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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

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xz-keg opened this issue Apr 8, 2024 · 5 comments

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@xz-keg
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xz-keg commented Apr 8, 2024

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)

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

@xz-keg xz-keg changed the title JN.1+C4777T+S:F456L(69 seqs, 12 countries) with S:R346T(31 seqs) and S:R346I( 16 seqs) misplaced under JN.1.16 and JN.1.16.1 JN.1+C4777T+S:F456L(71 seqs, 12 countries) with S:R346T(33 seqs) and S:R346I( 16 seqs) misplaced under JN.1.16 and JN.1.16.1 Apr 9, 2024
@xz-keg
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xz-keg commented Apr 12, 2024

84, Italy, Germany, Netherlands, Luxembourg

@xz-keg xz-keg changed the title JN.1+C4777T+S:F456L(71 seqs, 12 countries) with S:R346T(33 seqs) and S:R346I( 16 seqs) misplaced under JN.1.16 and JN.1.16.1 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 Apr 12, 2024
@FedeGueli
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FedeGueli commented Apr 15, 2024

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

@AngieHinrichs
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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

  • 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.

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