JN.1.39+S:F456L mostly misplaced under JN.1.16 (96 seqs, 10 countries, 3 with S:R346T, 5 with S:R346S)

[aviczhl2]

From branch 11 of sars-cov-2-variants/lineage-proposals#1253

JN.1.39+T22928C(S:F456L)

GISAID query: G2782T,T22926C,T22928C,-T111C,-23601,-C1594T,-26873,-21034, -10369
No. of seqs: 43( Germany 2 China 1 Japan 1 USA 39(1 from Japan, 1 from Switzerland, 1 from UAE)

First: EPI_ISL_18695414, USA, 2023-12-16
Latest: EPI_ISL_19005864, Japan, 2024-3-13

Mostly misplace as JN.1.16+G2782T, as S:F456L(T22928C) is much more of a convergent mutation than G2782T this shall be JN.1.39+S:F456L(T22928C). Seqs placed on other branches are excluded, maybe recombs.

@AngieHinrichs @corneliusroemer

usher

[Mydtlwn]

@corneliusroemer

[aviczhl2]

57, Canada,Australia

[aviczhl2]

68, Ireland

[FedeGueli]

it has now a FLiRS branch of 2
[JN.1.16> G2782T ] = JN.1.39 > S:F456L > S:R346S (A22600C), T25054C
Query: G2782T,T3565C,A22600C, T25054C

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_1b8fb_26cb10.json?c=userOrOld&label=id:node_11429162

Note that there is another likely misplaced JN.1.39 with S:S346S but this time it is anticipated by S:S31F and it chould not be the same lineage of the one found here even if there is Geographical contiguity (US):
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1cd44_2abef0.json?label=id:node_6934825

[aviczhl2]

96, Singapore