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Desigante JN.1.39 (G2782T)
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corneliusroemer committed Mar 25, 2024
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4 comments on commit c193ce6

@xz-keg
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@xz-keg xz-keg commented on c193ce6 Mar 25, 2024

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The correct trajectory of JN.1.33 shall be JN.1->G2782T->T111C->C5512T->S:A67V. Usher places it in a wrong place because some seqs have missing coverage on position 111.

So this one(JN.1.39) shall be parent of JN.1.33. Maybe designation shall be changed to JN.1.39.1 for JN.1.33.

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cc @corneliusroemer @AngieHinrichs important comment by @aviczhl2 that first noticed this thing

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JN.1.33 is currently placed at JN.1 > C5512T > G2782T > C21762T. JN.1 > C5512T has 90 sequences, with dates starting ~2023-11-09 (preceding JN.1.33 dates), without G2782T etc. So it's not impossible that C5512T came first for these. Why should two occurrences of G2782T be less plausible than two occurrences of C5512T? I think this is one of many cases where we can't tell between two occurrences of one mutation, two occurrences of a different mutation, or some other thing like recombination.

Also, the pangolin program masks all sites in the untranslated regions (UTR) at the beginning and end of the genome (1-265 and 29674-29903), so pangolin masks position 111, so that can't be part of the definition of a lineage that pangolin is going to call. I could mask position 111 in JN.1 in order to simplify these and perhaps make a hope of joining them, but still parsimony can't tell the difference between C5512T > G2782T and G2782T > C5512T when there are some sequences that have only C5512T, some sequences that have only G2782T, and some sequences that have both.

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@xz-keg xz-keg commented on c193ce6 Apr 13, 2024

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JN.1.33 is currently placed at JN.1 > C5512T > G2782T > C21762T. JN.1 > C5512T has 90 sequences, with dates starting ~2023-11-09 (preceding JN.1.33 dates), without G2782T etc. So it's not impossible that C5512T came first for these. Why should two occurrences of G2782T be less plausible than two occurrences of C5512T? I think this is one of many cases where we can't tell between two occurrences of one mutation, two occurrences of a different mutation, or some other thing like recombination.

Also, the pangolin program masks all sites in the untranslated regions (UTR) at the beginning and end of the genome (1-265 and 29674-29903), so pangolin masks position 111, so that can't be part of the definition of a lineage that pangolin is going to call. I could mask position 111 in JN.1 in order to simplify these and perhaps make a hope of joining them, but still parsimony can't tell the difference between C5512T > G2782T and G2782T > C5512T when there are some sequences that have only C5512T, some sequences that have only G2782T, and some sequences that have both.

Don't need that, just add the T111C to seqs on JN.1 > C5512T > G2782T > C21762T but without T111C due to missing coverage on 111.
I guess usher will automatically change the tree as G2782T>T111C is 2 mutations while C5512T is only 1 mutation.

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