B.1.1.529 Omicron variant

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Re: B.1.1.529 variant

Post by shpalman » Fri Nov 26, 2021 1:46 pm

Looks like it's already in Europe because of course it is.
A first case in Europe of the new variant of Covid-19 has been identified in Belgium in an unvaccinated young adult woman who developed mild flu-like symptoms 11 days after traveling to Egypt via Turkey.

The patient did not report any links with South Africa or other countries in southern Africa.
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Re: B.1.1.529 variant

Post by Woodchopper » Fri Nov 26, 2021 1:56 pm

Woodchopper wrote:
Fri Nov 26, 2021 12:14 pm
jimbob wrote:
Fri Nov 26, 2021 8:17 am
shpalman wrote:
Fri Nov 26, 2021 7:21 am
A tracker of new Nu variant news around the world: https://newsnodes.com/nu_tracker

Frankly it's probably all over the place already.
Yup

Prime Minister Naftali Bennett has said that Israel is “on the verge of an emergency, and I ask everyone to be fully prepared and harnessed for work around the clock” after a case of the South African B.1.1.529 coronavirus variant was discovered in Israel.
https://www.jpost.com/breaking-news/sou ... ael-687074

Belgium has detected the first case of the new coronavirus variant which was first found in South Africa, a virologist said on Friday.

Marc Van Ranst, whose laboratory works closely with Belgium's public health body Sciensano, said on Twitter that the variant was found in a traveller returning in Belgium from Egypt on Nov 11. The person developed the first symptoms on Nov. 22, the virologist said
https://www.reuters.com/business/health ... 021-11-26/

Kind of a long incubation period. Perhaps he caught it in Belgium.

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Re: B.1.1.529 variant

Post by Woodchopper » Fri Nov 26, 2021 3:32 pm


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Re: B.1.1.529 variant

Post by Woodchopper » Fri Nov 26, 2021 3:45 pm

Woodchopper wrote:
Fri Nov 26, 2021 3:02 am
Woodchopper wrote:
Thu Nov 25, 2021 11:00 pm
Detailed thread on the mutations: https://twitter.com/jcbarret/status/146 ... 97923?s=21
And another: https://twitter.com/jbloom_lab/status/1 ... 84705?s=21
And some more:
https://twitter.com/firefoxx66/status/1 ... 07491?s=21

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Re: B.1.1.529 variant

Post by jdc » Fri Nov 26, 2021 4:55 pm

Woodchopper wrote:
Fri Nov 26, 2021 3:32 pm
Good summary by some experts

https://www.sciencemediacentre.org/expe ... time-on-t/
A crumb of comfort in that loaf of doom:
B.1.1.529 is most unlikely to fully escape immunisation provided by vaccination and prior infection. The objective now should be to further increase vaccination rates, including administration of a third dose for anyone most at risk. With high vaccination rates and promising drugs on the horizon, a possible B.1.1.529 wave should be far less painful to weather than the alpha and delta ones
I'm going to calm myself by making this my mantra. I'll prob just do "unlikely to fully escape immunisation" as the whole thing is a bit long for a mantra, like.

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Re: B.1.1.529 variant

Post by nezumi » Fri Nov 26, 2021 5:13 pm

Not seen any mention of the world community helping South Africa blanket the area with vaccinations though. That would certainly be my first step.
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Re: B.1.1.529 variant

Post by jimbob » Fri Nov 26, 2021 5:37 pm

nezumi wrote:
Fri Nov 26, 2021 5:13 pm
Not seen any mention of the world community helping South Africa blanket the area with vaccinations though. That would certainly be my first step.
I have seen epidemiologists on Twitter asking for that.
Have you considered stupidity as an explanation

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Re: B.1.1.529 variant

Post by raven » Fri Nov 26, 2021 6:19 pm

What slightly concerns me is that a case has been picked up in Belgium, apparently with no connection to South Africa.

When I saw graphs of the recent meteoric rises in cases in Germany, Belgium, & eastern European countries, my first thought was 'new variant'. And compared to our roughly steady state -- well, Germany is only a couple of % points lower than us in vaccination coverage aren't they, which doesn't seem enough to account for the difference.

But I assume they do enough sequencing in those countries to have picked a variant up by now.

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Re: B.1.1.529 variant

Post by shpalman » Fri Nov 26, 2021 6:20 pm

raven wrote:
Fri Nov 26, 2021 6:19 pm
What slightly concerns me is that a case has been picked up in Belgium, apparently with no connection to South Africa.

When I saw graphs of the recent meteoric rises in cases in Germany, Belgium, & eastern European countries, my first thought was 'new variant'. And compared to our roughly steady state -- well, Germany is only a couple of % points lower than us in vaccination coverage aren't they, which doesn't seem enough to account for the difference.

But I assume they do enough sequencing in those countries to have picked a variant up by now.
I was wondering a similar thing. The UK does the most sequencing though, right?
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Re: B.1.1.529 variant

Post by Woodchopper » Fri Nov 26, 2021 6:21 pm

Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern
https://www.who.int/news/item/26-11-202 ... of-concern
This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant. Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.

