Covid Mutations
- Thread starter Supine
- Start date
2hats
Dust.
From Japan (Tokyo/Kyoto/Chiba) the first study of vaccine evasion of mu/B.1.621 compared to other recent VOC.
A study using both convalescent and vaccine (BNT162b2) sera determined that mu appears to have the highest degree of immune evasion yet.
However, delta/B.1.617.2 has a transmission fitness advantage over mu (pre-activation of the furin cleavage site mediating more efficient, rapid cell entry) so appears to have demonstrated a propensity to dominate and outcompete mu (and others).
DOI: https://doi.org/10.1101/2021.09.06.459005.
A study using both convalescent and vaccine (BNT162b2) sera determined that mu appears to have the highest degree of immune evasion yet.
However, delta/B.1.617.2 has a transmission fitness advantage over mu (pre-activation of the furin cleavage site mediating more efficient, rapid cell entry) so appears to have demonstrated a propensity to dominate and outcompete mu (and others).
DOI: https://doi.org/10.1101/2021.09.06.459005.
2hats
Dust.
Looks like delta/B.1.617.2/AY.x has pretty much crushed beta/B.1.351 across many regions of Africa.
From the Genomics Africa dashboard.
From the Genomics Africa dashboard.
Aladdin
Well-Known Member
Looks like delta/B.1.617.2/AY.x has pretty much crushed beta/B.1.351 across many regions of Africa.
From the Genomics Africa dashboard.
Is this...good?
Sorry..I am assuming it is...?
2hats
Dust.
In that delta (for now) seems to be usurping VOCs that appear to exhibit higher degrees of immune evasion (eg beta, mu), arguably yes. See also South America.
Aladdin
Well-Known Member
2hats
Dust.
Until a more fit one arrives on the scene.
2hats
Dust.
Perhaps a new variant worth keeping an eye on. AY.33 descended from delta/B.1.617.2. Four key defining mutations in spike - S:29A, S:250I, S:T299I and S:Q613H (note proximity to the key D614G backbone that has been a feature of many previous variants and came to dominate across Europe in summer 2020). May have originated in North Africa (perhaps Morocco), now gradually growing on the near continent (Belgium, Denmark, France, Germany, Netherlands) as well as the UK (over 100 sequences recorded). Too early to say what degree of growth advantage it might have over delta.
Last edited:
elbows
Well-Known Member
Ah I see.
github.com
New fast growing Delta sublineage with 4 distinct Spike mutations observed in multiple European countries · Issue #215 · cov-lineages/pango-designation
Proposal for new sublineage within B.1.617.2 by Cornelius Roemer and @chaoran-chen Defining AA mutations Occurred first: S:29A, S:250I Followed by: S:T299I Last (defining): S:Q613H First observatio...
github.com
retribution
Jack of Dubs
I was wondering about this yesterday. It seems to be policy that COVID will become endemic. What do we know about how variants play out in this picture? The flu produces variants that we produce new vaccines for each year, but is there anything about COVID that makes likely new variants more risky? Do policymakers anticipate that we will produce new vaccines for COVID like we do the flu? What are the risks of this approach?
Supine
Newt Member
It’s looking like new strain vaccines will be required every year or two. But that is very much subject to seeing how things develop. It could be annual, hopefully less frequently will be enough.
2hats
Dust.
The vast majority of new variants aren't "more risky", in that they don't necessarily lead to worse episodes of disease. They may (more correctly) evade immunity to a better degree and so ultimately place a higher load on healthcare systems (and cause an increase in poor outcomes to some degree).
As regards the endemic endgame, see part three herein:
How the Pandemic Now Ends
Cases of COVID-19 are rising fast. Vaccine uptake has plateaued. The pandemic will be over one day—but the way there is different now.
2hats
Dust.
Another descendent of delta/B.1.617.2 designated - AY.4.2 - might be one to watch. It appears to be growing rapidly in the UK and Romania, with a number of cases also in Germany and Denmark. Features S:Y145H (previously seen in mu/B.617 and sometimes beta/B.1.351) plus S:A222V (seen in numerous B.1.177-related lineages which drove a lot of cases across Europe in summer 2020). Might have a fitness advantage; perhaps might even have a chance of possessing slightly elevated immune evasion.
Also designated - AY4.1 (largely in UK & Ireland) with S:G446S and T814I and I6704L in ORF1ab.
Other recent delta descendents that might be worth keeping tabs on:
AY.34 (circulating in at least the UK, US, France, Germany) with S:Q677H, S:L1265F, ORF1a:C3059F, ORF1b:M1596I, ORF1a:V2930L, ORF3a:ins104P, and N:L230F.
AY.35 (seen in the UK & US) with S:E484Q (note: mutation seen on 484 in beta/B.1.351 and gamma/P.1) plus S:K77T, and P309L, P1921Q, D2980N, F3138S all in ORF1a.
Also designated - AY4.1 (largely in UK & Ireland) with S:G446S and T814I and I6704L in ORF1ab.
Other recent delta descendents that might be worth keeping tabs on:
AY.34 (circulating in at least the UK, US, France, Germany) with S:Q677H, S:L1265F, ORF1a:C3059F, ORF1b:M1596I, ORF1a:V2930L, ORF3a:ins104P, and N:L230F.
