Sciolus » Wed Dec 01, 2021 6:02 pm

Per capita, Denmark, Portugal and Netherlands are well ahead.

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Wed Dec 01, 2021 6:21 pm

Woodchopper wrote:
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
Update by the excellent Trevor Bedford: https://twitter.com/trvrb/status/146607 ... 04453?s=21

tl;dr estimates that Rt in Gauteng for Omicron is 2-2.5 whereas for Delta it’s about 0.8 (Rt being a consequence of vaccination, natural immunity and NPIs like wearing masks and distancing).

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Wed Dec 01, 2021 9:43 pm

S.African data suggests Omicron gets around some, not all immunity

The Omicron variant appears able to get around some immunity but vaccines should still offer protection against severe disease, according to the latest data from South Africa where it is fast overtaking Delta to become the dominant variant.

[...]

Omicron accounted for 74% of the 249 virus genomes sequenced in South Africa in November, according to the National Institute for Communicable Diseases (NICD), which is collecting data as part of a wider national network for genomic surveillance.

South Africa conducts genome sequencing on only a small proportion of total samples collected each week. The NICD did not give a total number of confirmed cases of Omicron infection.

"(The) mutation profile and epidemiological picture suggests Omicron is able to get around some of our immune protection (to cause infection) but the protection against severe disease and death from vaccines should be less affected," the latest report from the surveillance network said.
https://www.reuters.com/world/africa/sa ... 021-12-01/

I haven't been able to find the original source though.

Some protection from vaccination is good. Though the key question is still how much.

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