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JN.1.11.1+C6070T with FLiRT (346T+456L) and S:K187R (32 sequences, 10 countries ) #2523

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FedeGueli opened this issue Mar 17, 2024 · 8 comments
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JN.1.11.1+C6070T with FLiRT (346T+456L) and S:K187R (32 sequences, 10 countries ) #2523

FedeGueli opened this issue Mar 17, 2024 · 8 comments

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@FedeGueli
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Previously tracked as Branch 52 in sars-cov-2-variants/lineage-proposals#1089
One more JN.1.11.1 sublineage got FliRT combo mutation S:F456L S:R346T and a further NTD mutation S:K187R

JN.1.11.1 > C6070T > S:K187R (A22122G), S:R346T (G22599C)
Query: C6070T,G22599C,C7113T,G24872T,-C19884T
Samples: 9
Countries: Australia, US ( NY, NJ), Lebanon, Singapore (via China), India (via GBW)
IDs:
EPI_ISL_18933442, EPI_ISL_18939081, EPI_ISL_18945988,
EPI_ISL_18953029, EPI_ISL_18961244-18961245, EPI_ISL_18983740,
EPI_ISL_18983801, EPI_ISL_18983814
Tree:
Screenshot 2024-03-17 alle 04 09 18
Screenshot 2024-03-17 alle 04 08 59
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_c546_5e69a0.json?c=gt-S_346,187&gmax=25384&gmin=21563&label=id:node_6944915
@FedeGueli FedeGueli mentioned this issue Mar 17, 2024
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@karyakarte
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@FedeGueli as discussed earlier, JN.1 and JN.1.1 are declining in February as JN.1.11.1 and JN.1.18 are on a rise.

@FedeGueli FedeGueli changed the title JN.1.11.1+C6070T with FLiRT (346T+456L) and S:K187R (9 sequences, 5 countries , 3 continents) JN.1.11.1+C6070T with FLiRT (346T+456L) and S:K187R (10 sequences, 5 countries , 3 continents) Mar 18, 2024
@FedeGueli
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+1 California

@FedeGueli FedeGueli changed the title JN.1.11.1+C6070T with FLiRT (346T+456L) and S:K187R (10 sequences, 5 countries , 3 continents) JN.1.11.1+C6070T with FLiRT (346T+456L) and S:K187R (16 sequences, 8 countries , 4 continents) Mar 24, 2024
@FedeGueli
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16 now also from Scotland , Singapore (GBW) and Canada

@krosa1910 krosa1910 mentioned this issue Mar 30, 2024
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@FedeGueli FedeGueli changed the title JN.1.11.1+C6070T with FLiRT (346T+456L) and S:K187R (16 sequences, 8 countries , 4 continents) JN.1.11.1+C6070T with FLiRT (346T+456L) and S:K187R (20 sequences, 8 countries , 4 continents) Apr 5, 2024
@FedeGueli
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20, @corneliusroemer i suggest to designate it.

@xz-keg
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xz-keg commented Apr 9, 2024

27 now

@FedeGueli FedeGueli changed the title JN.1.11.1+C6070T with FLiRT (346T+456L) and S:K187R (20 sequences, 8 countries , 4 continents) JN.1.11.1+C6070T with FLiRT (346T+456L) and S:K187R (27 sequences, 8 countries , 4 continents) Apr 10, 2024
@FedeGueli FedeGueli changed the title JN.1.11.1+C6070T with FLiRT (346T+456L) and S:K187R (27 sequences, 8 countries , 4 continents) JN.1.11.1+C6070T with FLiRT (346T+456L) and S:K187R (32 sequences, 10 countries ) Apr 14, 2024
@FedeGueli
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32 seqs

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.4.2 via 8fbd0bc

@FedeGueli
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One sequence of KP.4.2 popped up today in Texas with a further mutation at S:187 : S:K>R187S involving two nucleotides in two steps: A22122G (>R) > A22123T (>S)
Query: A22122G,A22123T (cause it is the first ever sample with it)

Interestingly it should create a N Glycan at S:N185
Screenshot 2024-05-02 alle 22 49 15
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_4a23b_3d3430.json?c=gt-S_187&label=id:node_6979126

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3 participants
@xz-keg @FedeGueli @karyakarte