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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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JN.1+C4777T+S:F456L(84 seqs, 16 countries) with S:R346T(36 seqs) and S:R346I( 20 seqs) misplaced under JN.1.16 and JN.1.16.1 #2555

Closed aviczhl2 closed 2 months ago

aviczhl2 commented 2 months ago

From branch 46 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253

JN.1+C4777T+T22928C(S:F456L)+G22599C(S:R346T)/G22599T(S:R346I)

This is a lineage with serious usher misplacement issue. C4777T shouldn't be a convergent mutation, however S:456L and S:346T/I are very convergent, everything with C4777T shall belong to the same branch of JN.1+C4777T.

There are 3 misplacements for this lineage @AngieHinrichs @corneliusroemer 1: Usher misplaces JN.1+C4777T+S:F456L as JN.1.16+C4777T 2: Usher misplaces JN.1+C4777T+S:F456L+S:R346T as JN.1.16.1+C4777T 3: Usher misplaces JN.1+C4777T+S:F456L+S:R346I as JN.1.16.1+C4777T+S:T346I

GISAID query: C4777T,T22926C, T22928C No. of seqs: 69(Australia 9 Canada 7 UK 38 France 2 Ireland 1 Israel 1 Malaysia 1 Pakistan 1 Singapore 1 USA 8(2 from Japan, 2 from UAE)) First: EPI_ISL_18885437, UK, 2024-1-31 Latest: EPI_ISL_19033862, UK, 2024-3-25 GISAID query for S:R346T branch: C4777T, T22926C, T22928C, G22599C (31 seqs) GISAID query for S:R346I branch: C4777T, T22926C, T22928C, G22599T (16 seqs)

usher

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FedeGueli commented 2 months ago

the FLiRI branch was Branch 76 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089

aviczhl2 commented 2 months ago

84, Italy, Germany, Netherlands, Luxembourg

FedeGueli commented 2 months ago

89 +2 Qatar today

this is fast:https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=JN.1*&nucMutations1=C4777T%2CT22926C%2CT22928C&analysisMode=CompareToBaseline&

FedeGueli commented 2 months ago

Designated JN.1.16.2, LA.1 (346T) and LA.2 (346I) via https://github.com/cov-lineages/pango-designation/commit/52f33370c5df719f0b25d0b8b78ced0727d1171b

AngieHinrichs commented 2 months ago

I don't see any sequences that are only JN.1+C4777T. C4777T has appeared multiple times after other mutations in JN.1 (green circles below), and from many different countries, so I don't think C4777T is an artifact:

image

So I think it's reasonable that Cornelius designated

The tree definitely has the wrong structure for those, and I may or may not be able to fix it. But I think the designations are reasonable, and having the lineage labels will help to compensate for suboptimal tree structure -- at least the correct lineages can be assigned.