EG.5.1.1 on A23539T branch with S:L455F (264 seqs, mainly in Australia, 10 countries)

[NkRMnZr]

Taken from Branch 48 of Multitask sars-cov-2-variants/lineage-proposals#537

Defining Mutations: EG.5.1.1 > A23539T(S:S659S) > G22927T(S:L455F)
Query: G13627A, G22927T, A23539T, -A708C, -T899C, -C2662T, -C4686T, -C10015T, -T12865C, -G22332A
Earliest seq: 2023-08-16 (EPI_ISL_18141107, Singapore)
Latest seq: 2023-10-22 (EPI_ISL_18440472, Netherlands)
Sampled Countries: Australia (32: NSW/14; SA/8; QLD/4; VIC/3; TAS/1; WA/1), China (10: SC/4; HB/2; SH/2; FJ/1; XJ/1), New Zealand (9), Singapore (4), Netherlands (3), USA (2), France (1)

Genomes:

EPI_ISL_18141107, EPI_ISL_18246326, EPI_ISL_18278997, EPI_ISL_18279955, EPI_ISL_18292475, EPI_ISL_18300669, EPI_ISL_18307132, EPI_ISL_18320781, EPI_ISL_18324527, EPI_ISL_18324537, EPI_ISL_18324951, EPI_ISL_18346779, EPI_ISL_18346805, EPI_ISL_18346818, EPI_ISL_18347516, EPI_ISL_18347639, EPI_ISL_18347703-18347704, EPI_ISL_18347710, EPI_ISL_18352381, EPI_ISL_18355046, EPI_ISL_18360352, EPI_ISL_18365605, EPI_ISL_18365672, EPI_ISL_18365874, EPI_ISL_18376439, EPI_ISL_18388898, EPI_ISL_18396188, EPI_ISL_18411419, EPI_ISL_18411467, EPI_ISL_18411551, EPI_ISL_18411564, EPI_ISL_18411674, EPI_ISL_18411695, EPI_ISL_18423924, EPI_ISL_18427871, EPI_ISL_18428112, EPI_ISL_18435043, EPI_ISL_18438373, EPI_ISL_18440466, EPI_ISL_18440472, EPI_ISL_18440476, EPI_ISL_18442757, EPI_ISL_18442774, EPI_ISL_18447732, EPI_ISL_18454463, EPI_ISL_18454489, EPI_ISL_18457508, EPI_ISL_18459380, EPI_ISL_18459604, EPI_ISL_18459721, EPI_ISL_18459855, EPI_ISL_18459912, EPI_ISL_18459940, EPI_ISL_18461585, EPI_ISL_18461782, EPI_ISL_18461792, EPI_ISL_18461895, EPI_ISL_18461916, EPI_ISL_18461956, EPI_ISL_18464115

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2e62_757100.json?label=id:node_3495970

Trivia:

• Please check potential misplacement: it seems only one seqs preceeding S:L455F branch, being Sichuan/BZCDC-043/2023|EPI_ISL_17988879|2023-06-12; however the mutations on the follow-up sub-branch G571A, C2263A, A28959G are "unique" to the EG.5.1.1* tree which may support it be a different lineage than HK.3.

[AngieHinrichs]

Please check potential misplacement: it seems only one seqs preceeding S:L455F branch, being Sichuan/BZCDC-043/2023|EPI_ISL_17988879|2023-06-12; however the mutations on the follow-up sub-branch G571A, C2263A, A28959G are "unique" to the EG.5.1.1* tree which may support it be a different lineage than HK.3.

Yes, I think it is plausible that this is yet another independent G22927T (S:L455F) in EG.5.1.1, distinct from HK.3.

[FedeGueli]

80 now it seems fast.

[xz-keg]

115 now

[NkRMnZr]

Tracking updates

23-11-18, 51 seqs from Australia, China, France, Netherlands, New Zealand, and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_b056_a45740.json?f_userOrOld=uploaded%20sample&label=id:node_3492915

EPI_ISL_18468963, EPI_ISL_18472325, EPI_ISL_18472330, EPI_ISL_18485204, EPI_ISL_18485207, EPI_ISL_18485302, EPI_ISL_18488290, EPI_ISL_18488323, EPI_ISL_18488443, EPI_ISL_18488451, EPI_ISL_18488471, EPI_ISL_18488556, EPI_ISL_18489121, EPI_ISL_18489129, EPI_ISL_18489144, EPI_ISL_18489157, EPI_ISL_18495003, EPI_ISL_18495103, EPI_ISL_18501701, EPI_ISL_18501752, EPI_ISL_18505552, EPI_ISL_18505597, EPI_ISL_18508295, EPI_ISL_18508504, EPI_ISL_18510875-18510876, EPI_ISL_18510890, EPI_ISL_18510918-18510919, EPI_ISL_18510922, EPI_ISL_18510925, EPI_ISL_18510928, EPI_ISL_18510931, EPI_ISL_18510933, EPI_ISL_18510935, EPI_ISL_18510977-18510979, EPI_ISL_18510981, EPI_ISL_18512369, EPI_ISL_18512373, EPI_ISL_18513310-18513312, EPI_ISL_18513316, EPI_ISL_18513386, EPI_ISL_18513465, EPI_ISL_18513702, EPI_ISL_18513766, EPI_ISL_18513801, EPI_ISL_18513849

