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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.1.4 with Orf1a:D4117N, S:T22N and S:R346T (54 seqs) #2602

Closed DailyCovidCases closed 3 months ago

DailyCovidCases commented 4 months ago

From branch 24 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089 JN.1.4 > T18453C > C7732T, Orf1a:D4117N (G12614A),S:T22N (C21627A), G22111A, S:R346T (G22599C), C27944T Query: T18453C ,C7732T, ,G12614A,G22599C Samples : 37 ( US 36 Mexico 1) First: EPI_ISL_18730727, 2023-12-16 Latest: PP774304.1, 2024-04-21 usher Screenshot (63)

FedeGueli commented 3 months ago

New Query: C27944T,G12614A,C774T, G22599C samples: 40 It seems S:T22N came before S:R346T but it is not possible to exclude it was acquired multiple times independently by this lineage Current tree:

Screenshot 2024-06-30 alle 16 14 04

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice13_genome_test_318ef_115640.json?label=id:node_7107010

ryhisner commented 3 months ago

Just 2 sequences since April 21 for a lineage that first appeared in December. Makes sense to close this issue I think.

DailyCovidCases commented 1 week ago

Tree now: usher Screenshot (220) @corneliusroemer Is this branch worth a designation?

FedeGueli commented 1 week ago

54 with the new query: C27944T,G12614A,C774T, G22599C 3 samples after July ( 1 in August)