Covid Mutations

[elbows]

By the way I note that the mobility data shown in that paper for the recent national measures period (shaded period) isnt exactly showing impressive behaviour, there was a fair amount of bounce back.

 

[2hats]

Essentially the new variant is modelled to be 56% [50-74 CI] more transmissible and the preprint basically says we need a full lockdown (tier 4+) with all educational establishments closed for 6 weeks or more, twinned with an aggressive vaccination programme (2M/wk) to avoid ICU saturation and keep additional deaths down to 30-something K.

 

[weltweit]

Essentially the new variant is modelled to be 56% [50-74 CI] more transmissible and the preprint basically says we need a full lockdown (tier 4+) with all educational establishments closed for 6 weeks or more, twinned with an aggressive vaccination programme (2M/wk) to avoid ICU saturation and keep additional deaths down to 30-something K.

Hmm, it isn't good news ..

 

[elbows]

Essentially the new variant is modelled to be 56% [50-74 CI] more transmissible and the preprint basically says we need a full lockdown (tier 4+) with all educational establishments closed for 6 weeks or more, twinned with an aggressive vaccination programme (2M/wk) to avoid ICU saturation and keep additional deaths down to 30-something K.

And as is usual with these sorts of papers and modelling exercises, they've modelled one period of lockdown of particular duration. If the sort of vaccination levels they suggest are necessary to have a big impact arent achieved, there is of course the possibility of 'lockdowns' lasting longer or being repeated, as an alternative way to keep various levels below the amounts they are trying to avoid reaching. But politically everyone seems to want solutions that dont involve an obvious repeat of draconian measures again later, they want to hear that this is the last time we'll need to go that far. I'm not complaining that they have not included such repeat scenarios in their work here, but when it is not mentioned I keep feeling the need to mention it as an obvious alternative possibility that we may end up having to live through.

Also not unusually they end up saying a couple of things that can play into the hands of those who want an excuse to delay or soften certain things, with warnings about the strongest measures leading to the biggest bounce back in areas relatively unscathed so far, and other aspects of wave timing in different regions that the authorities may be keen to avoid.

We found that regardless of control measures simulated, all NHS regions are projected to experience a subsequent wave of COVID-19 cases and deaths, peaking in spring 2021 for London, South East and East of England, and in summer 2021 for the rest of England (Fig. 4). In the absence of substantial vaccine roll-out, cases, hospitalisations, ICU admissions and deaths in 2021 may exceed those in 2020 (Table 1). School closures in January 2021 may delay the peak (Fig. 4) and decrease the total burden in the short term. However, implementation of more stringent measures now with a subsequent lifting of these restrictions in February 2021 leads to a bigger rebound in cases, particularly in those regions that have been least affected so far (Fig. 4 and Table 1). However, these delaying measures may buy time to reach more widespread population immunity through vaccination. Vaccine roll-out will further mitigate transmission, although the impact of vaccinating 200,000 people per week—similar in magnitude to the rates reached in December 2020—may be relatively small (Fig. 5). An accelerated uptake of 2 million people vaccinated per week is predicted to have a much more substantial impact. The most stringent intervention scenario with Tier 4 England-wide and schools closed during January, and 2 million individuals vaccinated per week, is the only scenario we considered which reduces peak ICU burden below the levels seen during the first wave.

 

[2hats]

Obvious question: what's the estimated transmissibility of 501.V2 ..? (Haven't been able to find a figure in the literature yet).

 

[elbows]

Part of a thread about differences in genome surveillance & reporting differences between USA and UK had some interesting info in about the lag.

 

[frogwoman]

On the latter point how do 'herd immunity' proponents explain that Brazil and Mexico which had almost uncontrolled COVID-19 epidemics earlier this year are now seeing a resurgence of cases and deaths?

 

[2hats]

Just to mention that a separate 501Y mutation has been picked up in Wales (blue line lower right) which differs from the 501Y in the SE (VOC-202012/01 aka 501Y.V1 - the lime green line underneath, far lower right) at a number of positions, in particular it is missing the 69/70 double deletion. Currently being analysed but not of as great a concern as does not seem to be as transmissible as either 501Y.V1 or 501.V2 (may indeed, as a result, provide insight to the advantages conferred on those two by the differences).

