JN.1+S:F456L with G17562T branch (311 seqs)

[DailyCovidCases]

From branch 62 of sars-cov-2-variants/lineage-proposals#1253
JN.1+G17562T+S:F456L
Query: G17562T,T3565C, T22928C,-8716
No. of seqs: 62 (Australia 1 Canada 13 China 1 Denmark 1 France 3 Germany 1 India 2 Japan 3 Kenya 1 Singapore 4 South Korea 4 Spain 4 UK 8 USA 16)
First: OY991457.1, 2023-12-12
Latest: EPI_ISL_19162513, 2024-5-16
usher

[FedeGueli]

87

[DailyCovidCases]

Is this branch worth to be designated?

[FedeGueli]

Is it monophyletic? let me check

[FedeGueli]

it is. not monphyletic close this down:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_435d8_7a1800.json?f_userOrOld=uploaded%20sample&label=id:node_6939286

[DailyCovidCases]

151 seqs now
Tracked in tracker62
Is it worth to be designated? @corneliusroemer

[FedeGueli]

151 seqs now Tracked in tracker62 Is it worth to be designated? @corneliusroemer

Thius is not monophyletic close it down please. cc @aviczhl2

[xz-keg]

it is. not monphyletic close this down: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_435d8_7a1800.json?f_userOrOld=uploaded%20sample&label=id:node_6939286

What? Now this 17562 thing also appears in KP*? Crazy.

[FedeGueli]

it is. not monphyletic close this down: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_435d8_7a1800.json?f_userOrOld=uploaded%20sample&label=id:node_6939286

What? Now this 17562 thing also appears in KP*? Crazy.

Yeah 17562 went completely crazy (to me some sort of artifact) so with time it appeared there in KP.2 too likely.

too se you can use taxonium to check it: https://taxonium.org/?backend=https%3A%2F%2Fapi.cov2tree.org&srch=%5B%7B%22key%22%3A%22aa1%22%2C%22type%22%3A%22meta_pango_lineage_usher%22%2C%22method%22%3A%22text_exact%22%2C%22text%22%3A%22BA.2.86%22%2C%22gene%22%3A%22nt%22%2C%22position%22%3A%2217562%22%2C%22new_residue%22%3A%22any%22%2C%22min_tips%22%3A0%7D%2C%7B%22key%22%3A%22bxc48vo70gc%22%2C%22type%22%3A%22mutation%22%2C%22method%22%3A%22mutation%22%2C%22text%22%3A%22%22%2C%22gene%22%3A%22nt%22%2C%22position%22%3A%22017562%22%2C%22new_residue%22%3A%22A%22%2C%22min_tips%22%3A0%7D%5D&enabled=%7B%22aa1%22%3Atrue%2C%22bxc48vo70gc%22%3Atrue%7D