2 XBB.1.9.1* sublineages with S:E554K (Branch A with 61 seqs in 13 countries; Branch B with 49 seqs mainly in South Korea)

[HynnSpylor]

I propose 2 XBB.1.9.1* sublineages with S:E554K

Branch A: 61 seqs Defining mutations: XBB.1.9.1>G23222A (S: E554K)

GISAID query: Spike_E554K, -Spike_A701V, G5720A, C11956T, -G2235A, -G2174A, -C12412T, -C230T (for excluding of convergent branch) Earliest seq: 2023-02-15 (USA, EPI_ISL_17053663) Most recent seq: 2023-05-19 (Finland, EPI_ISL_17763434) Countries detected: Finland (20), USA (14), Spain (6), France (4), South Korea (4), Canada (3), Egypt (3), Switzerland (2), UK (1), Australia (1), Netherland (1), Austria (1), Croatia (1)

Usher Tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_34fb6_de6040.json

Genomes: EPI_ISL_17053663-17053664, EPI_ISL_17172393, EPI_ISL_17229800, EPI_ISL_17294273, EPI_ISL_17424204, EPI_ISL_17424269, EPI_ISL_17427611, EPI_ISL_17464030, EPI_ISL_17515694, EPI_ISL_17547211, EPI_ISL_17554957, EPI_ISL_17584790, EPI_ISL_17617654, EPI_ISL_17657476, EPI_ISL_17661640, EPI_ISL_17677129, EPI_ISL_17677168, EPI_ISL_17678992, EPI_ISL_17679464, EPI_ISL_17679499, EPI_ISL_17679663, EPI_ISL_17680402, EPI_ISL_17680576, EPI_ISL_17689575, EPI_ISL_17689586, EPI_ISL_17689967, EPI_ISL_17696737, EPI_ISL_17699170, EPI_ISL_17701072, EPI_ISL_17707076, EPI_ISL_17719445, EPI_ISL_17721684, EPI_ISL_17722259, EPI_ISL_17726791, EPI_ISL_17727086, EPI_ISL_17727444, EPI_ISL_17728887, EPI_ISL_17731344, EPI_ISL_17734248, EPI_ISL_17734568, EPI_ISL_17738885, EPI_ISL_17738889, EPI_ISL_17763174, EPI_ISL_17763186, EPI_ISL_17763417, EPI_ISL_17763419, EPI_ISL_17763421-17763422, EPI_ISL_17763426-17763427, EPI_ISL_17763429, EPI_ISL_17763432, EPI_ISL_17763434, EPI_ISL_17763442-17763447, EPI_ISL_17763450

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Branch B: FL.10 (XBB.1.9.1.10) sublineage with S:E554K Defining mutations: FL.10>C4234T>G23222A (S: E554K)

GISAID query: Spike_E554K, G5720A, C11956T, G2235A, C4234T Earliest seq: 2023-03-02 (Egypt, EPI_ISL_17424021) Most recent seq: 2023-05-27 (South Korea, EPI_ISL_17762213) Countries detected: South Korea (40), USA (3), Egypt (3), France (2), Sweden (1) Usher Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_34fb6_de6050.json?c=gt-S_554

Genomes: EPI_ISL_17424002, EPI_ISL_17424020-17424021, EPI_ISL_17480594, EPI_ISL_17490035, EPI_ISL_17511580, EPI_ISL_17554675, EPI_ISL_17604298, EPI_ISL_17604366, EPI_ISL_17604617, EPI_ISL_17605978, EPI_ISL_17606018, EPI_ISL_17647314, EPI_ISL_17668941, EPI_ISL_17677427, EPI_ISL_17677746, EPI_ISL_17677780, EPI_ISL_17677949, EPI_ISL_17677951, EPI_ISL_17680525, EPI_ISL_17690724, EPI_ISL_17691493, EPI_ISL_17691970, EPI_ISL_17691977-17691978, EPI_ISL_17691988, EPI_ISL_17691994-17691995, EPI_ISL_17692000-17692002, EPI_ISL_17700359, EPI_ISL_17700462, EPI_ISL_17729445, EPI_ISL_17730493, EPI_ISL_17730521, EPI_ISL_17730573, EPI_ISL_17730591, EPI_ISL_17730652, EPI_ISL_17730683, EPI_ISL_17730750, EPI_ISL_17730846, EPI_ISL_17740982, EPI_ISL_17762023, EPI_ISL_17762054, EPI_ISL_17762056, EPI_ISL_17762168, EPI_ISL_17762183, EPI_ISL_17762213

The geographic distribution of two branches is highly overlapped, hence they are likely convergent.

[FedeGueli]

Branch B now Designated FL.10.1

[FedeGueli]

Branch 1 proposed here is now over 100 sequences i suggest toi designate this one too @InfrPopGen

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5bd97_4c33f0.json?c=userOrOld&label=id:node_6602448

[FedeGueli]

@HynnSpylor now also branch 1 has been designated FL.25 via https://github.com/cov-lineages/pango-designation/commit/cbbfabf06209eb65da5bb3aef839c90c2fce6241 please close down the issue: