Thread by @PeacockFlu

With the BA.5 in the rearview mirror in most places I thought I'd do a quick thread on 'whats next for SARS-CoV-2 variants?' (TL:DR - not really sure but probably a BA.2 offshoot?)

First off: BA.2.75 - this is by far the most prevelent new variant out there - its caused a bit of a wave in India but I'm not sure it has the right combination of properties to cause a global wave like BA.5 did..

More likely perhaps is a BA.2.75 sublineage (of which there are many) - BA.2.75.2 is the most prelevent of these and contains several additional potent antigenic mutations on top of normal BA.2.75 (in black).

Finally there are some potential dark horses - as many people are aware BA.2.75 is a 'second generation variant' - a variant that has gone through a second round of 'variant evolution' and is genetically distinct from anything else

https://twitter.com/PeacockFlu/status/1468626571791671304

However BA.2.75 isnt the only second generation BA.2 out there - 3 more such lineages have been identified in the past month or two - all are at low numbers of sequences currently (<50) but have troubling combos of potent antigenic mutations (particularly BJ.1 and BA.2.3.20).

This sudden appearance of multiple second generation BA.2s represents a changing phase of SARS2 evolution - albeit somewhat similar to early 2021 where lots of variants arose at once (though from an ancestral strain, rather than an existing variant like BA.2).

Finally there are a couple of long shots BA.2 x Delta recombinants that have appeared in the last few months - these arent showing any signs of growth but I wanted to acknowledge them

https://twitter.com/PeacockFlu/status/1563198682710740992

At the moment my feeling is BA.2.75.2 is most likely to win out, but I definitley wouldnt rule out one of the other second gen BA.2s coming from behind...

I have no idea how any of these will look in terms of causing future waves, etc - I think anything from a silent takeover to further waves (like earlier this year) is entirely possible.
I also strongly suspect we will see further second gen BA.2s appear in the coming months...

Full credit to the folks generating and sharing the sequences, as well as the folks trawling through looking for new lineages and variants - QTing @LongDesertTrain's (who spotted one of these 2nd gen BA.2s) great in-depth thread on BA.2.3.20 here

https://twitter.com/LongDesertTrain/status/1565184527428980737

Final stray throught - its now clear the jumping/variant/saltation evolution of SARS2 is an intrisic property of the virus - although we also see flu-like stepwise drift I think the 'variant evolution' will continue to be the main driver of variation going forwards.

Quick update with early data coming in: BA.2.75.2 definitley has the antigenic distance from prior variants that parental BA.2.75 lacks - I think this is probably most likely to be the next variant to take over (whether causing a wave or not).

https://twitter.com/BenjMurrell/status/1570862185819303937

Another quick update here - BQ.1.1 (a descendent of BA.5) has been showing very quick growth in the last couple of weeks, particularly in the UK - no data on antigenicity, etc yet but definitely yet another one to watch...

https://twitter.com/CorneliusRoemer/status/1572520978433060870

BQ.1.1 is BA.5 but has gained several additional mutations in the RBD - R346T, K444T and N460K - if those positions sound familiar its because they're very similar to whats appearing in a lot of other variants right now - some massive convergent evolution happening

(Also full credit to @siamosolocani for spotting BQ.1.1 extremely early and putting in the lineage request!)
github.com/cov-lineages/p…