BA.2 (+ C25416T) lineage with S:K417T common in India [>20%] and growing in UK [400 seq]

[corneliusroemer]

It's plausible that BA.2 + S:K417T has a growth advantage. So I went and checked out all the global lineages. There are multiple, which again points to growth advantage.

This is a lineage that appears smaller than the UK one #528, but in fact I think it's bigger because it makes up 2% in India - which has many more cases than UK for sure. It also looks like there's been import into UK from India. There are now 100 sequences from UK.

I think it's definitely worth designating this one.

I checked whether it's clean. It is, it lies on the big BA.2 branch with C25416T (@chrisruis you remember I wanted to give this one a label, but unfortunately it's synonymous). Anyways, this will help show that C25416T is a big branch. The other lineage on it is #499 (BA.2.12(.1)).

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_ddae_1d19f0.json?c=gt-nuc_22812&label=nuc%20mutations:C25416T

https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants/international-comparison?aaMutations=S%3AK417T&nucMutations=C25416T&pangoLineage=BA.2*&aaMutations1=s%3AK417T%2Corf7a%3As83l&pangoLineage1=BA.2*&

[FedeGueli]

There has been recently an uptick in cases and Rt in northern eastern india (Uttar Pradesh) , too few seqs to say if this is related with that but maybe it is worth designating this one to monitor better the epidemic situation there.

[silcn]

[off-topic]
Pretty sure what's happening in Delhi, Haryana and Uttar Pradesh right now is unrelated to this: it's been around too long to cause such a sharp uptick. The realistic options are either BA.4/BA.5 or something new - personally leaning towards something new, as it seems too sharp even for BA.4/BA.5. We should have sequences from Delhi in a week or so but if it is a new lineage I wouldn't be surprised if a sequence turns up somewhere else first.
[/off-topic]

[silcn]

Eating my words from two weeks ago right now.
We just got a big batch of uploads from Delhi and Uttar Pradesh. Looking at April sequences only, 30/113 from Delhi and 58/141 from Uttar Pradesh (including one where 417T mutated further to the very rare 417A, previously unseen in Omicron) belong to this lineage. There are only 4 from Delhi and none from Uttar Pradesh in March, so it looks like this lineage is at least partly responsible for the resurgence in cases. Pretty strong case for designation.

There is also a scattering of S:L452M in the Delhi/UP sequences, belonging to a couple of independent lineages, but probably not worth designating at the moment.

[FedeGueli]

thx @silcn for the very important update.

@corneliusroemer the sublineage in this issue isnt the same of #581 and #582 (with 6071T) ?

[AngieHinrichs]

@corneliusroemer it would be very helpful if in each issue you could provide at least one name/ID of a sequence on the branch you have in mind. Even with the cov-spectrum links, I can't really tell which sequences/branches you mean for this issue vs. #581 and #582 (thanks @FedeGueli for linking those). Especially when the link is to a comparison/growth graph, and it takes me a while to notice the "Back to overview" button on the right. :) I'm clicking through to UShER so I can try to guess which branches you're referring to in the single subtree view, but that takes a few minutes... However if you listed a sequence name, I would know exactly what branch you mean.

I think India/GJ-INSACOG-GBRC6525/2022 is at the base of the branch you're referring to in this issue, is that correct?

[corneliusroemer]

Oh I see, you designated it, thanks @chrisruis

If I see it correctly it's all of these, and not just the UK 6061 one

I'll close this and #581 #582 accordingly.