 

[elbows]

This is what the UK variant news caused the European Centre for Disease Control to come out with a few days ago. I do like to take an occasional look at the pandemic from their angle, especially as despite the UK press rarely if ever mentioning it, we have still been a part of this institution during the brexit transition phase.

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

 

[William of Walworth]

I've only just become aware of this thread, embarassingly , but even for the scientifically-challenged (moi! ) these posts have been pretty informative.
Some good links to mentions of my own area of interest, vaccine efficacy -- thanks 2hats !

For accessible summaries about the Covid variant, I thought this (below) was well worth a look (the below is my post #28,000 on the Covid UK thread -- apologies for cross-posting) :

I think it's one of those 'the hope that gets you' scenarios.
When the vaccine was approved, few people thought 'that's it, game over'.
But it did add the idea that there was a way out. The real worry now is the vaccines don't work or work as well I suppose.

There's a little bit on this vaccine question, and much more else about the new strain more generally, in today's Guardian piece by Sharon Peacock-- IMO it's pretty good, detailed, and explanatory.

Here's what we know about the new variant of coronavirus
My team at the Genomics UK consortium sequenced the new Sars-CoV-2 variant, but we’ll need more evidence to understand how it might change the pandemic

It was always predictable that the genome of Sars-CoV-2 would mutate. After all, that’s what viruses and other micro-organisms do. The Sars-CoV-2 genome accumulates around one or two mutations every month as it circulates. In fact, its rate of change is much lower than those of other viruses that we know about. For example, seasonal influenza mutates at such a rate that a new vaccine has to be introduced each year.
Even so, over time the virus population will accumulate a fair few mutations in different combinations. The striking feature of the Sars-CoV-2 lineage 1.1.7 that we discovered here at the Covid-19 Genomics UK Consortium (familiar now from headlines as the “new variant”), is that its genome has a large number of mutations compared with other lineages we’ve picked up in the UK. It has a total of 23, which is what sets it apart.

Also, just a small bit about possible vaccine resistance of the neww strain -- reassuring, I thought :

There is currently no evidence that lineage 1.1.7 causes more severe disease or that it evades the immune system. There is also no reason to think that the vaccines being rolled out or under development will be less effective against it. But what does look increasingly likely is that this lineage is more transmissible.

I know there's also been other scientists discussing the risk of vaccine resistance already, and in more detail.
Maybe others have relevant links? (I think 2hats posted a link earlier up??) ....... cheers

What I've seen has been all 'what's known so far' stuff, but I haven't yet seen any piece being really pessimistic about vaccine efficacy declines with the new strain ...
I said so far!

 

[2hats]

This is what the UK variant news caused the European Centre for Disease Control to come out with a few days ago. I do like to take an occasional look at the pandemic from their angle, especially as despite the UK press rarely if ever mentioning it, we have still been a part of this institution during the brexit transition phase.

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

Relevant to the LSHTM Davies paper from the above consider:

and from the ONS:

in the light of this commentary...

 

[LDC]

Oh shitting hell. That's not a cheerful read at all.

 

[Supine]

Oh shitting hell. That's not a cheerful read at all.

Happy Christmas

 

[Hyperdark]

Oh shitting hell. That's not a cheerful read at all.

Its also very speculative and alarmist

 

[LDC]

Its also very speculative and alarmist

What are your qualifications and background to dismiss it out of hand?

 

[William of Walworth]

Relevant to the LSHTM Davies paper from the above consider:
View attachment 245038
and from the ONS:
View attachment 245039
in the light of this commentary...

From that last link (I clicled Bill Hanage's Twitter and it went straight to a PDF of the paper), this is what jumped out at me (the rest was too technical for me really ).

Our estimates suggest that control measures of a similar stringency to the
national lockdown implemented in England in November 2020 are unlikely to reduce the
effective reproduction number R t to less than 1, unless primary schools, secondary schools,
and universities are also closed. We project that large resurgences of the virus are likely to
occur following easing of control measures. It may be necessary to greatly accelerate vaccine
roll-out to have an appreciable impact in suppressing the resulting disease burden.

 

[2hats]

The precursor work for this (prior to new variant analysis) has been peer reviewed and published.

