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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.1.38+Orf3a:G100S+S:G35S(343 seqs, 8 countries, 15 with S:R346T) #2475

Open aviczhl2 opened 6 months ago

aviczhl2 commented 6 months ago

From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1295

JN.1+G18674A(Orf1b:R1736K)+C11572T+G25690A(Orf3a:G100S)+G21665A(S:G35S)

GISAID query: G21665A,G25690A,C11572T No. of seqs: 101(Canada 2 UK 3 USA 96)

First: EPI_ISL_18730401, USA-IL,2023-11-1 Latest: EPI_ISL_18816545, USA-TX, 2024-1-15

GISAID query for S:R346T branch: G21665A,G25690A,C11572T,G22599C

usher

image

FedeGueli commented 5 months ago

125 now it seems fast

FedeGueli commented 5 months ago

160 it seems fast @corneliusroemer: i suggest to designate it, mutations round 30-36( that before were never fit: think at S:36 which was mutated very soon in XBB.1.5 failing to be successful even if it had a start advantage) seem to have some effect in JN.1 maybe due the insertion that affects the NTD configuration ? More the other two mutations one in NSP14 and Orf3a could have some impact. The branch starts with Orf1b:R1736K, maybe i would evaluate if starting the designation from there or not, being there also S:t732I lineage after Orf3a:G100S tht could turn to be interesting.

Screenshot 2024-02-08 alle 11 01 40

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_22540_4a5810.json?f_userOrOld=uploaded%20sample&label=id:node_6881525

FedeGueli commented 5 months ago

A sublineage of this one got S:R346T :

Screenshot 2024-02-12 alle 22 31 32

it will be branch 38

aviczhl2 commented 5 months ago

178, Japan

FedeGueli commented 5 months ago

@corneliusroemer i suggest to designate this one

aviczhl2 commented 4 months ago

254, Ecuador

aviczhl2 commented 4 months ago

276, Mexico

aviczhl2 commented 4 months ago

+1 Netherlands

aviczhl2 commented 2 months ago

334, Brazil