11-25, 15 seqs from Australia, Canada, China, France, South Korea and USA

EPI_ISL_18523320, EPI_ISL_18524588, EPI_ISL_18524661, EPI_ISL_18527214, EPI_ISL_18528541, EPI_ISL_18528822, EPI_ISL_18533658, EPI_ISL_18533945, EPI_ISL_18534517, EPI_ISL_18535368, EPI_ISL_18535422, EPI_ISL_18536577, EPI_ISL_18536603, EPI_ISL_18537953, EPI_ISL_18539238

12-02, 35 seqs from Australia, Canada, New Zealand, Singapore and USA

EPI_ISL_18544845, EPI_ISL_18550856, EPI_ISL_18551350-18551351, EPI_ISL_18553215, EPI_ISL_18554023, EPI_ISL_18554436, EPI_ISL_18554438, EPI_ISL_18558787, EPI_ISL_18558802, EPI_ISL_18561693, EPI_ISL_18561885, EPI_ISL_18561894, EPI_ISL_18561909, EPI_ISL_18562033, EPI_ISL_18562088, EPI_ISL_18562097, EPI_ISL_18562154, EPI_ISL_18562210, EPI_ISL_18562288, EPI_ISL_18562581, EPI_ISL_18562587, EPI_ISL_18562591, EPI_ISL_18562687, EPI_ISL_18562720, EPI_ISL_18562817, EPI_ISL_18566407, EPI_ISL_18566588, EPI_ISL_18566599, EPI_ISL_18566616, EPI_ISL_18566622, EPI_ISL_18566689, EPI_ISL_18567756, EPI_ISL_18567955, EPI_ISL_18567968

12-14, 24 seqs from Australia, Canada, China, S. Korea and USA

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_32273_c0a290.json?f_userOrOld=uploaded%20sample&label=id:node_3473361

EPI_ISL_18581074, EPI_ISL_18584288, EPI_ISL_18584681, EPI_ISL_18591963, EPI_ISL_18594900, EPI_ISL_18598176, EPI_ISL_18598200, EPI_ISL_18601586, EPI_ISL_18608913, EPI_ISL_18609584, EPI_ISL_18610695, EPI_ISL_18615773, EPI_ISL_18615780, EPI_ISL_18615857, EPI_ISL_18622249, EPI_ISL_18631937, EPI_ISL_18631950, EPI_ISL_18631954, EPI_ISL_18633181, EPI_ISL_18633313, EPI_ISL_18633406, EPI_ISL_18633443, EPI_ISL_18633507, EPI_ISL_18633584

24-01-13, 80 seqs from Australia, Canada, China, France, Greece, New Zealand, Singapore and USA

EPI_ISL_18637967, EPI_ISL_18643685, EPI_ISL_18646038, EPI_ISL_18651176, EPI_ISL_18651352, EPI_ISL_18651562, EPI_ISL_18654652, EPI_ISL_18662496, EPI_ISL_18663212, EPI_ISL_18664905, EPI_ISL_18665197, EPI_ISL_18665230, EPI_ISL_18665238, EPI_ISL_18665267, EPI_ISL_18665273, EPI_ISL_18667297, EPI_ISL_18667324-18667326, EPI_ISL_18667442, EPI_ISL_18667523, EPI_ISL_18667840-18667841, EPI_ISL_18667985, EPI_ISL_18669836, EPI_ISL_18670535, EPI_ISL_18670892, EPI_ISL_18671008, EPI_ISL_18671022, EPI_ISL_18671142, EPI_ISL_18671219, EPI_ISL_18671260, EPI_ISL_18679290, EPI_ISL_18679346, EPI_ISL_18679413, EPI_ISL_18686405, EPI_ISL_18686569, EPI_ISL_18686573, EPI_ISL_18689540, EPI_ISL_18690122, EPI_ISL_18690589, EPI_ISL_18691409, EPI_ISL_18695134, EPI_ISL_18699564, EPI_ISL_18699823, EPI_ISL_18699986, EPI_ISL_18700039, EPI_ISL_18700084, EPI_ISL_18703396, EPI_ISL_18703423, EPI_ISL_18712397, EPI_ISL_18714732, EPI_ISL_18715904, EPI_ISL_18716369, EPI_ISL_18716372, EPI_ISL_18716390, EPI_ISL_18717311, EPI_ISL_18717395, EPI_ISL_18717398, EPI_ISL_18720056, EPI_ISL_18723594, EPI_ISL_18725445, EPI_ISL_18725457, EPI_ISL_18731153, EPI_ISL_18733360, EPI_ISL_18735139, EPI_ISL_18745238-18745239, EPI_ISL_18745375, EPI_ISL_18745379, EPI_ISL_18745743, EPI_ISL_18745985, EPI_ISL_18745988-18745989, EPI_ISL_18745991, EPI_ISL_18746678, EPI_ISL_18750183, EPI_ISL_18756371, EPI_ISL_18756470, EPI_ISL_18756549

[FedeGueli]

118 now 10% in Tasmania in October

[FedeGueli]

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_47693_f449a0.json?c=userOrOld&label=id:node_3502518

137 now 97 in the branch with N:Q229R and 78 with further spike mutation S:G1267R i suggest a designation for this or at least for the G1267R branch.

[DailyCovidCases]

Please close this issue