New Variant Covid-19 VUI 202012/01

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 30, 2021 9:31 am

Transmission of SARS-CoV-2 variants in Switzerland
https://ispmbern.github.io/covid-19/variants/

SARS-CoV-2 Variants of Concern in Switzerland
https://ibz-shiny.ethz.ch/covidDashboar ... index.html

Similar story to everywhere else.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 30, 2021 9:36 am

On Denmark
Yes - @SSI_dk is estimating that Rt for B.1.1.7 is slightly above 1 (~1.1), while the Rt for non-B.1.1.7 is still below one (~0.8).
https://twitter.com/k_g_andersen/status ... 74273?s=21

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 30, 2021 9:38 am

Increased Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 to Antibody Neutralization

“ The recent emergence of B.1.1.7, B.1.351, and B.1.1.28 is a clear demonstration of SARS-CoV-2 antigenic drift. This conclusion is supported by data presented herein, illustrating how so many of these spike changes conferred resistance from antibody neutralization. Mutationally, this virus is traveling in a direction that could ultimately lead to escape from our current therapeutic and prophylactic interventions directed to the viral spike. If the rampant spread of the virus continues and more critical mutations accumulate, then we may be condemned to chasing after the evolving SARS-CoV-2 continually, as we have long done for influenza virus. Such considerations require that we stop virus transmission as quickly as is feasible, by redoubling our mitigation measures and by expediting vaccine rollout.”
https://www.biorxiv.org/content/10.1101 ... 2.full.pdf

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Tue Feb 02, 2021 12:43 pm

Monoclonal antibodies only work against one variant at a time

... because that's what "monoclonal" means?
molto tricky

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Feb 02, 2021 8:32 pm

Investigation of novel SARS-CoV-2 variant
Variant of Concern 202012/01
Technical briefing 5
https://assets.publishing.service.gov.u ... ngland.pdf

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Wed Feb 03, 2021 3:18 pm

Victorian health authorities are investigating how a hotel quarantine worker contracted coronavirus after they tested positive to the virus, because normally it's the other way around
a returned traveller in hotel quarantine had tested positive to the exact same UK variant of Covid as a family staying across the hall, with health authorities suspecting the viral load was “so high” it jumped across the corridor.
A family of five arrived on 20 January and they all tested positive on 23 January. A woman in another room across the hall then tested positive on 27 January. All were moved to health hotels designed for supporting positive cases.

Neville said the danger of community transmission was “exceptionally low” but authorities were still attempting to determine how the transmission occurred. CCTV footage showed there were no breaches of protocol by either guests or staff. Workers always wore personal protective equipment.
molto tricky

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Wed Feb 03, 2021 6:51 pm

Corzano is a small town in the province of Brescia. 10% of the inhabitants have the English covids

Even the mayor has it.

He's ordered the schools to stay closed until at least the 8th of February.
We have 140 positives and 60% of those are elementary school (ages 6-10 in Italy) and nursery school (ages 3-6) pupils* who have in turn infected their family members
Overall something like 20% of the positives in the province of Brescia are the variant, if I've read it right.
molto tricky

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Re: New Variant Covid-19 VUI 202012/01

Post by Martin Y » Thu Feb 04, 2021 10:11 am

In closer-to-home news, this morning's work team meeting included a request to inform our manager if any of us lives in one a list of 8 postcodes where urgent testing for the SA variant is beginning, after it popped up in cases with no direct link to SA. And an instruction for anyone thus affected not to travel to work until you get a negative PCR test. This on top of the lateral flow tests they're already using.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Thu Feb 04, 2021 5:21 pm

Danish scientists see tough times ahead as they watch more contagious COVID-19 virus surge

But B.1.1.7 still has an estimated R of 1.07; in other words, it’s growing exponentially. Meanwhile, the share of COVID-19 cases infected with the variant has increased from less than 0.5% in early December 2020 to 13% in late January.



https://www.sciencemag.org/news/2021/02 ... irus-surge

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Feb 06, 2021 8:31 am

UK coronavirus variant found in 74% of Slovak cases

Matovic told a news conference the government had checked all positive samples of PCR laboratory tests taken in the country on Wednesday and results showed 74% were the UK variant, a touch above the 71% in partial findings he had reported earlier on Friday.
https://www.reuters.com/article/us-heal ... SKBN2A52IJ

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Feb 06, 2021 8:52 am


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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Feb 06, 2021 8:32 pm


The Oxford/AstraZeneca Covid-19 vaccine does not appear to offer protection against mild and moderate disease caused by the viral variant first identified in South Africa, according to a study due to be published on Monday.

