JN.1+S:F456L with C27110T branch (22 seqs)

[DailyCovidCases]

From branch 73 of sars-cov-2-variants/lineage-proposals#1253
JN.1+C27110T+S:F456L
Query: T22928C, C27110T, T22926C
No. of seqs: 33 (Canada 16 France 1 Ireland 10 Nepal 1 Spain 1 USA 4)
First: EPI_ISL_19166147, 2024-3-7
Latest: EPI_ISL_19175717, 2024-5-27
usher

[FedeGueli]

39 now

[FedeGueli]

44

[FedeGueli]

T22928C, C27110T, T22926C

nope, this is still 15 it is not monophyletic
correct query: T22928C, C27110T, T22926C,-C7113T

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_1a6e5_2ab0.json?f_userOrOld=uploaded%20sample&label=id:node_6938835
Please close it.

[FedeGueli]

@DailyCovidCases
when you propose from multiple lineages issue before transferring here check it if monophyletic ( one only branch) if not or you find a better query or better just highlight it to the author.
Multiple lineages issue are just as notes , a work in progress, so please don't take it as true and check them (as you already do) if not monophyletic wait before proposing them highlighting the not perfect query to the author. Thank you.

[FedeGueli]

T22928C, C27110T, T22926C

nope, this is still 15 it is not monophyletic correct query: T22928C, C27110T, T22926C,-C7113T https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_1a6e5_2ab0.json?f_userOrOld=uploaded%20sample&label=id:node_6938835 Please close it.

Now the lineage with S:S31F has started to grow and it has some recent samples:
New tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_678d2_93ce00.json?label=id:node_6970971

I think you can change the proposal to JN.1 + C27710T FLiRT + S:M153I and S:S31F
Query: C21654T, C9169T, G22021C
Samples : 7
Countries: 5 ( Australia, US, Spain , Switzerland, Qatar)

[DailyCovidCases]

Tracked in tracker73

[FedeGueli]

Tracked in tracker73

please update the proposal it catches multiple unrelated lineages see comment above, or close it pls

[FedeGueli]

Already designated LF.8.1.1 please close this