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Another JN.1.11.1 lineage with FLiRT (456L 346T) 44 seqs , 6 countries with a branch with S:W258R (6) #2521

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FedeGueli opened this issue Mar 15, 2024 · 13 comments
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Another JN.1.11.1 lineage with FLiRT (456L 346T) 44 seqs , 6 countries with a branch with S:W258R (6) #2521

FedeGueli opened this issue Mar 15, 2024 · 13 comments

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@FedeGueli
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FedeGueli commented Mar 15, 2024 •
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This was previously tracked as Branch 53 of sars-cov-2-variants/lineage-proposals#1089

JN.1.11.1 > C6070T > C19884T > S:R346T (G22599C)
Query: C6070T,G22599C,C7113T,G24872T, C19884T
Samples: 7
Countries: Australia , Canada, US (Texas), India (GBW)
IDs:EPI_ISL_18912216, EPI_ISL_18937582, EPI_ISL_18937584,
EPI_ISL_18960842, EPI_ISL_18965320, EPI_ISL_18972869,
EPI_ISL_18980922

Tree as of April 8:

Screenshot 2024-04-08 alle 14 36 23 Screenshot 2024-04-08 alle 14 36 40 https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_139f2_3e3b50.json?label=id:node_6962173

There is further branch with S:W258R (T22334A) spotted by @aviczhl2
Query: T22334A,G24872T,T3565C Samples: 4
Screenshot 2024-04-08 alle 14 37 05
@FedeGueli FedeGueli mentioned this issue Mar 15, 2024
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@xz-keg
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xz-keg commented Mar 15, 2024

Why not proposing the K187R branch

@FedeGueli
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Why not proposing the K187R branch

i m waiting one more sequence

@FedeGueli FedeGueli changed the title Another JN.1.11.1 lineage with FLiRT combo (456L 346T) 7 seqs , 3 continents Another JN.1.11.1 lineage with FLiRT combo (456L 346T) 8 seqs , 3 continents Mar 16, 2024
@FedeGueli
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+1 India (GBW)

@FedeGueli FedeGueli changed the title Another JN.1.11.1 lineage with FLiRT combo (456L 346T) 8 seqs , 3 continents Another JN.1.11.1 lineage with FLiRT combo (456L 346T) 11 seqs , 5 countries Mar 24, 2024
@FedeGueli
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11 sequences now

@FedeGueli FedeGueli changed the title Another JN.1.11.1 lineage with FLiRT combo (456L 346T) 11 seqs , 5 countries Another JN.1.11.1 lineage with FLiRT combo (456L 346T) 15 seqs , 6 countries Mar 28, 2024
@FedeGueli
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15 seqs new country Vietnam

@krosa1910 krosa1910 mentioned this issue Mar 30, 2024
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@FedeGueli FedeGueli changed the title Another JN.1.11.1 lineage with FLiRT combo (456L 346T) 15 seqs , 6 countries Another JN.1.11.1 lineage with FLiRT combo (456L 346T) 26 seqs , 6 countries Apr 2, 2024
@FedeGueli
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26 now @corneliusroemer it is growing fast, as expected being a KP.2 homologous. i suggest to designate

@FedeGueli FedeGueli changed the title Another JN.1.11.1 lineage with FLiRT combo (456L 346T) 26 seqs , 6 countries Another JN.1.11.1 lineage with FLiRT combo (456L 346T) 34 seqs , 6 countries Apr 7, 2024
@FedeGueli
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34

@xz-keg
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xz-keg commented Apr 8, 2024

There is a S:W258R sub-branc of this.

@FedeGueli FedeGueli changed the title Another JN.1.11.1 lineage with FLiRT combo (456L 346T) 34 seqs , 6 countries Another JN.1.11.1 lineage with FLiRT combo (456L 346T) 36 seqs , 6 countries Apr 8, 2024
@FedeGueli FedeGueli changed the title Another JN.1.11.1 lineage with FLiRT combo (456L 346T) 36 seqs , 6 countries Another JN.1.11.1 lineage with FLiRT (456L 346T) 36 seqs , 6 countries with a branch with S:W258R (4) Apr 8, 2024
@FedeGueli
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There is a S:W258R sub-branc of this.

thx added it to the proposal

@FedeGueli FedeGueli changed the title Another JN.1.11.1 lineage with FLiRT (456L 346T) 36 seqs , 6 countries with a branch with S:W258R (4) Another JN.1.11.1 lineage with FLiRT (456L 346T) 44 seqs , 6 countries with a branch with S:W258R (6) Apr 14, 2024
@FedeGueli
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44 now and 6 with 258R

FedeGueli referenced this issue Apr 16, 2024
@corneliusroemer
Designate KP.4 (JN.1.11.1.4, C6070T, India), KP.4.1 (S:R346T, C19884T…
8fbd0bc 
…), KP.4.2 (S:R346T, S:K187R)

Note: I'm only designating this now because there was uncertainty whether 6070T happened
before or after the 346T. The 4.1 and 4.2 could also be sublineages of KP.2
After all, the fact that there's little 6070T with just 346T and that most have
an extra mutation (C19884T for KP.4.1, and S:K187R for KP.4.2) made me content
with making this a convergent lineage.

We likely won't ever know what the "truth" is but that's ok, Pango is not
perfect and doesn't have to be for it to be useful.
@FedeGueli
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Designated KP.4.1. via 8fbd0bc

@FedeGueli
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One interesting singlet in KP.4.1 with S:K182Q and S:A475V:
KP.4.1 >C5144T, 9328G, T11773A, C18687T, S:K182Q (A22106C), S:A475V (C22986T)
Query:A22106C,C22986T,A9328G
Samples: 1 UK

FedeGueli referenced this issue Jun 17, 2024
@corneliusroemer
Designate KP.4.1.1 (S:W258R, India), KP.4.1.2 (S:L441V), KP.4.1.3 (OR…
df86946 
…F1a:M598V, A5245G, S:31del)
@FedeGueli
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the sub branch with S:W258R designated KP.4.1.1 via df86946

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