Although none of the more than 2,000 patients in the study died or was hospitalised, the findings could complicate the race to roll out vaccines as new strains emerge.

In both the human trials and tests on the blood of those vaccinated, the jab showed significantly reduced efficacy against the 501Y.V2 viral variant, which is dominant in South Africa, according to the randomised, double-blind study seen by the Financial Times.

A two-dose regimen of [the vaccine] did not show protection against mild-moderate Covid-19 due to [the South African variant]”, the study says, adding that efficacy against severe Covid-19, hospitalisations and deaths was not yet determined.

The so-called Kent variant — which Oxford university said on Friday was just as susceptible to the vaccine as older variants of the virus — has now acquired the E484K mutation, which is present in the variants fuelling Covid-19 surges in Brazil and South Africa.

There are caveats to the study, which has not yet been peer-reviewed, as the sample sizes were relatively small. The study, led by South Africa’s University of the Witwatersrand and Oxford university, enrolled 2,026 HIV negative individuals, with a median age of 31. Half the group was given at least one dose of placebo, with the other half receiving at least one dose of vaccine.

Tulio de Oliveira, who heads the Network for Genomic Surveillance in South Africa, told the Financial Times the findings were a “wake-up call to control the virus and increase the response to Covid-19 in the world”.
https://www.ft.com/content/e9bbd4fe-e6b ... 64140a3f36

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Sun Feb 07, 2021 1:57 pm

Woodchopper wrote:
Sat Feb 06, 2021 8:32 pm

The Oxford/AstraZeneca Covid-19 vaccine does not appear to offer protection against mild and moderate disease caused by the viral variant first identified in South Africa, according to a study due to be published on Monday.

Although none of the more than 2,000 patients in the study died or was hospitalised, the findings could complicate the race to roll out vaccines as new strains emerge.

In both the human trials and tests on the blood of those vaccinated, the jab showed significantly reduced efficacy against the 501Y.V2 viral variant, which is dominant in South Africa, according to the randomised, double-blind study seen by the Financial Times.

A two-dose regimen of [the vaccine] did not show protection against mild-moderate Covid-19 due to [the South African variant]”, the study says, adding that efficacy against severe Covid-19, hospitalisations and deaths was not yet determined.

The so-called Kent variant — which Oxford university said on Friday was just as susceptible to the vaccine as older variants of the virus — has now acquired the E484K mutation, which is present in the variants fuelling Covid-19 surges in Brazil and South Africa.

There are caveats to the study, which has not yet been peer-reviewed, as the sample sizes were relatively small. The study, led by South Africa’s University of the Witwatersrand and Oxford university, enrolled 2,026 HIV negative individuals, with a median age of 31. Half the group was given at least one dose of placebo, with the other half receiving at least one dose of vaccine.

Tulio de Oliveira, who heads the Network for Genomic Surveillance in South Africa, told the Financial Times the findings were a “wake-up call to control the virus and increase the response to Covid-19 in the world”.
https://www.ft.com/content/e9bbd4fe-e6b ... 64140a3f36
Means that you can't rely on herd immunity, but really do have to vaccinate everybody
molto tricky

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Mon Feb 08, 2021 9:17 am

shpalman wrote:
Sun Feb 07, 2021 1:57 pm
Woodchopper wrote:
Sat Feb 06, 2021 8:32 pm

The Oxford/AstraZeneca Covid-19 vaccine does not appear to offer protection against mild and moderate disease caused by the viral variant first identified in South Africa, according to a study due to be published on Monday.

Although none of the more than 2,000 patients in the study died or was hospitalised, the findings could complicate the race to roll out vaccines as new strains emerge.

In both the human trials and tests on the blood of those vaccinated, the jab showed significantly reduced efficacy against the 501Y.V2 viral variant, which is dominant in South Africa, according to the randomised, double-blind study seen by the Financial Times.

