XBB.1.9.1 with S:F490P (206 seqs, 19 countries)

[NkRMnZr]

Transferred from sars-cov-2-variants/lineage-proposals#119

Defining mutations: (On XBB.1.9.1 Polytomy) > A20458G(ORF1b:I2331V) > T23030C(S:F490P) > Query: A20458G, T23030C, C11956T Earliest seq: 2023-02-16 (Finland, EPI_ISL_17077296) Latest seq: 2023-05-15 (Austria, EPI_ISL_17715256) Sampled in Countries: Finland (65), Sweden (22), Ireland (9), UK (7), Japan (5), Austria (4), USA (4), Spain (4, incl/ 1 from Canary Islands), France (4), Norway (1), Netherlands (1), Australia (1), Switzerland (1), Czech (1), Lithuania (1)

Genomes:

EPI_ISL_17077296, EPI_ISL_17222521, EPI_ISL_17222544, EPI_ISL_17222601, EPI_ISL_17222616, EPI_ISL_17222662, EPI_ISL_17300406, EPI_ISL_17323013, EPI_ISL_17323083, EPI_ISL_17323105, EPI_ISL_17376004, EPI_ISL_17382236, EPI_ISL_17382280, EPI_ISL_17382544, EPI_ISL_17394520, EPI_ISL_17415434, EPI_ISL_17415435, EPI_ISL_17415445, EPI_ISL_17415453, EPI_ISL_17426906, EPI_ISL_17440549, EPI_ISL_17440580, EPI_ISL_17469897, EPI_ISL_17470523, EPI_ISL_17485147, EPI_ISL_17485149, EPI_ISL_17488338, EPI_ISL_17509059, EPI_ISL_17509098, EPI_ISL_17512823, EPI_ISL_17528504, EPI_ISL_17528515, EPI_ISL_17528528, EPI_ISL_17528581, EPI_ISL_17528583, EPI_ISL_17528588, EPI_ISL_17528591, EPI_ISL_17528606, EPI_ISL_17528612, EPI_ISL_17540296, EPI_ISL_17540299, EPI_ISL_17540303, EPI_ISL_17540305, EPI_ISL_17540309, EPI_ISL_17540453, EPI_ISL_17540455, EPI_ISL_17540457, EPI_ISL_17540571, EPI_ISL_17540572, EPI_ISL_17540574, EPI_ISL_17540584, EPI_ISL_17540587, EPI_ISL_17540592, EPI_ISL_17540607, EPI_ISL_17540640, EPI_ISL_17547112, EPI_ISL_17565204, EPI_ISL_17565311, EPI_ISL_17565312, EPI_ISL_17565314, EPI_ISL_17565315, EPI_ISL_17593744, EPI_ISL_17593770, EPI_ISL_17598048, EPI_ISL_17598052, EPI_ISL_17598059, EPI_ISL_17598063, EPI_ISL_17598079, EPI_ISL_17598093, EPI_ISL_17598100, EPI_ISL_17598133, EPI_ISL_17598136, EPI_ISL_17598147, EPI_ISL_17598155, EPI_ISL_17630946, EPI_ISL_17640522, EPI_ISL_17640860, EPI_ISL_17640882, EPI_ISL_17640890, EPI_ISL_17660828, EPI_ISL_17661553, EPI_ISL_17661562, EPI_ISL_17661595, EPI_ISL_17661622, EPI_ISL_17661623, EPI_ISL_17661625, EPI_ISL_17661628, EPI_ISL_17661642, EPI_ISL_17661644, EPI_ISL_17661646, EPI_ISL_17664643, EPI_ISL_17666417, EPI_ISL_17667013, EPI_ISL_17669317, EPI_ISL_17672474, EPI_ISL_17678661, EPI_ISL_17679251, EPI_ISL_17679634, EPI_ISL_17683288, EPI_ISL_17684900, EPI_ISL_17689183, EPI_ISL_17692055, EPI_ISL_17692056, EPI_ISL_17699088, EPI_ISL_17699108, EPI_ISL_17699115, EPI_ISL_17699130, EPI_ISL_17699133, EPI_ISL_17699149, EPI_ISL_17699160, EPI_ISL_17699162, EPI_ISL_17699163, EPI_ISL_17699174, EPI_ISL_17700331, EPI_ISL_17700443, EPI_ISL_17704625, EPI_ISL_17706939, EPI_ISL_17710262, EPI_ISL_17710285, EPI_ISL_17710289, EPI_ISL_17710538, EPI_ISL_17713588, EPI_ISL_17715256, EPI_ISL_17715328, EPI_ISL_17722487, EPI_ISL_17731416, EPI_ISL_17732220, EPI_ISL_17732262, EPI_ISL_17732696, EPI_ISL_17732754

Trivia:

• XBB acquired F490S (T23031C) from one of the donor BM.1.1.1, further T23030C turns S to P at residue 490.
• XBB.1.13 and XBB.1.36 are the other XBB* with this convergent mutation.
• The growth advantage may got carried by XBB.1.9.1 itself.

