New Variant Covid-19 VUI 202012/01

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Woodchopper
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New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sun Dec 20, 2020 6:26 pm

I thought this deserved its own thread.

Here’s a link to the NERVTAG briefing.
https://khub.net/documents/135939561/33 ... 8470511452
Four analytic approaches were reviewed regarding the transmissibility of VUI-202012/01 o Growth rate from genomic data:which suggest a growth rate of VUI-202012/01 that is 71% (95%CI: 67%-75%) higher than other variants.
o Studies of correlation between R-values and detection of the variant: which suggest an absolute increase in the R-value of between 0.39 to 0.93.
o PCR ct values: which suggest a decrease of ct value of around 2 associated with the new variant.
o Viral load inferred from number of unique genome reads: which suggests 0.5 increase in median log10 inferred viral load in Y501 versus N501.
• It was noted that variations in observed ct values can change with epidemiology since the stage of illness at which infection is detected can vary with incidence of cases, awareness of transmission, and the availability of tests.
• It was noted that VUI-202012/01 can be challenging to sequence so estimates of frequency of this variant may be underestimates.
• It was noted that whilst previous variants have successfully emerged in periods of low prevalence without clear evidence of having a selective advantage, the emergence and subsequent dominance of VUI-202012/01 in a period of relatively high prevalence suggests VUI-202012/01 does have a selective advantage over other variants.
• It was noted that VUI-202012/01 has demonstrated exponential growth during a period when national lockdown measures were in place.
• In summary, NERVTAG has moderate confidence that VUI-202012/01 demonstrates a substantial increase in transmissibility compared to other variants.
• NERVTAG concluded that there are currently insufficient data to draw any conclusion on:
o Underlying mechanism of increased transmissibility (e.g. increased viral load, tissue distribution of virus replication, serial interval etc)
o The age distribution of cases
o Disease severity: 4 deaths in around 1000 cases have been identified but further work is needed to compare this fatality rate with comparable data sets.
o Antigenic escape. The location of the mutations in the receptor binding domain of the spike glycoprotein raises the possibility that this variant is antigenically distinct from prior variants. Four probable reinfections have been identified amongst 915 subjects with this variant but further work is needed to compare this reinfection rate with comparable data sets.
• The committee discussed the geographic extent of spread of the variant:
o Within the UK, the variant is concentrated in the London, South East and East of England but has been detected in various parts of the UK.
o Few cases of this variant have been reported internationally but one confirmed export from the UK to Australia has been reported. It was noted that other countries have lower sequencing capability than the UK.

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Woodchopper
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sun Dec 20, 2020 6:31 pm

Much higher viral load seems to be the main issue. Though so far that hasn’t resulted in higher mortality.

Increased r by up to .93. f.ck.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sun Dec 20, 2020 6:55 pm

European Centre for Disease Prevention and Control

Threat Assessment Brief: Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom

https://www.ecdc.europa.eu/en/publicati ... ed-kingdom

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Re: New Variant Covid-19 VUI 202012/01

Post by jimbob » Sun Dec 20, 2020 7:13 pm

Woodchopper wrote:
Sun Dec 20, 2020 6:31 pm
Much higher viral load seems to be the main issue. Though so far that hasn’t resulted in higher mortality.

Increased r by up to .93. f.ck.
So why the f.ck are we not back into a full national lockdown? Johnson has an excuse for introducing one with the tier 4 arrangements, admittedly one that's wearing* thin, that the situation has changed.

*We didn't need to see the new variant to know that the November pseudo-lockdown with schools open wasn't working particularly well. And if you always take the most optimistic forecasts, you are going to fail many times.
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Sun Dec 20, 2020 7:19 pm

Woodchopper wrote:
Sun Dec 20, 2020 6:26 pm
• It was noted that VUI-202012/01 has demonstrated exponential growth during a period when national lockdown measures were in place.
What national lockdown measures? London was in tier 2 for some f.cking reason. And the more I read about things which aren't allowed anymore in tier 4 the more I'm shocked at what was still allowed in that "lockdown".
molto tricky

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Re: New Variant Covid-19 VUI 202012/01

Post by lpm » Sun Dec 20, 2020 7:25 pm

We've f.cked up haven't we.