Association of tiered restrictions and a second lockdown with COVID-19 deaths and hospital admissions in England: a modelling study

A second wave of COVID-19 cases in autumn, 2020, in England led to localised, tiered restrictions (so-called alert levels) and, subsequently, a second…

www.sciencedirect.com

 

[teuchter]

" It may be necessary to greatly accelerate vaccine roll-out to have an appreciable impact in suppressing the resulting disease burden."

This statement suggests that rolling out the vaccine more quickly than currently planned, is an option. If it is, why aren't we doing it anyway?

 

[Hyperdark]

What are your qualifications and background to dismiss it out of hand?

I didnt, I exhibited a tempered point of view IMO the piece needs examining before crying 'Oh Shitting Hell'

 

[2hats]

Move the immunocompromised up the vaccine priority list.

Here’s a Plan to Stop the Coronavirus From Mutating

Prioritize people who are immunocompromised for early vaccination.

www.wired.com

 

[LDC]

I didnt, I exhibited a tempered point of view IMO the piece needs examining before crying 'Oh Shitting Hell'

No, you said it was 'alarmist', which isn't a tempered point of view. Anyway, I'll take what they say as possible models to think about over your complete lack of knowledge thanks.

 

[2hats]

New phylogenies of B.1.1.7 lineage samples from Denmark exhibit multiple additional mutations as well as sharing a mutation. Likewise for new B.1.1.7 samples in the Netherlands. This suggests an introduction followed by onward (community) transmission in each country.

 

[prunus]

New phylogenies of B.1.1.7 lineage samples from Denmark exhibit multiple additional mutations as well as sharing a mutation. Likewise for new B.1.1.7 samples in the Netherlands. This suggests an introduction followed by onward (community) transmission in each country.

Thank you for the continued information on this - may I ask where you’re getting it? You always seem to be first with the molecular phylogeny news.

 

[2hats]

Thank you for the continued information on this - may I ask where you’re getting it? You always seem to be first with the molecular phylogeny news.

It's just been uploaded to the Nextstrain database. Emma Hodcroft mentioned it.

PS Forgot to mention, also now reported in Ireland.

 

[Mation]

Another way that transmission could be increased by a mutation (although am not saying this is the case with this one, I don't have enough info and it doesn't seem to be the case) would be if the infection made people sneeze more than other strains - that sprays a large area at a time. I don't think that is necessarily the case with this one though, if it still has a higher transmission rate even when people aren't exhibiting symptoms.

Not data not data not data:

Most recent colleague to test positive was sneezing loads the day before he got properly ill.

Still not data. And there's no info yet on whether anyone around him has come down with it.

Worth keeping a small eye out for it though.

 

[muscovyduck]

Not data not data not data:

Most recent colleague to test positive was sneezing loads the day before he got properly ill.

Still not data. And there's no info yet on whether anyone around him has come down with it.

Worth keeping a small eye out for it though.

Could you have covid, also have something (like a dust allergy) that makes you sneeze, but then that sneeze not caused by covid could still transfer it? It's stuff like this I'm struggling to get my head around, I got confused earlier after so long and thought raw meat could contaminate other food via air alone

 

[2hats]

Obvious question: what's the estimated transmissibility of 501.V2 ..? (Haven't been able to find a figure in the literature yet).

To 'far from satisfactorily' answer this question I find this counter-claim. Obviously would like to see some modelling from the research group(s) concerned.

 

[Mation]

Could you have covid, also have something (like a dust allergy) that makes you sneeze, but then that sneeze not caused by covid could still transfer it? It's stuff like this I'm struggling to get my head around, I got confused earlier after so long and thought raw meat could contaminate other food via air alone

I'm no authority, but I can't think of any way that sneezing could be selective about what it expels that's already present in the mucus in your nose. So yes, I guess any cause of sneeze could potentially transmit covid.

Raw meat will require more direct contact to contaminate other food, though.

 

[2hats]

 

[Hyperdark]

There seems to be a lot of acceptance of this 71% figure for the increase in transmissibility of the new strain, apart from the very fact that its stated as an estimate yet they have given 71% (not 70 not 75) should immediately alert us that its not definitive.
Mainly though it should be kept in mind that the calculated rise being present at the same times and places as the new strain become widely detected is not proof that the new strain caused thhe increase wholly or partly.
Its highly probable that other factors are at play that will change this figure perhaps drasticaly.
Work is ongoing to find out.