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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.1.42 got S:R346T emerged in South America 65 seqs now with a FLiRT Branch (3seqs) #2494

Closed FedeGueli closed 1 month ago

FedeGueli commented 4 months ago

Former branch 35 of [#1089 in the pre proposals repo)](https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089)_

There is a sublineage of Jn.1 carrying S:R346T that apparently is spreading from South America . JN.1.42 ( C5581A) > S:R346T ( G22599C ) Query: C5581A ,G22599C,T3565C,-A405G Samples: 19 Countries: Peru', Guatemala, Costarica , US Tree:

Screenshot 2024-02-20 alle 15 05 35

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4e8fc_4a8be0.json?f_userOrOld=uploaded%20sample&label=id:node_6938550

IDs: EPI_ISL_18716147, EPI_ISL_18756797, EPI_ISL_18778096, EPI_ISL_18781004, EPI_ISL_18781137, EPI_ISL_18797803, EPI_ISL_18798375, EPI_ISL_18803869, EPI_ISL_18827552, EPI_ISL_18849452, EPI_ISL_18849645, EPI_ISL_18868297, EPI_ISL_18871427, EPI_ISL_18872327, EPI_ISL_18872484, EPI_ISL_18872523-18872524, EPI_ISL_18894858, EPI_ISL_18901899,

There is now (May 1) a FLiRT sublinegae of this one apparently misplaced by USher to Jn.1.16 JN.1.42> S:R346T (G22599C) > Orf1a.P1640S (C5183T), C7594T, ORF1a:A4285V (C13119T) Query: C5183T, C7594T,C13119T Samples: 3 (PuertoRico , Brazil via GBW)

Screenshot 2024-05-01 alle 21 51 46

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_1b8fb_26cb10.json?label=id:node_7057630

FedeGueli commented 4 months ago

Query edited i ve mistakenly pasted an unrelated query

FedeGueli commented 4 months ago

26

FedeGueli commented 3 months ago

30

FedeGueli commented 2 months ago

There is now (May 1) a FLiRT sublinegae of this one apparently misplaced by USher to Jn.1.16 JN.1.42> S:R346T (G22599C) > Orf1a.P1640S (C5183T), C7594T, ORF1a:A4285V (C13119T) Query: C5183T, C7594T,C13119T Samples: 3 (PuertoRico , Brazil via GBW)

Screenshot 2024-05-01 alle 21 51 46

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_1b8fb_26cb10.json?label=id:node_7057630

cc @AngieHinrichs

FedeGueli commented 1 month ago

Designated JN.1.42.2 via https://github.com/cov-lineages/pango-designation/commit/5d5d81ebf1b331827909839672097b5bbe548db1

FedeGueli commented 6 days ago

@corneliusroemer this has now a big sublineage with S:S31del growing and sampled multiple times from different countries in GBW pls take a look! query: del21653,C5581A ,A3084G