New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 18 sequences Uk, Canada

[FedeGueli]

Formerly tracked as Branch 94 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089 JN.1 > S:H1101Y > S:F456L > S:R346T > S:S71F Query: C24863T, G22599C, T3565C,C21774T Samples: 9 Uk, US, Canada EPI_ISL_19010354, EPI_ISL_19059574, EPI_ISL_19062909-19062913, EPI_ISL_19062915, EPI_ISL_19064899

It further gained S:L1203F: JN.1 > S:H1101Y > S:F456L > S:R346T > S:S71F > Orf1a:P1912S (C6026T) > A7285G > S:L1203F (C25169T) Query: C25169T,A7285G Samples: 2 (Scotland)

Tree: updated at 05/07:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice8_genome_2696e_95ba50.json?label=id:node_6958379

To be noted that there is another lineage that has JN.1 > S:S71F > S:R346T > S:F456L without S:H1101Y tracked as branch 99 in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089 View it here :

Same lineage???

Query:C21774T ,G22599C ,T22928C,T3565C,-C7113T,-C24863T [tree](https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_464f0_7af8b0.json?label=id:node_6936214)

cc @AngieHinrichs @corneliusroemer

[FedeGueli]

+2

[FedeGueli]

12 on Gisaid , 14 on Usher. Typical stepwise evolution tree (updated with new samples in the main proposal) with last sample carrying a further S2 mutation : S:L1203F

[FedeGueli]

13

[FedeGueli]

14

[FedeGueli]

18 seqs but not relevant for designation