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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 C6968T branch (30 seqs, 9 countries) #2682

Open DailyCovidCases opened 3 days ago

DailyCovidCases commented 3 days ago

From branch 79 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/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 Screenshot (131)

FedeGueli commented 3 days ago

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

Screenshot 2024-07-02 alle 18 50 49

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:

Screenshot 2024-07-02 alle 18 51 19

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

aviczhl2 commented 2 days ago

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 commented 2 days ago

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