It needs to be emphasized that what we're seeing with SARS-CoV-2 variant evolution now is something new. 🧵
In the past, we've had distinct waves caused by one variant rising quickly in frequency (percentage of infections by that variant) and abundance (total number of infections by that variant), then dropping off. Alpha, Delta, and the Omicron BA.1 and BA.2 waves were like that. 
Where one occurred, the third Omicron wave was driven by BA.5, but it did not reach the same frequency or abundance as BA.1 and BA.2 did. In some places, the summer BA.5 wave plateaued and never really came back down.
.@DGBassani proposed months ago that what we were beginning to see was multiple variants evolving and overlapping in parallel, rather than replacing each other in series. As he noted, the less we do to stop transmission, the more this will occur.
Seeing as how we did not try to mitigate transmission (quite the opposite -- many places dropped what protections we did have), it is not surprising that this is exactly what has happened.
We have not seen the evolution of major new, deeply divergent lineages of variants recently, but instead it has all been rapid diversification of lineages within the large Omicron clade. I talked about variant naming and evolution in this recent thread:
https://twitter.com/TRyanGregory/status/1576945959824523264?t=XFr3KKThtvM4guuvW62gZg&s=19
Mutations happen as chance errors, but what happens to them once they arise is non-random if they happen to confer some advantage in a particular environment.
For an overview of basic evolutionary concepts as applied to viruses, check out this thread:
For an overview of basic evolutionary concepts as applied to viruses, check out this thread:
https://twitter.com/TRyanGregory/status/1477332222206423041?t=XFr3KKThtvM4guuvW62gZg&s=19
The current environment for SARS-CoV-2 is a population of hosts with varying levels of immunity, be it from vaccination, prior infection, or both. Immunity wanes, but there is strong selective pressure whereby mutations that confer an ability to circumvent immunity are very fit.
What we're seeing as a result is the same mutations arising by chance in multiple variant lineages, with the variants that happen to have those mutations increasing in frequency as they escape immunity and outcompete variants that lack immune-evading traits.
Similar traits can occur in different species for a couple of reasons. First, they may be similar simply because they all inherited the same trait from a shared ancestor (this is known as "homology"). Fur in different mammal species is homologous, for example.
Similar traits can also evolve independently in different lineages, which is known as "homoplasy" or "convergent evolution" (or "analogous [vs. homologous] traits").
Convergent evolution often happens when separate lineages evolve under similar environmental pressures.
Convergent evolution often happens when separate lineages evolve under similar environmental pressures.
Bird wings and bat wings are homoplasious (though the bones in the limbs are homologous).
What is happening with Omicron lineages is convergent evolution in which clusters of mutations that confer immune escape in the current host environment are evolving repeatedly.
What is happening with Omicron lineages is convergent evolution in which clusters of mutations that confer immune escape in the current host environment are evolving repeatedly.
We don't know what this will mean for the upcoming fall/winter wave. Again, this situation is new. Very smart people are working hard to try to make predictions. You can follow many of them on Twitter:
twitter.com/i/lists/156947…
twitter.com/i/lists/156947…
The new situation also poses challenges for communication. We've previously talked about single variants (and I still think we need nicknames), but now we also need to convey what is happening with many variants at the same time.
Terms like "variant soup", "swarm", or "cloud" are being used. (There's a technical term, "viral quasispecies" as well, but that could be confusing because it uses the chemical rather than biological meaning of species pubmed.ncbi.nlm.nih.gov/31622336/).
Maybe we need to refer to the SARS-CoV-2 "variome" at this point, or think of it the way we consider microbiomes / metagenomics. (I know, everything is an 'ome nowadays.)
en.wikipedia.org/wiki/Variome
en.wikipedia.org/wiki/Variome
Or perhaps we need a new term. I am a fan of portmanteaux, so maybe something like:
* Convergent variants --> "Convars"
* Clouds of variants --> "Clovars" 🍀 (more leaves/mutations means worse luck for us)
Or maybe something like "Constels" (short for "constellations").
* Convergent variants --> "Convars"
* Clouds of variants --> "Clovars" 🍀 (more leaves/mutations means worse luck for us)
Or maybe something like "Constels" (short for "constellations").
I also wonder whether there can be some naming convention that indicates which soup/cloud/swarm/clovar is being discussed, when it appeared, how many mutations it involves, so on.
Huge thank you to the folks who continue to track new variants and share their expertise. There are many, but singling out a few with recent threads that are very useful:
https://twitter.com/yunlong_cao/status/1577343549120872448?t=Y1lAnJCgr5bbMIYN4Pj_Uw&s=19
Note that some of the current rise in infections looks to be due to a resurgence of BA.5 -- again, that wave has never really ended in many places. Maybe schools, people moving indoors more, etc.? The variant soup (clovar?) has not had its impact yet.
https://twitter.com/MoritzGerstung/status/1577667110385471488?s=20&t=46SaZ1sVLQrb2W7bfBxMFg
It also bears noting that some experts had suggested that this kind of thing was possible some time ago as well.
https://twitter.com/trvrb/status/1470420195567030274?s=20&t=ZCyMG03hwB14IxFz_56kUg
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