Thread by @firefoxx66

🗓️CoVariants.org now updated to data from 9 Mar🗓️

Plus, 2 new variants and 5 new mutations added!

Let's have a look at what's new...

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To help track variants of interest, we've added 20C/S:484K (B.1.526, sometimes called the 'New York variant') & 20A/S:484K (B.1.525)!

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20C/S:484K (blue) carries the S:E484K mutation as well as a mutation at S:A701V (shared with 501Y.V2). Interestingly, 2 independent sister-clades nearby (yellow) do *not* have 484, but have S:S477N (same mutation as is in 20A.EU2 & 20F.

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covariants.org/variants/20C.S…

All 3 of these variants are particularly prevalent in New York, USA, though they're found across the USA, & a few internationally.

20C/S:484K & its sister-clades also share a 3 amino acid deletion in ORF1a:3675-7 - seen in the 3 variants of concern & a few other variants.

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One of those others that shares ORF1a:3675-7 deletion is 20A/S:484K - the other new variant added.

It also carries 484K, along with the 69/70 & 144 deletion seen in 501Y.V1 (B.1.1.7) & S:Q677H, seen in multiple variants.

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covariants.org/variants/20A.S…

20A/S:484K is fairly internationally spread, including many countries in Europe, multiple states in the US, Nigeria & Ghana in Africa, & more. Like many clusters of current interest, it seems to have begun expanding in late 2020.

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Of course, these new variants are in our 'table of names' on the homepage, and included in our Per Country plots!

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covariants.org/per-country

Additionally, we've added 5 new mutation pages & focal builds:
S:L18
S:Y144-
S:K417
S:H655
S:P681
ORF1a:S3675- (the deletion mentioned above)

These mutations are some of those seen multiple times in variants of concern & of interest.

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The amount we knows about each of these mutations varies - if you can help by adding links, please do!

With dedicated builds, we can try to keep an eye on where they arise.
For example, we can see where S:655Y has appeared.

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nextstrain.org/groups/neherla…

Finally, a big thanks to @jamesscottbrown for helping us get links looking prettier, & a belated thanks to @hamesjadfield for the idea of splitting out Variants & Mutations (last push).

Thanks also to @YYCist for many links & resources, & @ivan_aksamentov as always!

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