There are a number of studies underway and the TAG-VE will continue to evaluate this variant. WHO will communicate new findings with Member States and to the public as needed.

Based on the evidence presented indicative of a detrimental change in COVID-19 epidemiology, the TAG-VE has advised WHO that this variant should be designated as a VOC, and the WHO has designated B.1.1.529 as a VOC, named Omicron.

As such, countries are asked to do the following:

enhance surveillance and sequencing efforts to better understand circulating SARS-CoV-2 variants.
submit complete genome sequences and associated metadata to a publicly available database, such as GISAID.
report initial cases/clusters associated with VOC infection to WHO through the IHR mechanism.
where capacity exists and in coordination with the international community, perform field investigations and laboratory assessments to improve understanding of the potential impacts of the VOC on COVID-19 epidemiology, severity, effectiveness of public health and social measures, diagnostic methods, immune responses, antibody neutralization, or other relevant characteristics.
Going straight to VoC and passing VoI does suggest that this is serious.

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Re: B.1.1.529 variant

Post by shpalman » Fri Nov 26, 2021 9:25 pm

I was today years old when I realized that omicron and omega mean "little o" and "big o".
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Re: B.1.1.529 variant

Post by Woodchopper » Fri Nov 26, 2021 9:53 pm

European CDC:

Implications of the emergence and spread of the SARS-CoV-2 B.1.1. 529 variant of concern (Omicron) for the EU/EEA
https://www.ecdc.europa.eu/sites/defaul ... ov2021.pdf

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Re: B.1.1.529 variant

Post by Martin_B » 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?
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Re: B.1.1.529 variant

Post by Woodchopper » Sat Nov 27, 2021 3:18 am

Woodchopper wrote:
Fri Nov 26, 2021 3:45 pm
Woodchopper wrote:
Fri Nov 26, 2021 3:02 am
Woodchopper wrote:
Thu Nov 25, 2021 11:00 pm
Detailed thread on the mutations: https://twitter.com/jcbarret/status/146 ... 97923?s=21
And another: https://twitter.com/jbloom_lab/status/1 ... 84705?s=21
And some more:
https://twitter.com/firefoxx66/status/1 ... 07491?s=21
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).

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Re: B.1.1.529 variant

Post by Woodchopper » Sat Nov 27, 2021 3:32 am

Possible evidence of community transmission in Belgium.
https://assets.uzleuven.be/files/2021-1 ... 211126.pdf
Over the last month, we identified 47 positive test results associated with both a Cq <26 and a SGTF [significant viral load and S gene dropout]. These samples were distributed over the last 23 days, with a higher frequency during the last week (Figure 6). These samples were analyzed in the 8 different federal platform laboratories.

[…]

These samples will be systematically investigated in the coming days.
And on the patient where it has been found:

The patient infected with B.1.1.529 is a young adult woman who developed symptoms 11 days after travelling to Egypt via Turkey. The patient had a high viral load at the time of diagnosis (Cq of 14,2) The patient did not report any link with South Africa or other Southern African countries. This patient had not previously been vaccinated and had not yet been infected. She developed flu-like symptoms, but does not present at this stage signs of severe disease.

The patient did not report high risk contacts outside her household. None of her household members have developed symptoms, but have nevertheless been referred for testing. An extended investigation will be launched.
I still think that with an 11 day incubation period she may have been infected in Belgium.

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Re: B.1.1.529 variant

Post by Woodchopper » Sat Nov 27, 2021 3:50 am

Chief executive of Pfizer claims that it’ll take 100 days for a new Omicron vaccine to be developed and get regulatory approval.
https://www.thetimes.co.uk/article/how- ... -dbnc5lmxm

Though production and rollout will obviously also take time.

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Sat Nov 27, 2021 4:35 am

Woodchopper wrote:
Sat Nov 27, 2021 3:50 am
Chief executive of Pfizer claims that it’ll take 100 days for a new Omicron vaccine to be developed and get regulatory approval.
https://www.thetimes.co.uk/article/how- ... -dbnc5lmxm

Though production and rollout will obviously also take time.
And from Moderna

Moderna will rapidly advance an Omicron-specific booster candidate (mRNA-1273.529). This candidate is part of the Company’s strategy to advance variant-specific candidates for a subset of variants of significant concern. During 2021 this has already included Beta- and Delta-specific boosters. The Company has repeatedly demonstrated the ability to advance new candidates to clinical testing in 60-90 days.
https://investors.modernatx.com/news-re ... ars-cov-2/

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Re: B.1.1.529 Omicron variant

Post by Brightonian » 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

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Re: B.1.1.529 Omicron variant

Post by Woodchopper » Sat Nov 27, 2021 7:01 am


Dutch health authorities said that dozens of people who arrived in Amsterdam on two flights from South Africa on Friday are likely infected with COVID-19, and they are conducting further testing to see if people are infected with the recently discovered Omicron coronavirus variant.

