B.1.1.529 Omicron variant

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Sat Nov 27, 2021 10:01 am

“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.”

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.

[...]

“It’s a huge concern. We all are terribly concerned about this virus,” Professor Willem Hanekom, director of the Africa Health Research Institute, told The Associated Press.

“This variant is mostly in Gauteng province, the Johannesburg area of South Africa. But we’ve got clues from diagnostic tests ... that suggest that this variant is already all over South Africa,” said Hanekom, who is also co-chair of the South African COVID Variant Research Consortium.

“The scientific reaction from within South Africa is that we need to learn as much as soon as possible. We know precious little,” he said. “For example, we do not know how virulent this virus is, which means how bad is this disease that it causes?”

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.
https://apnews.com/article/coronavirus- ... a371792ab7

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Re: B.1.1.529 Omicron variant

Post by shpalman » Sat Nov 27, 2021 10:36 am

Woodchopper wrote:
Sat Nov 27, 2021 10:01 am
... The new variant appears to be spreading most quickly among those who are unvaccinated....
Well f.ck a doodle do.
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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Sat Nov 27, 2021 10:44 am

shpalman wrote:
Sat Nov 27, 2021 10:36 am
Woodchopper wrote:
Sat Nov 27, 2021 10:01 am
... The new variant appears to be spreading most quickly among those who are unvaccinated....
Well f.ck a doodle do.
Suggests that vaccination does provide protection. Which is good.

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Re: B.1.1.529 variant

Post by lpm » Sat Nov 27, 2021 11:33 am

Woodchopper wrote:
Sat Nov 27, 2021 3:18 am
And another by the excellent Trevor Bedford: https://twitter.com/trvrb/status/146435 ... 25066?s=21

Recommend, highlights include that Omicron is descended from viruses that were last seen circulating in mid-2020, and so has either been circulating since then in an area where there isn’t genomic surveillance (not South Africa) or in a single individual. And:
median estimate of exponential doubling time of 4.8 days (95% CI between 2.6 and 8.7 days).
That is very interesting.

Trevor Bedford has to behave and not jump to unsupported conclusions. But we're free to be over conclusive on too little evidence.

This variant is the result of HIV.

No way can this variant have been circulating since mid-2020 in an unknown community. It matches Delta for pace or even beats it, so if it had been circulating it would have emerged from its little untested village and reached every corner of the world months ago.

It has to be a single individual. He or she was infected in May 2020 and has been struggling with permanent infection ever since. The virus kept churning over mutations day after day, some of which survived and prospered. This explains the absence of any side branches between May 2020 and October 2021 - just a long straight line.

Omicron then emerged from this individual in a single instance a month or two ago, probably in Gauteng somewhere, spread as fast as Delta, and started loads of minor variants in the thousands of new cases.

The individual must surely have immune deficiencies. It's no surprise variants are coming out of southern Africa - the awful burden of HIV cases doesn't just leave millions with immunity problems, it also over burdens the healthcare systems and suppresses the economy to make Covid detection unaffordable. This individual will have probably have had waves of acute Covid illness, interspersed with better periods where the virus was only partially held in check, and probably other illnesses to go with it. Lack of healthcare for the poor in Africa leads directly to the entire world getting hit. The health inequalities of 30 and 40 years ago and the focus on producing drugs for the rich has come back to haunt us - and obviously we are making exactly the same mistakes right now.
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Re: B.1.1.529 Omicron variant

Post by jimbob » Sat Nov 27, 2021 11:50 am

Brightonian wrote:
Sat Nov 27, 2021 6:44 am
Someone on Twitter claiming his mate in Bootle has tested positive for Omicron. Others doubt the story.
https://twitter.com/Marklovesfoods/stat ... 4299048960
He's not very convincing.
Have you considered stupidity as an explanation

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Re: B.1.1.529 variant

Post by Lydia Gwilt » Sat Nov 27, 2021 12:05 pm

Martin_B wrote:
Fri Nov 26, 2021 10:31 pm
Lydia Gwilt wrote:
Fri Nov 26, 2021 9:53 am
Woodchopper wrote:
Thu Nov 25, 2021 4:58 pm
Dramatic thread by Tulio de Olivera:
https://twitter.com/tuliodna/status/146 ... 60130?s=21

If you haven’t been following him over the past couple of years he’s South Africa’s leading virologist.
According to himself! He's also a smug self-publicising loose cannon.
He started a baseless panic in the summer that led to more than a million doses of perfectly good vaccine being trashed, and put back the SA vaccination programme by at least 6 months ( who knows how many people died as a result) - as a result of misinterpreting sequence data and going straight to the press, before discussing it with public health or anyone else. If you mention this to him he is completely unrepentant.