AY.35 (seen in the UK & US) with S:E484Q (note: mutation seen on 484 in beta/B.1.351 and gamma/P.1) plus S:K77T, and P309L, P1921Q, D2980N, F3138S all in ORF1a.
petee
no gods, no malarkey
Looks like delta/B.1.617.2/AY.x has pretty much crushed beta/B.1.351 across many regions of Africa.
From the Genomics Africa dashboard.
i took that at first to be a map of china, mongolia, the pacific, and central asia, and wondered what a chart in that shape was good for.
26S which features in the VOC gamma/P.1 (which dominated infections in Brazil until delta rocked up in early summer). Not insignificant numbers turning up in UK, Sweden, Switzerland and Germany.
2hats
Dust.
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elbows
Well-Known Member
Yes I've managed to stumble upon the small bunch of people on twitter who noticed that Delta descendent and are nervous about some of its attributes. I will keep an eye on it but they and everyone else arent quite sure what to make of it yet. I get the idea that there is no point in me winding myself up about such mutations until they demonstrate that any advantage they have is leading to them trending towards dominance. I still find it interesting and worth taking seriously, just have to be careful not to cry wolf.
elbows
Well-Known Member
It made it onto the BBC. I'm not sure it was entirely sensible for them to say "Experts say it is unlikely to take off in a big way".
Covid-19: New mutation of Delta variant under close watch in UK
Scientists are studying it to better understand how much of a threat it may pose.
www.bbc.co.uk
elbows
Well-Known Member
Such concerns are an understsandable side-effect of a bad pandemic, especially at certain moments.
However humans and society are adaptable even in the face of nuch adversity and horror. I suspect that even if the pandemic had been much worse, with a far higher death rate across a broader range of age groups, something resembling society would still have come out the other side. It would just be a changed society. And huge chunks of the economy and political and security order could of collapsed or been radically changed under certain scenarios.
I do expect that the big stories of this century will involve all manner of heavy shit leading to much change over time. Especially when various different structural problems rise to the surface, triggered by particular crises but then seeping far beyond those triggers.
All of the ramifications of this pandemic have not played out yet, thats for sure.
Big global events certainly bring about change, what that change will look like is hard to know.
One thing is for certain is that humanity has come back from a lot worse. The history of previous pandemics have been so much worse that this. The Spanish flu for example was killing all ages, in fact one subsequent wave was more likely to kill people in their 20's. People were going from healthy to dead in 48 hours. Also pick your death toll on that one anywhere from 20m to 100m.
All thing considered so far covid has been bad but not utterly terrible. Plus we have so much more weaponry in our armour these days to fight things like this.
_Russ_
Never not Knowingly Misunderstood
Yea Im not just considering this Pandemic in my worries, lots of other shit going down and the division between the haves and have nots surely cant get much wider without something snapping?
In all honesty I cant see life for most people in this country improving at all under this serfdom, but we would need the armed forces on side to change it
In all honesty I cant see life for most people in this country improving at all under this serfdom, but we would need the armed forces on side to change it
Dogsauce
I’ve got Skol but I’m not a Scholar
Like Alpha, another gift to the world from a country where they just happily ‘let it rip’. Cunts.View attachment 292896Read and Share Twitter Threads easily!
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Quick, scrap PCR tests for travel and put them all on the green list.
2hats
Dust.
UKHSA (ex-PHE) have now designated AY.4.2 a Variant Under Investigation (VUI-21OCT-01).
www.gov.uk
COVID-19 variants identified in the UK – latest updates
Latest updates on SARS-CoV-2 variants detected in the UK.
2hats
Dust.
UKHSA Technical Briefing number 26 has been released covering AY.4.2/VUI-21OCT-01. Modest growth rate compared to delta/B.1.617.2. It is now defined as delta/B.1.617.2 plus any two of orf1ab:A2529V; S:Y145H; S:A222V.
Secondary attack rate (SAR) for household contacts has been deemed to be 12.4% (95%CI:11.9-13.0) higher than parent delta. In non-household settings the SAR is also higher, 4.4% (95%CI:3.8-5.1), but this is not significant. It is still not clear if the advantage is biologically or behaviourally driven.
Initial analyses do not (at least yet) strongly suggest AY.4.2/VUI-21OCT-01 leads to any greater risk of hospitalisation or death than delta/B.1.617.2.
Lambda/C.37 and C36.3 have been 'downgraded' to variants in monitoring.
Secondary attack rate (SAR) for household contacts has been deemed to be 12.4% (95%CI:11.9-13.0) higher than parent delta. In non-household settings the SAR is also higher, 4.4% (95%CI:3.8-5.1), but this is not significant. It is still not clear if the advantage is biologically or behaviourally driven.
Initial analyses do not (at least yet) strongly suggest AY.4.2/VUI-21OCT-01 leads to any greater risk of hospitalisation or death than delta/B.1.617.2.
Lambda/C.37 and C36.3 have been 'downgraded' to variants in monitoring.
Dogsauce
I’ve got Skol but I’m not a Scholar
Delta is pretty good at evasion already, people I know who’ve had cases round here have all been vaccinated.
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