Thread by @TRyanGregory

On January 1, I said "Omicron is not a Pokemon-style final evolution of SARS-CoV-2", in response to way too many people acting like Omicron (BA.1) was the last variant we'd have to contend with. Time to check in on this after 5 months. 🧵

The original tweet from January.

https://twitter.com/TRyanGregory/status/1477325635618058246?s=20&t=ntRMeE-NWlHyF0u0YVdSwA

Since the BA.1 wave, we've already had another wave caused by BA.2. The fascinating (and concerning) thing about Omicron is that it is evolving extremely quickly and we keep seeing subvariants that have transmission advantages/immune escape versus previous variants.

Incidentally, I also noted the very close correspondence between what happens in the UK and what happens a few weeks later in Canada. That was borne out once again.

Whereas previously we were getting new variants that were only distantly related the one ones they were replacing, now we have a growing number of highly transmissible and genetically divergent subvariants within the Omicron clade.

This phylogeny shows (rectangular or radial show the same information) the different variants of concern and their evolutionary relationships. Omicron was not derived from Delta, and Delta was not derived from Alpha -- they had distant shared ancestors.

By contrast, Omicron BA.1 and BA.2 are descended from a relatively recent common ancestor (i.e., they're sister lineages). However, BA.2.12 (22C), BA.4 (22A), and BA.5 (22B), which are now of increasing concern, are all derived recently from different sublineages of BA.2.

BA.4 (22A) and BA.5 (22B), in particular, are very closely related.

There are early reports that BA.4 and BA.5 have mutations that make them likely to escape prior immunity, setting us up for another wave on the heels of BA.2.

secureservercdn.net/166.62.108.196…

In any case, SARS-CoV-2 continues to evolve very rapidly, with Omicron being especially prone to mutation. You can see that Omicron is well above the regression line of mutations over time compared to other variants.

And this is especially the case for spike protein (S1) mutations.

Sorry to say it, but the pandemic still isn't over.

More info:

nextstrain.org/ncov/gisaid/gl…

covariants.org

Follow @MarionKoopmans, @firefoxx66, @RajlabN, @nextstrain, @Tuliodna, @trvrb, @Gab_H_R, @DGBassani, @sigallab (I'm definitely missing bunch of others -- please post in comment).