He's done the same with this, there was a slight rise in cases in Gauteng province, he sequenced 2000 samples of which 22 were this new variant - 0.1% so most unlikely to be the cause of the rise. His first port of call was the press - international panic, 6 southern African countries completely blocked and economies well on the way to being trashed again. Well done, de Olivera!
22 of 2000 would be 1.1%, not 0.1%, wouldn't it?
You are quite right, my bad. And I also made two other errors - a) there were many more than 2000 sequenced to find the 22; b) he didn't misinterpret sequence data but overinterpreted one plaque assay to cause the vaccine panic in the summer. He is not really a virologist, he is a sequencer.

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Re: B.1.1.529 variant

Post by Woodchopper » Sat Nov 27, 2021 12:13 pm

lpm wrote:
Sat Nov 27, 2021 11:33 am
Woodchopper wrote:
Sat Nov 27, 2021 3:18 am
And another by the excellent Trevor Bedford: https://twitter.com/trvrb/status/146435 ... 25066?s=21

Recommend, highlights include that Omicron is descended from viruses that were last seen circulating in mid-2020, and so has either been circulating since then in an area where there isn’t genomic surveillance (not South Africa) or in a single individual. And:
median estimate of exponential doubling time of 4.8 days (95% CI between 2.6 and 8.7 days).
That is very interesting.

Trevor Bedford has to behave and not jump to unsupported conclusions. But we're free to be over conclusive on too little evidence.

This variant is the result of HIV.

No way can this variant have been circulating since mid-2020 in an unknown community. It matches Delta for pace or even beats it, so if it had been circulating it would have emerged from its little untested village and reached every corner of the world months ago.

It has to be a single individual. He or she was infected in May 2020 and has been struggling with permanent infection ever since. The virus kept churning over mutations day after day, some of which survived and prospered. This explains the absence of any side branches between May 2020 and October 2021 - just a long straight line.

Omicron then emerged from this individual in a single instance a month or two ago, probably in Gauteng somewhere, spread as fast as Delta, and started loads of minor variants in the thousands of new cases.

The individual must surely have immune deficiencies. It's no surprise variants are coming out of southern Africa - the awful burden of HIV cases doesn't just leave millions with immunity problems, it also over burdens the healthcare systems and suppresses the economy to make Covid detection unaffordable. This individual will have probably have had waves of acute Covid illness, interspersed with better periods where the virus was only partially held in check, and probably other illnesses to go with it. Lack of healthcare for the poor in Africa leads directly to the entire world getting hit. The health inequalities of 30 and 40 years ago and the focus on producing drugs for the rich has come back to haunt us - and obviously we are making exactly the same mistakes right now.
That is a plausible hypothesis. I think that if that happened the AIDS patient may not have been in South Africa. We are looking there because they have the surveillance capacity to find it.

Other probably less plausible hypotheses that come to mind are firstly that it was circulating in a very remote part of Africa. But that wouldn’t explain the large number of mutations, and Africa isn’t that remote. For example people still go to markets.

Secondly, could the mutations have occurred in an animal population? We know that Covid infects animals. But I don’t know whether Omicron is consistent with that having happened.

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Sat Nov 27, 2021 12:24 pm

On the Hong Kong cases:

We know a lot about the Hong Kong cases because of their impeccable contact tracing. Health authorities published a report of these two cases yesterday.

The first case in Hong Kong was a 36 year old, fully vaccinated (two Pfizer doses in May/June 2021) male. He was traveling through South Africa from October 22 to November 11. Before returning to Hong Kong, he tested negative on a PCR. As per usual, once he landed in Hong Kong he was required to quarantine. On day 4 of quarantine (November 13), he tested positive on a PCR.

Another guest across the hallway was also infected with B.1.1.529. He was Pfizer vaccinated in May/June 2021 too. In both of these rooms, 25 out of 87 swabs were positive for the virus.

These Hong Kong cases tell us two things:

Confirms that COVID19 is airborne (we knew this)

During their PCR tests, the viral loads were VERY high considering they were negative on previous PCR tests. They had a Ct value of 18 and 19 value. So, this tell us that B.1.1.529 is likely highly contagious.
https://yourlocalepidemiologist.substac ... ant-b11529

Of course we should be wary of reading too much from two cases.

