FY.5 with ORF1a:M2796I (nsp4_M33I) and S:T572I (160 seqs, 8 countries)

[NkRMnZr]

Taken from Branch 1 of multitask sars-cov-2-variants/lineage-proposals#929

Defining Mutations: FY.5 > A6019G > G8653C(ORF1a:M2796I), T9616C, T18408C > C23277T(S:T572I)
Query: G8653C, T9616C, C23277T, -A20634G
Earliest seq: 2023-06-19 (EPI_ISL_18065370, Mississippi, USA)
Latest seq: 2023-10-23 (EPI_ISL_18470344, Ontario, Canada)
Sampled Countries: USA (35: CA/33; MN/8; FL/5; UT/5; AZ/4; TX/4; MS/3; NY/3; MD/2; NJ/2; CO; GA; LA; MO; PA; WA), Canada (28: AB/11; BC/9; ON/6; NB/2), UK (21: EN/20; WS), Australia (7: QLD/2; SA/2; NSW; VIC; WA), New Zealand (3), Spain (2), France (1), Ireland (1)

Genomes:

EPI_ISL_18037673, EPI_ISL_18065363, EPI_ISL_18065370, EPI_ISL_18076501, EPI_ISL_18080203, EPI_ISL_18093353, EPI_ISL_18137237, EPI_ISL_18144922, EPI_ISL_18145717, EPI_ISL_18147831, EPI_ISL_18213587, EPI_ISL_18225095, EPI_ISL_18225408, EPI_ISL_18227137, EPI_ISL_18231691, EPI_ISL_18234320, EPI_ISL_18237621, EPI_ISL_18240196, EPI_ISL_18240585, EPI_ISL_18240605, EPI_ISL_18240944, EPI_ISL_18243590, EPI_ISL_18251270, EPI_ISL_18251286, EPI_ISL_18252720, EPI_ISL_18260598, EPI_ISL_18266738, EPI_ISL_18266941, EPI_ISL_18267264, EPI_ISL_18273868, EPI_ISL_18276817, EPI_ISL_18278644, EPI_ISL_18279999, EPI_ISL_18284545, EPI_ISL_18284638, EPI_ISL_18292316, EPI_ISL_18296925, EPI_ISL_18301677, EPI_ISL_18304606, EPI_ISL_18306051, EPI_ISL_18311801, EPI_ISL_18312155, EPI_ISL_18316276, EPI_ISL_18316739, EPI_ISL_18318989, EPI_ISL_18322274, EPI_ISL_18322541, EPI_ISL_18332176, EPI_ISL_18332271, EPI_ISL_18333729, EPI_ISL_18340027, EPI_ISL_18340262, EPI_ISL_18340934, EPI_ISL_18341077, EPI_ISL_18342218, EPI_ISL_18344785, EPI_ISL_18346146, EPI_ISL_18347232, EPI_ISL_18347551, EPI_ISL_18350049, EPI_ISL_18351511, EPI_ISL_18358363, EPI_ISL_18363565, EPI_ISL_18364460, EPI_ISL_18364467, EPI_ISL_18366711, EPI_ISL_18369794, EPI_ISL_18371040, EPI_ISL_18377973, EPI_ISL_18381776, EPI_ISL_18383579, EPI_ISL_18384152-18384158, EPI_ISL_18385805, EPI_ISL_18389955, EPI_ISL_18392229, EPI_ISL_18392248, EPI_ISL_18392827, EPI_ISL_18398086, EPI_ISL_18398090, EPI_ISL_18398104, EPI_ISL_18398243, EPI_ISL_18398572, EPI_ISL_18399980, EPI_ISL_18403772, EPI_ISL_18403791, EPI_ISL_18407508, EPI_ISL_18410377, EPI_ISL_18411719, EPI_ISL_18412668, EPI_ISL_18413165, EPI_ISL_18413175, EPI_ISL_18413266, EPI_ISL_18413463, EPI_ISL_18413619, EPI_ISL_18413639, EPI_ISL_18414207, EPI_ISL_18414282, EPI_ISL_18414419, EPI_ISL_18414891, EPI_ISL_18415306, EPI_ISL_18416207, EPI_ISL_18416507, EPI_ISL_18416663, EPI_ISL_18420319, EPI_ISL_18424611, EPI_ISL_18425618, EPI_ISL_18425620, EPI_ISL_18425909, EPI_ISL_18427910, EPI_ISL_18430960, EPI_ISL_18436211, EPI_ISL_18437643, EPI_ISL_18439724, EPI_ISL_18439830, EPI_ISL_18448767, EPI_ISL_18452825, EPI_ISL_18453156, EPI_ISL_18453189, EPI_ISL_18455328, EPI_ISL_18456203-18456204, EPI_ISL_18456217, EPI_ISL_18456269, EPI_ISL_18456290, EPI_ISL_18456329, EPI_ISL_18456575, EPI_ISL_18456585, EPI_ISL_18456915, EPI_ISL_18456917, EPI_ISL_18456934, EPI_ISL_18469204, EPI_ISL_18470344

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_11444_e2ee80.json?f_userOrOld=uploaded%20sample&label=id:node_3216430

[FedeGueli]

CC @corneliusroemer @AngieHinrichs @thomasppeacock following the recent discoveries by Bloom and Dadonaite i suggest to designate it after FY.5.1 and FY.8:
It looks like S:T572I is a strong binding enhancing mutation :https://x.com/jbloom_lab/status/1724940201032560920?s=20

More the same study found that S:Y200C is a strong escape mutation with high ace2 binding cost : https://x.com/jbloom_lab/status/1724940211778412824?s=20 explaining the rise of XBB.1.22.1
but also why it was never able to compete and restored its fitness when gaining S:T572I

https://twitter.com/jbloom_lab/status/1724940222360682629

cc @HynnSpylor who tracked XBB.1.22.1 evolution from the start.

[NkRMnZr]

Tracking updates

11-18, 22 seqs from Canada, New Zealand and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_6ce3_a44380.json?f_userOrOld=uploaded%20sample&label=id:node_3215432

EPI_ISL_18488265, EPI_ISL_18488298, EPI_ISL_18492756, EPI_ISL_18492990, EPI_ISL_18493050, EPI_ISL_18494001, EPI_ISL_18502321, EPI_ISL_18502689, EPI_ISL_18504914, EPI_ISL_18507010, EPI_ISL_18507200, EPI_ISL_18512865, EPI_ISL_18512953, EPI_ISL_18516868, EPI_ISL_18517245, EPI_ISL_18517319, EPI_ISL_18517452, EPI_ISL_18517597, EPI_ISL_18517655, EPI_ISL_18517798, EPI_ISL_18518219, EPI_ISL_18519459

[HynnSpylor]

One branch further gets S:P807S and circulates in US recently (17 seqs)

[FedeGueli]

Designated FY.5.5.1 via c91bcf1