Sorry world.
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 shpalman » Sun Dec 20, 2020 7:35 pm

it's already in Italy

And that's just the one that was found, presumably specifically looking at people having come from London recently.

Means it's probably all over the place by now.
molto tricky

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Woodchopper
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sun Dec 20, 2020 8:41 pm

35 928 UK cases reported today. Which is a new record.

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Re: New Variant Covid-19 VUI 202012/01

Post by discovolante » Sun Dec 20, 2020 9:08 pm

lpm wrote:
Sun Dec 20, 2020 7:25 pm
We've f.cked up haven't we.

Sorry world.
Yes it's fair to point out that the prime minister's responsibilities extend beyond the country's borders, especially in this context.
socialism is when the government does stuff

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Re: New Variant Covid-19 VUI 202012/01

Post by sTeamTraen » Sun Dec 20, 2020 9:52 pm

This shows up, once again, the utter folly of the herd immunity idea. The virus has the potential to mutate on every transmission (or of course, at every reproduction within someone's body), and it's completely to be expected that some of those mutations would be adaptive. More transmission, more mutations.

I don't know how bad this mutation is, but imagine one that brought about a substantial increase in mortality in the age group that we might denote by the range [Julia Hartley-Brewer < N < Allison Pearson]. They would be screaming blue f.cking murder about how nobody told them that this could happen, although they've been strutting around with their newly-minted PhDs in Amateur Epidemiology for the past year.

One bright spot, I suppose, is that Tier 4 continues to enjoy the same overwhelming popular support that every lockdown measure so far has done (and this has been repeated across all European countries that I've looked at). The "skeptics" are very much in the minority still.
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Re: New Variant Covid-19 VUI 202012/01

Post by Brightonian » Mon Dec 21, 2020 12:07 am

Some people on Twitter suggesting the government's announcement of the new strain was primarily a news management thing, and that countries are only imposing 48-hour travel bans to give them time to assess whether to take it seriously.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Mon Dec 21, 2020 5:59 am

Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations
https://virological.org/t/preliminary-g ... ations/563

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Mon Dec 21, 2020 6:02 am

COG-UK update on SARS-CoV-2 Spike mutations of special interest Report 1
https://www.cogconsortium.uk/wp-content ... ations.pdf

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Mon Dec 21, 2020 6:06 am

Mutant coronavirus in the United Kingdom sets off alarms but its importance remains unclear
https://www.sciencemag.org/news/2020/12 ... ns-unclear

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Mon Dec 21, 2020 7:04 am

In the above there’s surprise that so many genetic mutations could have appeared so quickly in a single variant. There’s a suggestion that they could have happened in a single person who had some kind of long term chronic Covid infection. I’ll speculate that perhaps it could also have been in a sub-population that weren’t getting tested and treated for whatever reason (hypothetically perhaps people who don’t believe that Covid is a severe public health problem).

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Mon Dec 21, 2020 7:14 am

Thread by virologist Trevor Bedford (gets to this variant half way through)
https://twitter.com/trvrb/status/134040 ... 71616?s=21

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Mon Dec 21, 2020 7:20 am

Analysis of genetics and comparison with the SA variant
https://twitter.com/firefoxx66/status/1 ... 61506?s=21

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Mon Dec 21, 2020 7:22 am

Thread on why it’s likely to be more transmissible (and not just luck and a founder effect). https://twitter.com/jcbarret/status/134 ... 72416?s=21

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Re: New Variant Covid-19 VUI 202012/01

Post by headshot » Mon Dec 21, 2020 7:44 am

Brightonian wrote:
Mon Dec 21, 2020 12:07 am
Some people on Twitter suggesting the government's announcement of the new strain was primarily a news management thing, and that countries are only imposing 48-hour travel bans to give them time to assess whether to take it seriously.
This freight ban makes no sense. There’s definitely more to it than fears of the new variant. Truck drivers taking freight back and forth aren’t going to have *that* many close contacts or be particularly big spreaders. (unless there’s a trucker sub-culture I’m entirely unaware of).