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Re: B.1.1.529 Omicron variant

Post by lpm » Sat Nov 27, 2021 2:07 pm

Two cases found in Britain.

Which implies twenty cases already here? Two hundred? Two thousand? What multiple should we guess at?
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Re: B.1.1.529 Omicron variant

Post by shpalman » Sat Nov 27, 2021 3:11 pm

lpm wrote:
Sat Nov 27, 2021 2:07 pm
Two cases found in Britain.

Which implies twenty cases already here? Two hundred? Two thousand? What multiple should we guess at?
Well luckily thanks to your vaccination program plus the general use of masks indoors and vaccination/recovery/negativity protocols for crowded indoor events you don't have that many cases so you'll be able to effectively trace contacts and sequence a substantial proportion of the positives.

And since you weren't trying to be sure of killing 1000 people per week your hospitals aren't too stretched so you'll be able to cope for the 3-4 weeks over which hospitalizations will keep rising even after the lockdown you'll quickly implement to keep this under control.
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Re: B.1.1.529 Omicron variant

Post by dyqik » Sat Nov 27, 2021 3:39 pm

The US not stopping travelers from SA until Monday is looking a bit slow

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Re: B.1.1.529 Omicron variant

Post by lpm » Sat Nov 27, 2021 3:52 pm

Travel bans never worked and won't this time. Buy a bit of time, but for what? It's not like March 2021 or something, when buying a couple of weeks allowed 1 million extra vaccinations.
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Re: B.1.1.529 Omicron variant

Post by lpm » Sat Nov 27, 2021 3:56 pm

shpalman wrote:
Sat Nov 27, 2021 3:11 pm
lpm wrote:
Sat Nov 27, 2021 2:07 pm
Two cases found in Britain.

Which implies twenty cases already here? Two hundred? Two thousand? What multiple should we guess at?
Well luckily thanks to your vaccination program plus the general use of masks indoors and vaccination/recovery/negativity protocols for crowded indoor events you don't have that many cases so you'll be able to effectively trace contacts and sequence a substantial proportion of the positives.

And since you weren't trying to be sure of killing 1000 people per week your hospitals aren't too stretched so you'll be able to cope for the 3-4 weeks over which hospitalizations will keep rising even after the lockdown you'll quickly implement to keep this under control.
The UK plan was clearly to get a high case load to October, then hope immunity levels high enough to cut hospital numbers across November. Go into flu season with a falling hospitalisation rate.

That has obviously failed. We're at risk of flu+Covid crushing the NHS. It's not clear what flu is doing so far, though. Any reports from any countries?

The big threat to the UK is probably still flu not Omicron. Delta's done so well in infecting and killing there's not much room for Omicron to add anything - unless it has a changed aged profile in how it kills.
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Re: B.1.1.529 Omicron variant

Post by bob sterman » Sat Nov 27, 2021 4:11 pm

In the original an alien takes over the body of an Earthman in order to learn about the planet so his race can take it over.

Image

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Re: B.1.1.529 Omicron variant

Post by dyqik » Sat Nov 27, 2021 4:29 pm

lpm wrote:
Sat Nov 27, 2021 3:52 pm
Travel bans never worked and won't this time. Buy a bit of time, but for what? It's not like March 2021 or something, when buying a couple of weeks allowed 1 million extra vaccinations.
They buy a bit of time to evaluate.

But reacting to a rapidly rising variant/event with a travel ban that starts half a week later doesn't even do that.

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Re: B.1.1.529 Omicron variant

Post by lpm » Sat Nov 27, 2021 4:57 pm

A few days won't make any difference. Omicron was in Britain, and almost certainly in the US, days before Woodchopper even started this thread.

