JN.1.24.1 (346T) > FLiRT with S:F456L (83 seqs) likely emerged in Texas

FedeGueli commented 3 months ago

Originally tracked in Branch 37 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089

JN.1.24.1 [ S:C1243F (G25290T)] > S:R346T (G22599C)] > S:F456L (T22928C)

Query for the S:R346T branch : G22599C, G25290T, A6183G Samples: 22 Countries: Us (mainly Texas), Canada, Sweden IDs: EPI_ISL_18811311, EPI_ISL_18816744, EPI_ISL_18816982, EPI_ISL_18817077, EPI_ISL_18817110, EPI_ISL_18874220, EPI_ISL_18874505, EPI_ISL_18874870, EPI_ISL_18920907, EPI_ISL_18928072, EPI_ISL_18947689, EPI_ISL_18981402

Query for FLiRT Combo S:R346T + S:F456L :G22599C, G25290T, A6183G,T22928C or G22599C, T22928C, G25290T,T3565C Samples: 10 Country : US (All Texas), Canada EPI_ISL_18874396, EPI_ISL_18933600, EPI_ISL_18980900, EPI_ISL_18980941, EPI_ISL_18980948, EPI_ISL_18980957, EPI_ISL_18981020, EPI_ISL_18981101, EPI_ISL_18981255, EPI_ISL_18981378

Query for Irish FLiRT branch with S:A288T :C20178T,A27489G,G22424A JN.1.24.1 [ S:C1243F (G25290T)] > S:R346T (G22599C)] > S:F456L (T22928C) >C20178T>A27489G> S:A288T (G22424A)

Samples:14

Tree as of May 2:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice3_genome_test_4a23b_3d3430.json?label=id:node_6937346

Tree for the S:A288T branch

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice3_genome_test_4a23b_3d3430.json?label=id:node_6937346

krosa1910 commented 3 months ago

It was lineage 9 of my issue 1421, and just two days ago it was a doublet there. I updated the issue to include an usher tree for it regularly but did not pay attention to lineage updates or change on weekday updates so I missed it. Anyway this would be a good FLirt+ extra S mutation example and let's see if it is comparable with other FLirts.

FedeGueli commented 3 months ago

this is now 25 , 12 with FLiRT . last came from Israel so internationally spread now.

@corneliusroemer i suggest a designation of this one.