There’s zero chance a new variant first detected in Sept has not spread far and wide by now...so what gives?
Last edited by headshot on Mon Dec 21, 2020 7:45 am, edited 1 time in total.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Mon Dec 21, 2020 7:51 am


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Re: New Variant Covid-19 VUI 202012/01

Post by bob sterman » Mon Dec 21, 2020 8:01 am

Woodchopper wrote:
Mon Dec 21, 2020 7:22 am
Thread on why it’s likely to be more transmissible (and not just luck and a founder effect). https://twitter.com/jcbarret/status/134 ... 72416?s=21
As he notes - the alternative hypothesis is that...

"A lineage can get "lucky" and increase in frequency because it happened to be present in local circumstances that favour growth (e.g. poor compliance with social distancing)."

Well, a lineage couldn't get much more lucky than being present in a nation with one of the most useless track-and-trace systems in the world, during the consumerist frenzy that precedes Christmas, while the government was intent on relaxing as many restrictions as possible to "save Christmas".

I walked down a Tier 4 high street yesterday - it was packed and every other person was clutching a takeaway coffee. For this new variant all its Christmases come at once!

I don't think we can dismiss the alternative hypothesis just yet.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Mon Dec 21, 2020 9:02 am

headshot wrote:
Mon Dec 21, 2020 7:44 am
Brightonian wrote:
Mon Dec 21, 2020 12:07 am
Some people on Twitter suggesting the government's announcement of the new strain was primarily a news management thing, and that countries are only imposing 48-hour travel bans to give them time to assess whether to take it seriously.
This freight ban makes no sense. There’s definitely more to it than fears of the new variant. Truck drivers taking freight back and forth aren’t going to have *that* many close contacts or be particularly big spreaders. (unless there’s a trucker sub-culture I’m entirely unaware of).

There’s zero chance a new variant first detected in Sept has not spread far and wide by now...so what gives?
IMHO Macron doesn't want to be seen to have not done everything possible. He has an election in 18 months and the last thing he wants are accusations that his dithering let the Super Covid spread in France.

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Re: New Variant Covid-19 VUI 202012/01

Post by headshot » Mon Dec 21, 2020 9:05 am

Yes. It definitely seems to more of a politically motivated decision. Which is, of course, perfectly valid.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Mon Dec 21, 2020 9:10 am

headshot wrote:
Mon Dec 21, 2020 7:44 am

There’s zero chance a new variant first detected in Sept has not spread far and wide by now...
I agree. As far as I recall, only Denmark and the Netherlands have found it so far. But most places haven't been actively looking for it. The rest of the world will be lucky if it hasn't spread further already. But travel restrictions can slow the spread (eg ten people bringing it into a country rather than a hundred).

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Mon Dec 21, 2020 9:17 am

Woodchopper wrote:
Mon Dec 21, 2020 9:10 am
headshot wrote:
Mon Dec 21, 2020 7:44 am

There’s zero chance a new variant first detected in Sept has not spread far and wide by now...
I agree. As far as I recall, only Denmark and the Netherlands have found it so far. But most places haven't been actively looking for it. The rest of the world will be lucky if it hasn't spread further already. But travel restrictions can slow the spread (eg ten people bringing it into a country rather than a hundred).
Like I said somewhere, it was just found in an Italian returning from London to Rome who is already in isolation. I'm assuming that Rome Fiumicino does testing on arrival, because if he'd tested himself in the 72 hours before leaving England he should have resulted positive already and therefore not got on the flight at all.
molto tricky

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