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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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Another JN.1+S:S31F(111 seqs, 7 countries, 39 with S:R346T, 20 with FLiRT) #2530

Open aviczhl2 opened 3 months ago

aviczhl2 commented 3 months ago

From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1445 JN.1+C24023T+C21654T(S:S31F)

GISAID query:C24023T,C21654T,C18894T No. of seqs: 59(South Korea 57 Japan 1 USA 1) 58 on GISAID , 1 USA seq PP077093.1 not. GISAID query for S:R346T branch: C24023T,C21654T,C18894T,G22599C (9 seqs) GISAID query for further S:F456L: C24023T,C21654T,C18894T,G22599C ,T22928C (1 seq)

First: EPI_ISL_18687243, South Korea 2023-11-21 Latest: EPI_ISL_19001311, South Korea, 2024-2-26

usher

image

aviczhl2 commented 2 months ago

One FLiRT seq emerges from this branch.

FedeGueli commented 2 months ago

79 now for S:S31F 17 for S:R346T (all from S.Korea) 3 for S:F456L (All south Korea)

cc @corneliusroemer i suggest to designate this one.

aviczhl2 commented 2 months ago

new country of Netherlands

FedeGueli commented 2 months ago

now: 90 > 27 > 10

Big upload today of samples from South Korea belonging to the FLiRT branch:

Screenshot 2024-04-29 alle 13 07 17

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_129bc_f78670.json?c=userOrOld&label=id:node_7027376

FedeGueli commented 2 months ago

98 31F > 31 346T > 14 FLiRT ping @corneliusroemer i think this should be designated.

FedeGueli commented 2 months ago

16 with FLiRT

FedeGueli commented 1 month ago

18 for FLiRT

FedeGueli commented 1 month ago

105 , 18 FLiRT, slowed down a lot in my view but it could be also delayed uploading by S.Korea

FedeGueli commented 3 weeks ago

109 S:S31F 38 R346T 19 for FLiRT (+1 after one month hiatus)

aviczhl2 commented 1 week ago

111, Spain, China, France