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

cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme

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JN.1+S:F456L with C27110T branch (22 seqs) #2645

Closed DailyCovidCases closed 4 weeks ago

DailyCovidCases commented 3 months ago

From branch 73 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/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 Screenshot (165)

FedeGueli commented 3 months ago

39 now

FedeGueli commented 3 months ago

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 commented 3 months ago

@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 commented 2 months ago

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 commented 2 months ago

Tracked in tracker73

FedeGueli commented 2 months ago

Tracked in tracker73

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

FedeGueli commented 4 weeks ago

Already designated LF.8.1.1 please close this