A two-dose regimen of [the vaccine] did not show protection against mild-moderate Covid-19 due to [the South African variant]”, the study says, adding that efficacy against severe Covid-19, hospitalisations and deaths was not yet determined.

The so-called Kent variant — which Oxford university said on Friday was just as susceptible to the vaccine as older variants of the virus — has now acquired the E484K mutation, which is present in the variants fuelling Covid-19 surges in Brazil and South Africa.

There are caveats to the study, which has not yet been peer-reviewed, as the sample sizes were relatively small. The study, led by South Africa’s University of the Witwatersrand and Oxford university, enrolled 2,026 HIV negative individuals, with a median age of 31. Half the group was given at least one dose of placebo, with the other half receiving at least one dose of vaccine.

Tulio de Oliveira, who heads the Network for Genomic Surveillance in South Africa, told the Financial Times the findings were a “wake-up call to control the virus and increase the response to Covid-19 in the world”.
https://www.ft.com/content/e9bbd4fe-e6b ... 64140a3f36
Means that you can't rely on herd immunity, but really do have to vaccinate everybody
Proper rather that live blog link: https://www.theguardian.com/society/202 ... d-immunity

So instead of trying to vaccinate everyone to achieve herd immunity, you should protect people from severe illness and death from covid by vaccinating them all.

In particular, I think it means you should concentrate on first vaccinating older people, people with comorbidities, and people at risk of heavy exposure (i.e. health care workers) rather than, erm, what was the UK's and indeed everyone's vaccination strategy so far?
molto tricky

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Mon Feb 08, 2021 9:20 am

Ok it might be a bit more subtle than that: use a highly efficacious vaccine for the most at-risk, even if limited amounts of it are available, because mass-vaccinating using a vaccine available in large numbers which isn't that efficacious is a bit of a waste of time. The latter strategy won't make much of a dent in transmission anyway and it won't protect the at-risk groups as much.
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Tue Feb 09, 2021 11:56 am

Our world-beating UK variant will protect us from the upstart SA variant
One way in which the Kent (B117) variant might help us vs SA variant... Both are more transmissible that older variants & so quickly become dominant.

BUT SA not more transmissible than Kent (we think) - so Kent, already dominant in UK, should stay dominant.

This is good because all vaccines work well against Kent (B117) & it doesn't seem to be re-infecting people who've already had covid.

But SA can re-infect people & evade (somewhat) AZ vax. Unknown is how that might help SA over time as it has more people it can spread to.
It's not like the Kent variant has been fighting with the wild type over the chance to infect people - without the Kent variant, there would have been fewer infections in the UK at this point* since the half-arsed restrictions in place worked ok against the wild type. They didn't work against the variant. So the variant hasn't "become dominant" against the wild type through direct competition, it has become dominant in the population since the restrictions worked to kill off the wild type.

The idea in these two tweets seems to be that the SA variant will have a hard time in the UK because people who are infected already are mainly infected with the UK variant... that's just... I can't even.

(And isn't already known that the SA variant can re-infect people who've had the wild type in the same way that it can evade vaccines? So it wouldn't even be true that "it's good to catch covid because then you won't catch covid".)

* - except there wouldn't be because the f.cking morons in charge would have ordered fewer restrictions, to keep the number of deaths up.

Also, I know that there's all sorts of variants and not just "wild type" vs. Kent variant vs. SA variant, but I'm using "wild type" to mean "not those two variants".
molto tricky

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Re: New Variant Covid-19 VUI 202012/01

Post by headshot » Tue Feb 09, 2021 12:23 pm

Look mate, our Patriotic Home-Grown Kent version will give this South African variant a good kicking and send it packing. The people of Kent survived the Blitz. They stuck two fingers up at Hitler from the top of the White Cliffs of Dover. The people of Margate won't let some poxy African virus infect them when they have a proper British virus they can get instead. That's what sovereignty's about mate. That's why we won the f.cking war mate.

