JN.1+S:F456L with C6968T branch (169 seqs)

[DailyCovidCases]

From branch 79 of sars-cov-2-variants/lineage-proposals#1253
JN.1+C6968T+S:F456L
Query: C6968T, T22928C, C18894T
No. of seqs: 30 (Canada 1 China 3 France 1 Singapore 3 South Korea 2 Spain 2 Sweden 1 UK 10 USA 7)
First: EPI_ISL_19051595, 2024-3-23
Latest: PP934275.1, 2024-6-10
usher

[FedeGueli]

thanks for proposing but i suggest to close this down , the query catches multiple lineages

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_462b3_42fab0.json?f_userOrOld=uploaded%20sample&label=id:node_6939135
the one proposed here seems very small:

When a multiple lineages issue is open it is like a notebook where initial queries are annotated, sometimes they are very good , while more usually they then have to be updated to exclude convergent lineages, so when you go to propose a lineage and you see that the sequences are widespread in the tree better stopping and highlighiting that in the comments before proposing it. thank you for your work anyway

[xz-keg]

When a multiple lineages issue is open it is like a notebook where initial queries are annotated, sometimes they are very good , while more usually they then have to be updated to exclude convergent lineages, so when you go to propose a lineage and you see that the sequences are widespread in the tree better stopping and highlighiting that in the comments before proposing it. thank you for your work anyway

Yeah. But it is quite shocking that C6968T is so convergent as a synonym mutation.

[FedeGueli]

When a multiple lineages issue is open it is like a notebook where initial queries are annotated, sometimes they are very good , while more usually they then have to be updated to exclude convergent lineages, so when you go to propose a lineage and you see that the sequences are widespread in the tree better stopping and highlighiting that in the comments before proposing it. thank you for your work anyway

Yeah. But it is quite shocking that C6968T is so convergent as a synonym mutation.

agree

[DailyCovidCases]

Tracked in tracker79

[FedeGueli]

C6968T, T22928C, C18894T

did you update the query? @DailyCovidCases if not it is not monophyletic as highlighted in a comment above. please check