Around 600 passengers arrived at Amsterdam's Schiphol Airport on the two KLM flights on Friday and then faced hours of delays and testing due to concerns over thenew virus variant. On the basis of initial testing, the Dutch health ministry estimated there may be around 85 positive cases among the passengers.
https://www.reuters.com/world/europe/pa ... 021-11-26/

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Re: B.1.1.529 variant

Post by bob sterman » Sat Nov 27, 2021 7:50 am

Woodchopper wrote:
Sat Nov 27, 2021 3:32 am
I still think that with an 11 day incubation period she may have been infected in Belgium.
OR she was infected with B.1.1.529 abroad and the flu-like symptoms were caused by a different virus (e.g. influenza co-infection). The report from Belgium states that a young adult woman developed flu-like symptoms 11 days after travel but it doesn't state when or why she was tested.

With young people, particularly kids, where testing for co-infection does happen it's often found they are full of other things (e.g. rhinovirus, adenovirus, RSV, influenza) which complicates matching symptoms to causes and working out incubation periods.

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Re: B.1.1.529 Omicron variant

Post by shpalman » Sat Nov 27, 2021 7:59 am

Woodchopper wrote:
Sat Nov 27, 2021 7:01 am

Dutch health authorities said that dozens of people who arrived in Amsterdam on two flights from South Africa on Friday are likely infected with COVID-19, and they are conducting further testing to see if people are infected with the recently discovered Omicron coronavirus variant.

Around 600 passengers arrived at Amsterdam's Schiphol Airport on the two KLM flights on Friday and then faced hours of delays and testing due to concerns over thenew virus variant. On the basis of initial testing, the Dutch health ministry estimated there may be around 85 positive cases among the passengers.
https://www.reuters.com/world/europe/pa ... 021-11-26/
Many passengers on the two flights that arrived from South Africa to the Netherlands last night did not wear face coverings, New York Times reporter Stephanie Nolen says.

Nolen, who was on one plane, said many passengers did not follow the health guidelines despite a mask mandate by Dutch airline KLM, which operated both flights.

We now now that dozens of those passengers tested positive for Covid, although authorities have yet to confirm the presence of the Omicron variant.

Passengers were stuck on the airport tarmac for about four hours before being sent to be swabbed, tweeted Nolen, who later said she tested negative.

“... still probably 30% of ppl are wearing no mask or only over mouth. Dutch authorities not enforcing. We’re just all in this unventilated room at hour 12, breathing on each other,” she added.

“After all that time with maskless yellers in an unventilated space - we shall see what the next days bring.”
Guardian live blog
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Re: B.1.1.529 variant

Post by shpalman » Sat Nov 27, 2021 8:32 am

nezumi wrote:
Fri Nov 26, 2021 5:13 pm
Not seen any mention of the world community helping South Africa blanket the area with vaccinations though. That would certainly be my first step.
In November South Africa asked Johnson & Johnson and Pfizer to delay delivery of COVID-19 vaccines because it had too much stock.
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Re: B.1.1.529 variant

Post by Woodchopper » Sat Nov 27, 2021 8:58 am

bob sterman wrote:
Sat Nov 27, 2021 7:50 am
Woodchopper wrote:
Sat Nov 27, 2021 3:32 am
I still think that with an 11 day incubation period she may have been infected in Belgium.
OR she was infected with B.1.1.529 abroad and the flu-like symptoms were caused by a different virus (e.g. influenza co-infection). The report from Belgium states that a young adult woman developed flu-like symptoms 11 days after travel but it doesn't state when or why she was tested.

With young people, particularly kids, where testing for co-infection does happen it's often found they are full of other things (e.g. rhinovirus, adenovirus, RSV, influenza) which complicates matching symptoms to causes and working out incubation periods.
Yes, that could have happened.

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Re: B.1.1.529 variant

Post by Woodchopper » Sat Nov 27, 2021 9:00 am

shpalman wrote:
Sat Nov 27, 2021 8:32 am
nezumi wrote:
Fri Nov 26, 2021 5:13 pm
Not seen any mention of the world community helping South Africa blanket the area with vaccinations though. That would certainly be my first step.
In November South Africa asked Johnson & Johnson and Pfizer to delay delivery of COVID-19 vaccines because it had too much stock.
Yes, I was talking to a South African friend about it last week. The problem there isn’t lack of vaccines but that people don’t want them. Conspiracy theories are a major public health hazard there as well as in the US etc

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Re: B.1.1.529 variant

Post by Martin Y » Sat Nov 27, 2021 10:00 am

shpalman wrote:
Fri Nov 26, 2021 9:25 pm
I was today years old when I realized that omicron and omega mean "little o" and "big o".
Weird, isn't it? They have all this baggage of ancient history, wisdom, seriousness and solemnity and then you spot they're like something from play school.

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