UShER:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2d00c_6972e0.json?c=pango_lineage&f_userOrOld=uploaded%20sample&label=id:node_6685197

downsampled

detailed

[NkRMnZr]

Tracking updates

Update 1: 23-06-05, 5 seqs from 2 countries

4 more seqs from Sweden EPI_ISL_17742434, EPI_ISL_17742446, EPI_ISL_17742477, EPI_ISL_17742520 1 from Ukraine: EPI_ISL_17742950

Update 2: 23-06-06, 16 seqs from Finland

EPI_ISL_17763074, EPI_ISL_17763093, EPI_ISL_17763170, EPI_ISL_17763171, EPI_ISL_17763184, EPI_ISL_17763188, EPI_ISL_17763191, EPI_ISL_17763197, EPI_ISL_17763224, EPI_ISL_17763385, EPI_ISL_17763404, EPI_ISL_17763405, EPI_ISL_17763406, EPI_ISL_17763409, EPI_ISL_17763423, EPI_ISL_17763424

Update 3: 23-06-08, 3 seqs from 2 countries

2 more from Sweden: EPI_ISL_17769739, EPI_ISL_17769766 1 more from the USA: EPI_ISL_17768966

Update 4: 23-06-14, 3 seqs from 3 countries

1 England EPI_ISL_17786662 1 California EPI_ISL_17788906 1 Western Australia EPI_ISL_17790996

Update 5: 23-06-16, 4 seqs from 3 countries

1 Wales EPI_ISL_17796712 2 Germany EPI_ISL_17803496, EPI_ISL_17803501 1 Israel EPI_ISL_17803605

Update 6: 23-06-17, 3 seqs from 3 countries

Austria, EPI_ISL_17808478 Sweden, EPI_ISL_17809290 France, EPI_ISL_17809609

Update 7: 23-06-21, 6 seqs from 2 countries

5 from Sweden: EPI_ISL_17818795, EPI_ISL_17818836, EPI_ISL_17818844, EPI_ISL_17818846, EPI_ISL_17818859 1 from England: EPI_ISL_17813134

Update 8: 23-06-26, 3 seqs from 3 countries

New York: EPI_ISL_17821193 Switzerland: EPI_ISL_17830509 Ukraine: EPI_ISL_17833467

UShER tree after 8 updates:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2bcd9_961480.json?f_userOrOld=uploaded%20sample 

Update 9: 23-07-07, 3 seqs from 3 countries

1 from Israel: EPI_ISL_17954937 1 from Germany: EPI_ISL_17964462 1 from France: EPI_ISL_17971777

Update 10: 23-07-10, 16 seqs from Finland

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2cc1d_bd86e0.json?f_userOrOld=uploaded%20sample&showBranchLabels=all  EPI_ISL_17974267, EPI_ISL_17974337, EPI_ISL_17974418, EPI_ISL_17974421, EPI_ISL_17974432, EPI_ISL_17974435, EPI_ISL_17974437, EPI_ISL_17974446, EPI_ISL_17974484, EPI_ISL_17974488, EPI_ISL_17974520, EPI_ISL_17974525, EPI_ISL_17974526, EPI_ISL_17974544, EPI_ISL_17974549, EPI_ISL_17974572

Update 11: 23-07-18, 12 seqs from Finland and Denmark

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_10942_6480a0.json?f_userOrOld=uploaded%20sample&showBranchLabels=all  1 from Denmark: EPI_ISL_17975282 11 from Finland: EPI_ISL_17994737, EPI_ISL_17994746, EPI_ISL_17994750, EPI_ISL_17994752, EPI_ISL_17994780, EPI_ISL_17994782, EPI_ISL_17994790, EPI_ISL_17994801, EPI_ISL_17994812, EPI_ISL_17994833, EPI_ISL_17994836

Update 12: 23-07-23, 3 seqs from 3 countries

1 from Minnesota, USA: EPI_ISL_17998449 1 from South Australia: EPI_ISL_18000331 1 from British Columbia, Canada: EPI_ISL_18005457

[ryhisner]

There's an interesting branch in this one with S:A879T and S:P479L. Perhaps S:P479L helps reintroduce some needed flexibility to make up for S:S490P?

Within this smaller branch, there are two sequences with a rare and unusual ORF8 mutational pattern that's popped up in 7 sequences from three different lineages. This pattern always includes T27995A and G27996A plus one other mutation, either G27993T (as here) or C27998T (as in four recent South Korean XBB.1.5 sequences). And there was one Delta from August 2021 from Croatia that had all four: G27993T, T27995A, G27996A, C27998T. There's no TRS signal really, so I can't explain it. Except for the Delta, it's all behind a stop codon, so the practical effect is probably nil, but I'm still curious about it.

[HynnSpylor]

Now there are 2 concerned branches: Branch A with S:P1162L and some further get S:S98F and N:S235Y

Branch B with S:A879T(and 5 nuc mutations) then further get S:P479L (mentioned by @ryhisner )

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1fd07_2ae0e0.json

[NkRMnZr]

Designated as FL.29, would be nice to have a milestone.