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

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FedeGueli opened this issue Feb 20, 2024 · 6 comments
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JN.1.42 got S:R346T emerged in South America 65 seqs now with a FLiRT Branch (3seqs) #2494

FedeGueli opened this issue Feb 20, 2024 · 6 comments

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@FedeGueli
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FedeGueli commented Feb 20, 2024 •
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Former branch 35 of #1089 in the pre proposals repo)_

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
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Query edited i ve mistakenly pasted an unrelated query

@FedeGueli FedeGueli mentioned this issue Feb 21, 2024
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@FedeGueli FedeGueli changed the title JN.1 Plus S:R346T sublineage emerging in South America (Former branch 35 of #1089 in the pre proposals repo) JN.1 Plus S:R346T sublineage emerging in South America 19seqs (Former branch 35 of #1089 in the pre proposals repo) Feb 26, 2024
@FedeGueli FedeGueli changed the title JN.1 Plus S:R346T sublineage emerging in South America 19seqs (Former branch 35 of #1089 in the pre proposals repo) JN.1 Plus S:R346T sublineage emerging in South America 26 seqs (1 % in Peru') Mar 7, 2024
@FedeGueli
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26

@FedeGueli FedeGueli changed the title JN.1 Plus S:R346T sublineage emerging in South America 26 seqs (1 % in Peru') JN.1 Plus S:R346T sublineage emerging in South America 30 seqs (1 % in Peru') Mar 17, 2024
@FedeGueli
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30

@FedeGueli FedeGueli changed the title JN.1 Plus S:R346T sublineage emerging in South America 30 seqs (1 % in Peru') JN.1.42 got S:R346T emerging in South America 30 seqs (1 % in Peru') Mar 25, 2024
@FedeGueli FedeGueli changed the title JN.1.42 got S:R346T emerging in South America 30 seqs (1 % in Peru') JN.1.42 got S:R346T emerging in South America 37 seqs (1 % in Peru') Mar 28, 2024
@FedeGueli FedeGueli changed the title JN.1.42 got S:R346T emerging in South America 37 seqs (1 % in Peru') JN.1.42 got S:R346T emerging in South America 37 seqs - 7 countries Mar 28, 2024
@FedeGueli FedeGueli changed the title JN.1.42 got S:R346T emerging in South America 37 seqs - 7 countries JN.1.42 got S:R346T emerged in South America 47 seqs - 7 countries Apr 17, 2024
@FedeGueli FedeGueli changed the title JN.1.42 got S:R346T emerged in South America 47 seqs - 7 countries JN.1.42 got S:R346T emerged in South America 50 seqs - 7 countries Apr 27, 2024
@FedeGueli FedeGueli changed the title JN.1.42 got S:R346T emerged in South America 50 seqs - 7 countries JN.1.42 got S:R346T emerged in South America 61 seqs now with a FLiRT Branch (3seqs) May 1, 2024
@FedeGueli
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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 FedeGueli changed the title JN.1.42 got S:R346T emerged in South America 61 seqs now with a FLiRT Branch (3seqs) JN.1.42 got S:R346T emerged in South America 65 seqs now with a FLiRT Branch (3seqs) May 8, 2024
FedeGueli referenced this issue May 16, 2024
@corneliusroemer
Designate JN.1.42.2 (S:R346T, Peru)
5d5d81e
@FedeGueli
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Designated JN.1.42.2 via 5d5d81e

@FedeGueli
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FedeGueli commented Jul 4, 2024 •
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@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 proposed in sars-cov-2-variants/lineage-proposals#1692

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