EG.5.1.1 with S:L455F on C10015T branch (286 seqs, 23 countries)

[NkRMnZr]

Taken from Branch 51 of multitask sars-cov-2-variants/lineage-proposals#537

Defining Mutations: EG.5.1.1 > C10015T > G22927T(S:L455F) Query: C6541T, C10015T, G22927T, -C4586T Earliest seq: 2023-07-31 (EPI_ISL_18246153, Heilongjiang) Latest seq: 2023-10-31 (EPI_ISL_18473950, Spain) Sampled Countries: China (20: SH/6; HL/5; LN/3; AH/1; BJ/1; GS/1; HB/1; SC/1; SX/1; XJ/1), Canada (10: ON/9; NS/1), Australia (5: NSW/4; QLD/1), Singapore (5), Spain (5), Croatia (4), USA (3: NY/2; HI/1), Denmark (2), Japan (2), Belgium (1), France (1), Italy (1), Switzerland (1)

Genomes:

`EPI_ISL_18246153, EPI_ISL_18268220, EPI_ISL_18284760, EPI_ISL_18289806, EPI_ISL_18304238, EPI_ISL_18307185, EPI_ISL_18309728, EPI_ISL_18320892, EPI_ISL_18333882, EPI_ISL_18354453, EPI_ISL_18356455, EPI_ISL_18362071, EPI_ISL_18382338, EPI_ISL_18384364, EPI_ISL_18388937, EPI_ISL_18388943, EPI_ISL_18392626, EPI_ISL_18392641, EPI_ISL_18395616, EPI_ISL_18398918, EPI_ISL_18401900, EPI_ISL_18422863, EPI_ISL_18425076, EPI_ISL_18433557, EPI_ISL_18438020, EPI_ISL_18438314, EPI_ISL_18438838, EPI_ISL_18445101, EPI_ISL_18445501, EPI_ISL_18446144, EPI_ISL_18448315, EPI_ISL_18448907-18448908, EPI_ISL_18448913-18448914, EPI_ISL_18461557, EPI_ISL_18461608, EPI_ISL_18461684, EPI_ISL_18461722, EPI_ISL_18464481, EPI_ISL_18464633, EPI_ISL_18465094, EPI_ISL_18465113, EPI_ISL_18465171, EPI_ISL_18465395, EPI_ISL_18465403, EPI_ISL_18466062, EPI_ISL_18466326-18466327, EPI_ISL_18466420, EPI_ISL_18466590, EPI_ISL_18470572, EPI_ISL_18471609, EPI_ISL_18471611, EPI_ISL_18473319, EPI_ISL_18473421, EPI_ISL_18473950, EPI_ISL_18475156, EPI_ISL_18475172, EPI_ISL_18475181, EPI_ISL_18475190, EPI_ISL_18475453`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_25e8a_b47430.json?label=id:node_3494261

[NkRMnZr]

Tracking updates

11-18, 42 seqs from Australia, Belgium, Canada, China, Denmark, France, South Korea, Spain, Switzerland, UK and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2b4ba_a39cf0.json?f_userOrOld=uploaded%20sample&label=id:node_3489797  `EPI_ISL_18481026, EPI_ISL_18481033, EPI_ISL_18481125, EPI_ISL_18481209, EPI_ISL_18494077, EPI_ISL_18494687, EPI_ISL_18495482, EPI_ISL_18495534-18495536, EPI_ISL_18496915, EPI_ISL_18497244, EPI_ISL_18499556, EPI_ISL_18501516, EPI_ISL_18504362, EPI_ISL_18504442, EPI_ISL_18504471-18504472, EPI_ISL_18504477, EPI_ISL_18505411, EPI_ISL_18505415-18505416, EPI_ISL_18505644, EPI_ISL_18507754, EPI_ISL_18508179, EPI_ISL_18509101, EPI_ISL_18509986, EPI_ISL_18511298, EPI_ISL_18513290, EPI_ISL_18513305, EPI_ISL_18513309, EPI_ISL_18513337, EPI_ISL_18513407, EPI_ISL_18513729, EPI_ISL_18513874, EPI_ISL_18513904, EPI_ISL_18514908, EPI_ISL_18515301, EPI_ISL_18517066, EPI_ISL_18518263, EPI_ISL_18518365, EPI_ISL_18518377`

11-25, 21 seqs from Belgium, Canada, China, France, Germany, Japan, S. Korea, Netherlands, Sweden and USA

`EPI_ISL_18522509, EPI_ISL_18522729, EPI_ISL_18523229, EPI_ISL_18523429, EPI_ISL_18523515-18523516, EPI_ISL_18523523, EPI_ISL_18523603, EPI_ISL_18523608-18523609, EPI_ISL_18523764, EPI_ISL_18524265, EPI_ISL_18524409, EPI_ISL_18525030, EPI_ISL_18525796, EPI_ISL_18528808, EPI_ISL_18529540, EPI_ISL_18535399, EPI_ISL_18535857, EPI_ISL_18537999, EPI_ISL_18539303`

12-02, 45 seqs from Australia, Canada, Croatia, France, Israel, S. Korea, New Zealand, Singapore and Spain