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Tue Feb 09, 2021 6:03 pm

Four cases of a mutation of the more transmissible Kent variant were detected in two unconnected households in the Moss Side area of Manchester
There is no evidence that this variant will be resistant to the vaccines or causes a more severe illness, and it is not yet known if the strain can be passed more easily between people.
molto tricky

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Wed Feb 10, 2021 8:22 pm

Austria to isolate province in EU's worst outbreak of South African coronavirus variant
https://www.reuters.com/article/us-heal ... SKBN2A92JX

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Wed Feb 10, 2021 8:40 pm

Another report of the virus evolving during a long term infection of one person. This time for 154 days: https://www.wbur.org/hereandnow/2021/02 ... s-variants

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Wed Feb 10, 2021 8:52 pm

BMJ summary on the South African variant

Covid-19: The E484K mutation and the risks it poses
https://www.bmj.com/content/372/bmj.n359

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Re: New Variant Covid-19 VUI 202012/01

Post by hakwright » Thu Feb 11, 2021 1:24 pm

Woodchopper wrote:
Wed Feb 10, 2021 8:52 pm
BMJ summary on the South African variant

Covid-19: The E484K mutation and the risks it poses
https://www.bmj.com/content/372/bmj.n359
That's a really useful summary, I've been struggling to keep on top of the various mutations, variants and names used.

If I've understood correctly, the E484K mutation has evolved independently at least 4 separate times? Once in South Africa, once in Brazil, and twice in the UK (the article says testing has shown that both the more contagious "Kent variant" as well as the "original" SARS-CoV-2 virus have both evolved E484K mutations in the UK).

Given the article about Austria and the Tyrol, and the fact that they don't yet understand how the "South African variant" took hold there, it's possible this is a 5th independent evolution of the same mutation.

If we are to maintain a good understanding of how the virus spreads and evolves, we (and the media) will need to get much better at our terminology in referring to the various mutations and "variants".

Howard

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Feb 12, 2021 7:15 am

A SARS-CoV-2 lineage A variant (A.23.1) with altered spike has emerged and is dominating the current Uganda epidemic

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first detected in March 2020 in Uganda. Recently the epidemic showed a shift of SARS-CoV-2 variant distribution and we report here newly emerging A sub-lineages, A.23 and A.23.1, encoding replacements in the spike protein, nsp6, ORF8 and ORF9, with A.23.1 the major virus lineage now observed in Kampala. Although the clinical impact of the A.23.1 variant is not yet clear it is essential to continue careful monitoring of this variant, as well as rapid assessment of the consequences of the spike protein changes for vaccine efficacy.
https://www.medrxiv.org/content/10.1101 ... 21251393v1

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Re: New Variant Covid-19 VUI 202012/01

Post by lpm » Fri Feb 12, 2021 8:05 am

hakwright wrote:
Thu Feb 11, 2021 1:24 pm
Woodchopper wrote:
Wed Feb 10, 2021 8:52 pm
BMJ summary on the South African variant

Covid-19: The E484K mutation and the risks it poses
https://www.bmj.com/content/372/bmj.n359
That's a really useful summary, I've been struggling to keep on top of the various mutations, variants and names used.

If I've understood correctly, the E484K mutation has evolved independently at least 4 separate times? Once in South Africa, once in Brazil, and twice in the UK (the article says testing has shown that both the more contagious "Kent variant" as well as the "original" SARS-CoV-2 virus have both evolved E484K mutations in the UK).

Given the article about Austria and the Tyrol, and the fact that they don't yet understand how the "South African variant" took hold there, it's possible this is a 5th independent evolution of the same mutation.

If we are to maintain a good understanding of how the virus spreads and evolves, we (and the media) will need to get much better at our terminology in referring to the various mutations and "variants".

Howard
This number of repeats is a good thing, isn't it?

The virus keeps doing the same mutation path. Doesn't this show its evolution possibilities are very limited? It's not jumping randomly in all directions, which would give a huge range of risks, but it's constrained to a narrow set of options.

I'm thinking of a pinball game (does anyone play pinball these days?)

A tricky pinball machine would be highly chaotic. The ball would be flung about in crazy random ways by those cushion things, the ball could come at your flippers at any unpredictable direction or speed. An easy pinball machine would see the ball continually reverting to a couple of known pathways, usually reaching you from the same direction and speed.

Or is this too simplistic?
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Re: New Variant Covid-19 VUI 202012/01

Post by jdc » Fri Feb 12, 2021 5:50 pm

I'm fairly sure I saw the same point being made by An Expert a couple of weeks ago. Said if new strains kept appearing with e484k it would be convenient for vaccine mfrs as they wouldn't have to think about how to tweak their vaccines it'd be nice and obvious.

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