XBB.1.9.1 with ORF1a:A876S / nsp3_A58S (230 seqs, 27 countries)

[NkRMnZr]

Defining Mutations: XBB.1.9.1 > G2891T(ORF1a:A876S) Query: G5720A, C11956T, G2891T Earliest seq: 2023-02-07 (EPI_ISL_17017836, Austria) Latest seq: 2023-06-14 (EPI_ISL_17954793, Portugal) Sampled Countries: Australia, Austria, Brunei, Canada, China, Czech, Denmark, Finland, Georgia, Germany, Ireland, Israel, Italy, Japan, Malaysia, Mauritius, New Zealand, Portugal, Russia, South Korea, Spain, Sweden, Thailand, Ukraine, UK, USA

Genomes:

EPI_ISL_17006000, EPI_ISL_17017836, EPI_ISL_17017891, EPI_ISL_17079936, EPI_ISL_17208746, EPI_ISL_17289050, EPI_ISL_17289167, EPI_ISL_17289194, EPI_ISL_17319325, EPI_ISL_17327765, EPI_ISL_17344456, EPI_ISL_17367352, EPI_ISL_17389991, EPI_ISL_17390042, EPI_ISL_17401528, EPI_ISL_17412393, EPI_ISL_17423031, EPI_ISL_17423248, EPI_ISL_17440492, EPI_ISL_17441131, EPI_ISL_17446180, EPI_ISL_17446478, EPI_ISL_17462015, EPI_ISL_17465386, EPI_ISL_17465403, EPI_ISL_17469519, EPI_ISL_17474865, EPI_ISL_17474869, EPI_ISL_17480956, EPI_ISL_17481011, EPI_ISL_17481903, EPI_ISL_17488253, EPI_ISL_17488256, EPI_ISL_17499330, EPI_ISL_17499782, EPI_ISL_17499844, EPI_ISL_17499865, EPI_ISL_17499889, EPI_ISL_17500000, EPI_ISL_17504722, EPI_ISL_17510839, EPI_ISL_17510908, EPI_ISL_17510964, EPI_ISL_17511837, EPI_ISL_17514143, EPI_ISL_17528955-17528956, EPI_ISL_17535504, EPI_ISL_17535540, EPI_ISL_17535553, EPI_ISL_17544782, EPI_ISL_17549831, EPI_ISL_17552476, EPI_ISL_17552640, EPI_ISL_17558344, EPI_ISL_17559021, EPI_ISL_17563022, EPI_ISL_17565671, EPI_ISL_17566431, EPI_ISL_17566488, EPI_ISL_17566493, EPI_ISL_17567052, EPI_ISL_17567114-17567115, EPI_ISL_17567136, EPI_ISL_17567155, EPI_ISL_17579027, EPI_ISL_17592486, EPI_ISL_17592590, EPI_ISL_17592597, EPI_ISL_17596749, EPI_ISL_17598350, EPI_ISL_17602347, EPI_ISL_17605521, EPI_ISL_17605542, EPI_ISL_17605564, EPI_ISL_17614605, EPI_ISL_17622522, EPI_ISL_17630312, EPI_ISL_17630379, EPI_ISL_17634082-17634083, EPI_ISL_17638067, EPI_ISL_17642705-17642706, EPI_ISL_17642710, EPI_ISL_17642730, EPI_ISL_17644106, EPI_ISL_17644532, EPI_ISL_17645747, EPI_ISL_17646720, EPI_ISL_17652646, EPI_ISL_17653795, EPI_ISL_17659431, EPI_ISL_17659962, EPI_ISL_17660028, EPI_ISL_17662141, EPI_ISL_17662143, EPI_ISL_17664743, EPI_ISL_17664776, EPI_ISL_17664802, EPI_ISL_17664934, EPI_ISL_17664993, EPI_ISL_17665103, EPI_ISL_17665159, EPI_ISL_17665194, EPI_ISL_17665214, EPI_ISL_17665219, EPI_ISL_17665236, EPI_ISL_17665313, EPI_ISL_17665316-17665317, EPI_ISL_17665319, EPI_ISL_17665333, EPI_ISL_17665476, EPI_ISL_17665785, EPI_ISL_17665823, EPI_ISL_17672025, EPI_ISL_17680297, EPI_ISL_17682169, EPI_ISL_17682187, EPI_ISL_17682189-17682190, EPI_ISL_17682229, EPI_ISL_17684854, EPI_ISL_17684872, EPI_ISL_17684891, EPI_ISL_17684893, EPI_ISL_17687736, EPI_ISL_17701300, EPI_ISL_17701426, EPI_ISL_17707800, EPI_ISL_17707919, EPI_ISL_17713603-17713604, EPI_ISL_17713606, EPI_ISL_17713611, EPI_ISL_17715407, EPI_ISL_17716513, EPI_ISL_17716550, EPI_ISL_17716577, EPI_ISL_17716645, EPI_ISL_17720215, EPI_ISL_17722592, EPI_ISL_17736238, EPI_ISL_17761573, EPI_ISL_17761585, EPI_ISL_17761602, EPI_ISL_17761608, EPI_ISL_17761750, EPI_ISL_17761753-17761754, EPI_ISL_17761807, EPI_ISL_17764584, EPI_ISL_17767515, EPI_ISL_17779100, EPI_ISL_17780143, EPI_ISL_17780282, EPI_ISL_17781120, EPI_ISL_17781128, EPI_ISL_17781132, EPI_ISL_17781136-17781138, EPI_ISL_17783037, EPI_ISL_17784122, EPI_ISL_17786209, EPI_ISL_17786220, EPI_ISL_17786717, EPI_ISL_17786725, EPI_ISL_17789861, EPI_ISL_17791962, EPI_ISL_17801784, EPI_ISL_17802413, EPI_ISL_17802928, EPI_ISL_17803043, EPI_ISL_17803442, EPI_ISL_17803878, EPI_ISL_17808476, EPI_ISL_17818032-17818033, EPI_ISL_17818038, EPI_ISL_17818170, EPI_ISL_17818289, EPI_ISL_17818293, EPI_ISL_17818295, EPI_ISL_17818353, EPI_ISL_17826769, EPI_ISL_17831431, EPI_ISL_17831469, EPI_ISL_17831477, EPI_ISL_17831492, EPI_ISL_17831494, EPI_ISL_17832680, EPI_ISL_17832684, EPI_ISL_17834835, EPI_ISL_17836158, EPI_ISL_17836166, EPI_ISL_17836182, EPI_ISL_17837270-17837272, EPI_ISL_17837294-17837295, EPI_ISL_17837303, EPI_ISL_17860913, EPI_ISL_17860920, EPI_ISL_17879261, EPI_ISL_17879311, EPI_ISL_17879314, EPI_ISL_17879335, EPI_ISL_17885326, EPI_ISL_17885370, EPI_ISL_17954790-17954791, EPI_ISL_17954793, EPI_ISL_17959046, EPI_ISL_17971211, EPI_ISL_17974310, EPI_ISL_17974424, EPI_ISL_17975291