In March 2020 the question "have you travelled recently from Wuhan" was asked in the US and UK long after local community transmission was established.
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Re: B.1.1.529 Omicron variant

Post by lpm » Sat Nov 27, 2021 5:07 pm

Johnson announcement:

- 10 days isolation for all contacts of identified Omicron cases
- tightened face mask rules
- "boost the booster campaign", speeding up and reducing gap from 2nd vax

No work from home guidance, so only a bit of Plan B.
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Re: B.1.1.529 Omicron variant

Post by shpalman » Sat Nov 27, 2021 5:19 pm

lpm wrote:
Sat Nov 27, 2021 5:07 pm
Johnson announcement:

- 10 days isolation for all contacts of identified Omicron cases
- tightened face mask rules
- "boost the booster campaign", speeding up and reducing gap from 2nd vax

No work from home guidance, so only a bit of Plan B.
International arrivals have to take a PCR test by the second day of their arrival and self-isolate until they have a negative result.
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 shpalman » Sat Nov 27, 2021 5:30 pm

lpm wrote:
Sat Nov 27, 2021 5:07 pm
Johnson announcement:

- 10 days isolation for all contacts of identified Omicron cases
- tightened face mask rules
- "boost the booster campaign", speeding up and reducing gap from 2nd vax

No work from home guidance, so only a bit of Plan B.
No need to be more Plan B about it apparently because Omicron is different to Delta or something.
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Re: B.1.1.529 Omicron variant

Post by lpm » Sat Nov 27, 2021 5:49 pm

The logic should be:

Omicron could reduce vaccine effectiveness against hospitalisations a bit - therefore hospitalisations would rise once it spreads - therefore get the Delta hospitalisation rate down now to build some breathing space - therefore all of Plan B and consider further measures just in case.

The actual logic applied is SAVE CHRISTMAS THAT IS THE ONLY THING WE MUST DO SAVE CHRISTMAS SAVE CHRISTMAS SAVE CHRISTMAS.
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Re: B.1.1.529 Omicron variant

Post by Stranger Mouse » Sat Nov 27, 2021 5:59 pm

lpm wrote:
Sat Nov 27, 2021 5:49 pm
The logic should be:

Omicron could reduce vaccine effectiveness against hospitalisations a bit - therefore hospitalisations would rise once it spreads - therefore get the Delta hospitalisation rate down now to build some breathing space - therefore all of Plan B and consider further measures just in case.

The actual logic applied is SAVE CHRISTMAS THAT IS THE ONLY THING WE MUST DO SAVE CHRISTMAS SAVE CHRISTMAS SAVE CHRISTMAS.
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Re: B.1.1.529 Omicron variant

Post by Martin Y » Sat Nov 27, 2021 6:03 pm

I see the "dozens are likely infected" on those flights from SA held at Schipol has now become "yup, dozens are infected".

About 60-odd from 600, though no info on variants involved as yet.

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Re: B.1.1.529 Omicron variant

Post by bob sterman » Sat Nov 27, 2021 6:41 pm

shpalman wrote:
Sat Nov 27, 2021 5:19 pm
lpm wrote:
Sat Nov 27, 2021 5:07 pm
Johnson announcement:

- 10 days isolation for all contacts of identified Omicron cases
- tightened face mask rules
- "boost the booster campaign", speeding up and reducing gap from 2nd vax

No work from home guidance, so only a bit of Plan B.
International arrivals have to take a PCR test by the second day of their arrival and self-isolate until they have a negative result.
After they've travelled home from Heathrow through London on the tube.

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Re: B.1.1.529 Omicron variant

Post by shpalman » Sat Nov 27, 2021 6:50 pm

bob sterman wrote:
Sat Nov 27, 2021 6:41 pm
shpalman wrote:
Sat Nov 27, 2021 5:19 pm
lpm wrote:
Sat Nov 27, 2021 5:07 pm
Johnson announcement:

- 10 days isolation for all contacts of identified Omicron cases
- tightened face mask rules
- "boost the booster campaign", speeding up and reducing gap from 2nd vax

No work from home guidance, so only a bit of Plan B.
International arrivals have to take a PCR test by the second day of their arrival and self-isolate until they have a negative result.
After they've travelled home from Heathrow through London on the tube.
True, they're far more likely to catch it on the tube.
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Re: B.1.1.529 Omicron variant

Post by bob sterman » Sat Nov 27, 2021 7:06 pm

shpalman wrote:
Sat Nov 27, 2021 6:50 pm
bob sterman wrote:
Sat Nov 27, 2021 6:41 pm
shpalman wrote:
Sat Nov 27, 2021 5:19 pm

International arrivals have to take a PCR test by the second day of their arrival and self-isolate until they have a negative result.
After they've travelled home from Heathrow through London on the tube.
True, they're far more likely to catch it on the tube.
Perhaps - and we may be getting to a point where the Omicron incubation period is shorter than the international arrival queue times at Heathrow. So community transmission may get established in the arrivals hall.

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