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Covid Mutations

In other words this is sadly not an area where I have much expectation of getting ahead of the curve in ways that allow me to give people advanced warning of where the pandemic story is heading next.
 
Delta sub-lineage classification is quite dynamic right now (AY.25 was just assigned a couple of hours ago; AY.10-AY.24 have only been recognised in the last 9 days), so it might be a little premature to draw any firm conclusions.
 
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.
Neutralisation assay performed using pseudoviruses harbouring the SARS-CoV-2 spike proteins of the alpha, beta, gamma, delta, epsilon, lambda, mu variants and the D614G-harbouring parental virus. Eight COVID-19 convalescent sera (B) and ten sera from BNT162b2-vaccinated individuals (C).

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.
 
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.
 
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Until a more fit one arrives on the scene.
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?
 
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?

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.
 
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?
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:
 
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.
AY.4.2 UK cases, transmission advantage.
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.
 
AY.4.3 designated: has a delta-like spike with S:p26S 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.
 
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.
Tweet@BallouxFrancois: To summarise, the recent rise in the UK of AY.4.2 would be compatible with a transmissibility advantage of ~10%. As such, it feels worthwhile keeping an eye on it. Though, based on its genetic make-up, it is not a priori an obvious VoC candidate.
 
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.
 
I'm beginning to wonder if this is the end game for society as we know it
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.
 
I'm beginning to wonder if this is the end game for society as we know it

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.
 
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
 
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.
 
Its got a mutation of the spike protein-thing that means the spike is not a perfect match to exisiting antibody-thing, does this equal partial vaccine evasion?
 
Its got a mutation of the spike protein-thing that means the spike is not a perfect match to exisiting antibody-thing, does this equal partial vaccine evasion?
Delta is pretty good at evasion already, people I know who’ve had cases round here have all been vaccinated.
 
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