Another (?) XBB.1.11 lineage acquired S:F486P, with ORF1a:S2103F/nsp3_S1285F (22 seqs, 7 countries)

[NkRMnZr]

Defining Mutations: XBB.1.11 > C3241T > C29095T > C2536T, C6573T(ORF1a:S2103F), C15045T > C6997T, T23018C(S:F486P) Query: C3241T, C6573T, C6997T, T23018C Earliest seq: 2023-04-06 (EPI_ISL_17780640, Hanoi, Vietnam) Latest seq: 2023-07-06 (EPI_ISL_18041466, Miyazaki, Japan) Sampled Countries: South Korea (7), Japan (6), China (5, Sichuan/2, Anhui/1, Shanghai/1, Yunnan/1), Austria (1), Israel (1), Spain (1), Vietnam (1)

Genomes:

EPI_ISL_17554729, EPI_ISL_17558200, EPI_ISL_17618864, EPI_ISL_17633003, EPI_ISL_17650861, EPI_ISL_17690500, EPI_ISL_17691135, EPI_ISL_17691275, EPI_ISL_17718440, EPI_ISL_17730411, EPI_ISL_17730517, EPI_ISL_17736084, EPI_ISL_17780640, EPI_ISL_17785360, EPI_ISL_17883071, EPI_ISL_17883192, EPI_ISL_17958600, EPI_ISL_17959662, EPI_ISL_17969972, EPI_ISL_18041261, EPI_ISL_18041459, EPI_ISL_18041466

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2a92e_1e8cd0.json?f_userOrOld=uploaded%20sample&label=id:node_6779293

view from XBB.1.11 polytomy with nuc 2536 filter, upper hightlight branch is FP.4, lower is this proposal

details

Trivia:

• Need help to identify if it really is the sibling branch to cov-lineages/pango-designation#1490 that also acquired S:F486P, it shares the homoplastic C3241T, C2536T (and of course T23018C) with FP.4 (XBB.1.11.1.4), but they seems to be on different phylogenetic paths. Could this be a subset of FP.4 simply misplaced due to certain samples with dropout, or something new?
• I've checked there's no SGTF like FP.1 so far.

[FedeGueli]

FP.4 anf this one has 2536,3241,in common and differ for ,6573,15045 and C29095T

but in my view they are kept divided just by two/three sequences: EPI_ISL_17719711,EPI_ISL_17481626,EPI_ISL_17427836.

but i think only @angiehinrichs could really tell us.

[AngieHinrichs]

but in my view they are kept divided just by two/three sequences: EPI_ISL_17719711,EPI_ISL_17481626,EPI_ISL_17427836.

Yep, I'll prune those, re-optimize (which should put the branch in FP.4) and then let them be added back. Thanks!

[FedeGueli]

but in my view they are kept divided just by two/three sequences: EPI_ISL_17719711,EPI_ISL_17481626,EPI_ISL_17427836.

Yep, I'll prune those, re-optimize (which should put the branch in FP.4) and then let them be added back. Thanks!

Thanks!

[FedeGueli]

@NkRMnZr please recheck this one in some days. if it has been merged back in FP.4 please close this one.

[NkRMnZr]

Now it's fixed, seems to be false alarm then. https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1ee26_4c8110.json?c=gt-nuc_6997&f_userOrOld=uploaded%20sample&label=id:node_6796396

thanks @AngieHinrichs @FedeGueli

[FedeGueli]

Thank you @NkRMnZr for checking! Thx @AngieHinrichs for fixing it!