`EPI_ISL_18544634, EPI_ISL_18548695, EPI_ISL_18548727, EPI_ISL_18549106, EPI_ISL_18549219, EPI_ISL_18549434, EPI_ISL_18551283, EPI_ISL_18551675-18551676, EPI_ISL_18553962, EPI_ISL_18559397, EPI_ISL_18561775, EPI_ISL_18561778, EPI_ISL_18561867, EPI_ISL_18561917, EPI_ISL_18562193, EPI_ISL_18562239, EPI_ISL_18562245, EPI_ISL_18562248-18562249, EPI_ISL_18562335, EPI_ISL_18562614, EPI_ISL_18562616, EPI_ISL_18562620, EPI_ISL_18565086, EPI_ISL_18566443, EPI_ISL_18566469-18566470, EPI_ISL_18566477, EPI_ISL_18566551, EPI_ISL_18566643, EPI_ISL_18566646, EPI_ISL_18566709, EPI_ISL_18567026, EPI_ISL_18567036-18567037, EPI_ISL_18567054-18567055, EPI_ISL_18567130, EPI_ISL_18567141, EPI_ISL_18567156, EPI_ISL_18567166, EPI_ISL_18567192, EPI_ISL_18568832, EPI_ISL_18572391`

12-06, 21 seqs from Canada, Netherlands, Russia, Singapore and USA

`EPI_ISL_18576975, EPI_ISL_18579959, EPI_ISL_18580023, EPI_ISL_18580930, EPI_ISL_18581568, EPI_ISL_18581632, EPI_ISL_18581729, EPI_ISL_18581740, EPI_ISL_18581847, EPI_ISL_18582275, EPI_ISL_18582277, EPI_ISL_18582972, EPI_ISL_18583150, EPI_ISL_18583291, EPI_ISL_18590228, EPI_ISL_18590239, EPI_ISL_18590254, EPI_ISL_18590343, EPI_ISL_18590421, EPI_ISL_18591571, EPI_ISL_18593070`

12-14, 21 seqs from Australia, Austria, Canada, China, Germany, Israel, Japan, S. Korea, Luxembourg and USA

`EPI_ISL_18594305, EPI_ISL_18596927, EPI_ISL_18597425, EPI_ISL_18600020, EPI_ISL_18602920, EPI_ISL_18603438, EPI_ISL_18610536, EPI_ISL_18610543, EPI_ISL_18610546, EPI_ISL_18610548, EPI_ISL_18610747, EPI_ISL_18610750, EPI_ISL_18614616, EPI_ISL_18616028, EPI_ISL_18620711, EPI_ISL_18624379, EPI_ISL_18625199, EPI_ISL_18625216, EPI_ISL_18625221, EPI_ISL_18633395, EPI_ISL_18633417`

24-01-13, 74 seqs from Australia, Austria, Canada, China, Croatia, France, Israel, Japan, S. Korea, Luxembourg, Netherlands, New Zealand, Russia, UK and USA

`EPI_ISL_18637370, EPI_ISL_18638377, EPI_ISL_18638410, EPI_ISL_18639898, EPI_ISL_18639956, EPI_ISL_18643441, EPI_ISL_18643495, EPI_ISL_18645249, EPI_ISL_18645374, EPI_ISL_18645587, EPI_ISL_18645598-18645599, EPI_ISL_18646708, EPI_ISL_18654538, EPI_ISL_18655474, EPI_ISL_18656719, EPI_ISL_18656880, EPI_ISL_18663601, EPI_ISL_18666637, EPI_ISL_18667540, EPI_ISL_18671666, EPI_ISL_18674530, EPI_ISL_18678968, EPI_ISL_18679894, EPI_ISL_18683330, EPI_ISL_18683587, EPI_ISL_18686924, EPI_ISL_18694627, EPI_ISL_18695735, EPI_ISL_18696466, EPI_ISL_18696504, EPI_ISL_18696903-18696904, EPI_ISL_18697037, EPI_ISL_18697381, EPI_ISL_18697384-18697385, EPI_ISL_18697665, EPI_ISL_18704496, EPI_ISL_18711078, EPI_ISL_18712302, EPI_ISL_18714046, EPI_ISL_18717122, EPI_ISL_18719636, EPI_ISL_18725405, EPI_ISL_18727917, EPI_ISL_18728760, EPI_ISL_18729281, EPI_ISL_18729909, EPI_ISL_18730989, EPI_ISL_18731965, EPI_ISL_18731985-18731986, EPI_ISL_18731989, EPI_ISL_18731991-18731992, EPI_ISL_18732021-18732022, EPI_ISL_18732117, EPI_ISL_18732119, EPI_ISL_18732282, EPI_ISL_18736654, EPI_ISL_18738096, EPI_ISL_18738805, EPI_ISL_18738949, EPI_ISL_18740438, EPI_ISL_18744812, EPI_ISL_18744829, EPI_ISL_18744863, EPI_ISL_18746557, EPI_ISL_18750182, EPI_ISL_18754121, EPI_ISL_18756274, EPI_ISL_18756478`

[FedeGueli]

110 now . it seems faster than most of the designated Flip. https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=JN.1*&nucMutations1=C6541T%2CC10015T%2CG22927T&analysisMode=CompareToBaseline&

[FedeGueli]

213 now

[FedeGueli]

one small cluster with defining C10015T apaparently reverted popped up in Japan with S:K478E:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_12197_113a70.json?c=userOrOld&label=id:node_3474825

[FedeGueli]

333 now