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Another JN.1+S:S31F(119 seqs, 8 countries, 47 with S:R346T, 27 with FLiRT) #2530

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xz-keg opened this issue Mar 23, 2024 · 11 comments
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Another JN.1+S:S31F(119 seqs, 8 countries, 47 with S:R346T, 27 with FLiRT) #2530

xz-keg opened this issue Mar 23, 2024 · 11 comments

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@xz-keg
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xz-keg commented Mar 23, 2024 •
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From sars-cov-2-variants/lineage-proposals#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

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@FedeGueli FedeGueli mentioned this issue Mar 24, 2024
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@xz-keg xz-keg changed the title Another JN.1+S:S31F(59 seqs, 3 countries, 9 with S:R346T) Another JN.1+S:S31F(63 seqs, 3 countries, 10 with S:R346T) Apr 2, 2024
@xz-keg xz-keg changed the title Another JN.1+S:S31F(63 seqs, 3 countries, 10 with S:R346T) Another JN.1+S:S31F(68 seqs, 3 countries, 12 with S:R346T) Apr 6, 2024
@xz-keg xz-keg changed the title Another JN.1+S:S31F(68 seqs, 3 countries, 12 with S:R346T) Another JN.1+S:S31F(71 seqs, 3 countries, 14 with S:R346T, 1 with FLiRT) Apr 12, 2024
@xz-keg
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xz-keg commented Apr 12, 2024

One FLiRT seq emerges from this branch.

@FedeGueli
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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.

@xz-keg
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xz-keg commented Apr 24, 2024

new country of Netherlands

@xz-keg xz-keg changed the title Another JN.1+S:S31F(71 seqs, 3 countries, 14 with S:R346T, 1 with FLiRT) Another JN.1+S:S31F(79 seqs, 4 countries, 17 with S:R346T, 3 with FLiRT) Apr 24, 2024
@FedeGueli
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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
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98 31F > 31 346T > 14 FLiRT ping @corneliusroemer i think this should be designated.

@xz-keg xz-keg changed the title Another JN.1+S:S31F(79 seqs, 4 countries, 17 with S:R346T, 3 with FLiRT) Another JN.1+S:S31F(98 seqs, 4 countries, 31 with S:R346T, 14 with FLiRT) May 8, 2024
@FedeGueli
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16 with FLiRT

@FedeGueli
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18 for FLiRT

@FedeGueli
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FedeGueli commented May 23, 2024 •
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105 , 18 FLiRT, slowed down a lot in my view but it could be also delayed uploading by S.Korea

@xz-keg xz-keg changed the title Another JN.1+S:S31F(98 seqs, 4 countries, 31 with S:R346T, 14 with FLiRT) Another JN.1+S:S31F(107 seqs, 4 countries, 36 with S:R346T, 18 with FLiRT) May 29, 2024
@FedeGueli
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FedeGueli commented Jun 14, 2024 •
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109 S:S31F
38 R346T
19 for FLiRT (+1 after one month hiatus)

@xz-keg
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xz-keg commented Jul 1, 2024

111, Spain, China, France

@xz-keg xz-keg changed the title Another JN.1+S:S31F(107 seqs, 4 countries, 36 with S:R346T, 18 with FLiRT) Another JN.1+S:S31F(111 seqs, 7 countries, 39 with S:R346T, 20 with FLiRT) Jul 1, 2024
@xz-keg xz-keg changed the title Another JN.1+S:S31F(111 seqs, 7 countries, 39 with S:R346T, 20 with FLiRT) Another JN.1+S:S31F(112 seqs, 7 countries, 40 with S:R346T, 21 with FLiRT) Jul 13, 2024
@xz-keg xz-keg changed the title Another JN.1+S:S31F(112 seqs, 7 countries, 40 with S:R346T, 21 with FLiRT) Another JN.1+S:S31F(114 seqs, 7 countries, 42 with S:R346T, 23 with FLiRT) Jul 31, 2024
@xz-keg xz-keg changed the title Another JN.1+S:S31F(114 seqs, 7 countries, 42 with S:R346T, 23 with FLiRT) Another JN.1+S:S31F(118 seqs, 7 countries, 46 with S:R346T, 27 with FLiRT) Aug 5, 2024
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xz-keg commented Aug 10, 2024

119,Canada

@xz-keg xz-keg changed the title Another JN.1+S:S31F(118 seqs, 7 countries, 46 with S:R346T, 27 with FLiRT) Another JN.1+S:S31F(119 seqs, 8 countries, 47 with S:R346T, 27 with FLiRT) Aug 10, 2024
@xz-keg xz-keg closed this as not planned Won't fix, can't repro, duplicate, stale Aug 15, 2024
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