JN.1.24.1 (346T) > FLiRT with S:F456L (101 seqs) emerged in Texas (NOTE: unreliable query)

[FedeGueli]

Originally tracked in Branch 37 of sars-cov-2-variants/lineage-proposals#1089

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

JN.1.24.1 ( Parent) proposal

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 :G22599C, T22928C, G25290T,T3565C,-A1308G,-C7113T,-C774T,-G2782T
Samples: 89
Countries : 9 Including Guadaloupe
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

Tree as July 19:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_60e2f_a9fc70.json?f_userOrOld=uploaded%20sample&label=id:node_6956545

[krosa1910]

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]

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

@corneliusroemer i suggest a designation of this one.

[FedeGueli]

the S:R346T branch designated JN.1.24.1 via 2a82248

[FedeGueli]

+2 Minnesota , Ireland

[FedeGueli]

+1 Ontario

[FedeGueli]

+1 Texas

[FedeGueli]

+2 Ireland (with S:A288T) and Ohio

[FedeGueli]

+2 Ireland and Wisconsin

[FedeGueli]

30 now with a big upload from Texas yesterday

[FedeGueli]

Big upload today from Ireland in the area of Dublin all carrying the additional S:A288T mutation
JN.1.24.1 [ S:C1243F (G25290T)] > S:R346T (G22599C)] > S:F456L (T22928C) >C20178T>A27489G> S:A288T (G22424A)
Query:C20178T,A27489G,G22424A
Samples:14

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

[FedeGueli]

56 now (FLiRT)

[FedeGueli]

57 Hawaii

[FedeGueli]

79

[FedeGueli]

dying off closing this

[FedeGueli]

83 still around in Texas not worth reopening, interestingly one from NZL has DeFLIRT

[xz-keg]

4/10 in the most recent batch of Guadeloupe.

[FedeGueli]

4/10 in the most recent batch of Guadeloupe.

Rearranged the proposal with a new query and reopened the issue thank you for spotting!

[DailyCovidCases]

Tree now:
usher

It shows 91 seqs

[FedeGueli]

yeah likely new samples are from other lineages.

[FedeGueli]

As supsected all from other lineages.