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3eb90_d84bf0.json?f_userOrOld=uploaded%20sample

view from XBB.1.9.1's polytomy

details from ORF1a:A876S branch, with filter to samples collected since May 1st

Trivia:

• 91 out of 221 seqs collected since May 1st, with 5-20% prevalence in Russia and Denmark (too little seqs to confirm)
• 2 seqs got S:T478R follows: main proposal >C23053T > C22995G(S:T478R), query: C23053T, C22995G, G2891T finds 2

[FedeGueli]

I dont think all the branch is fast , but some of its sublineages could be, as the one with N:L219F or with S:E554Q or with Orf1b:P1727S

[NkRMnZr]

23-07-18: 9 seqs from countries

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3429e_6581c0.json?f_userOrOld=uploaded%20sample  2 from Slovakia: EPI_ISL_17980676-17980677 2 from Ukraine: EPI_ISL_17982477-17982478 1 from Shanghai, China: EPI_ISL_17987486 2 from Brunei: EPI_ISL_17989199, EPI_ISL_17989209 2 from Finland: EPI_ISL_17994818-17994819

[FedeGueli]

A branch of this one with S:Q493L popped up in Finland : https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_38d49_65e830.json?c=userOrOld&label=id:node_6704936 Please propose it , highlighting the fact it is showing a lot of diversity with relevant or interesting spike mutations further acquired.

[FedeGueli]

ping @corneliusroemer

[NkRMnZr]

Transferred to cov-lineages/pango-designation#2110