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

[xz-keg]

From branch 46 of sars-cov-2-variants/lineage-proposals#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

[FedeGueli]

the FLiRI branch was Branch 76 of sars-cov-2-variants/lineage-proposals#1089

[xz-keg]

84, Italy, Germany, Netherlands, Luxembourg

[FedeGueli]

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]

Designated JN.1.16.2, LA.1 (346T) and LA.2 (346I) via 52f3337

[AngieHinrichs]

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:

So I think it's reasonable that Cornelius designated

• JN.1 > T22928C(S:F456L) > C4777T as JN.1.16.2
• JN.1 > T22928C(S:F456L) > C4777T > G22599C (S:R346T) as JN.1.16.2.1 (LA.1) even though the tree has it erroneously placed in JN.1.16.1 because of G22599C
• JN.1 > T22928C(S:F456L) > C4777T > G22599T(S:R346I) as JN.1.16.2.2 (LA.2) even though the tree has it erroneously placed in JN.1.16.1 with a subsequent C22599T, yuck.

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.