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

Closed FedeGueli closed 2 months ago

FedeGueli commented 3 months ago

Previously tracked as Branch 52 in https://github.com/sars-cov-2-variants/lineage-proposals/issues/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

karyakarte commented 3 months ago

@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 commented 3 months ago

+1 California

FedeGueli commented 3 months ago

16 now also from Scotland , Singapore (GBW) and Canada

FedeGueli commented 3 months ago

20, @corneliusroemer i suggest to designate it.

aviczhl2 commented 3 months ago

27 now

FedeGueli commented 2 months ago

32 seqs

FedeGueli commented 2 months ago

designated KP.4.2 via https://github.com/cov-lineages/pango-designation/commit/8fbd0bccca8b93f0293ab4139818fbd28d41cf74

FedeGueli commented 2 months ago

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