EG.5.1.1 with S:L455F on C5812T branch, mostly with M:K15Q and N:T166R (159 seqs, mainly in South Korea, 10 countries) further with S:A475V (50 seqs, 5 countries)

[NkRMnZr]

Main branch taken from Branch 28 of Multitask sars-cov-2-variants/lineage-proposals#537
Follow-up branch taken from Branch 2 of Multitask sars-cov-2-variants/lineage-proposals#978

Defining Mutations: EG.5.1.1 > C5812T > G22927T(S:L455F), mostly with >> A26565C(M:K15Q), C28770G(N:T166R)
Query: C5812T, G22927T, C28770G (for major A26565C(M:K15Q), C28770G(N:T166R) sub-branch only)

Defining Mutations for follow-up S:A475V sub-branch: Main proposal > A26565C(M:K15Q), C28770G(N:T166R) > A10323G(ORF1a:K3353R), C22986T(S:A475V)
Query for follow-up S:A475V sub-branch: C5812T, C22986T, A26565C

Earliest seq: 2023-08-09 (EPI_ISL_18214077, South Korea)
Latest seq: 2023-11-09 (EPI_ISL_18547984, Nevada, USA)
Sampled Countries: South Korea (68), USA (5: NV/2; NC/1; ex. S. Korea/2), Australia (2: NSW; QLD), China (2: SC/1; ex. S. Korea/1), Denmark (2), Hungary (2), Finland (1), Japan (1)

Genomes:

EPI_ISL_18214077, EPI_ISL_18236938, EPI_ISL_18293068, EPI_ISL_18293497, EPI_ISL_18347905, EPI_ISL_18353940, EPI_ISL_18354370, EPI_ISL_18354403, EPI_ISL_18355265, EPI_ISL_18355547, EPI_ISL_18368528, EPI_ISL_18382157, EPI_ISL_18382304, EPI_ISL_18382505, EPI_ISL_18382615, EPI_ISL_18386641, EPI_ISL_18408701-18408702, EPI_ISL_18408814, EPI_ISL_18408878, EPI_ISL_18411301, EPI_ISL_18415920, EPI_ISL_18435710, EPI_ISL_18438964, EPI_ISL_18439203, EPI_ISL_18439262-18439263, EPI_ISL_18439368, EPI_ISL_18439436, EPI_ISL_18460639, EPI_ISL_18460726, EPI_ISL_18460826, EPI_ISL_18461023, EPI_ISL_18461030, EPI_ISL_18461109, EPI_ISL_18461117, EPI_ISL_18461139, EPI_ISL_18488790, EPI_ISL_18488878, EPI_ISL_18488904, EPI_ISL_18489119, EPI_ISL_18501908, EPI_ISL_18502007, EPI_ISL_18503617, EPI_ISL_18503624, EPI_ISL_18503755, EPI_ISL_18503952, EPI_ISL_18503974, EPI_ISL_18511170, EPI_ISL_18511222, EPI_ISL_18511248, EPI_ISL_18511257, EPI_ISL_18511484, EPI_ISL_18513699, EPI_ISL_18518361, EPI_ISL_18535616, EPI_ISL_18535618, EPI_ISL_18535641, EPI_ISL_18535643-18535644, EPI_ISL_18535683, EPI_ISL_18539076, EPI_ISL_18539319, EPI_ISL_18539641, EPI_ISL_18539827, EPI_ISL_18540358, EPI_ISL_18544082, EPI_ISL_18547609, EPI_ISL_18547984, EPI_ISL_18550336, EPI_ISL_18552522, EPI_ISL_18559930, EPI_ISL_18564453, EPI_ISL_18564477, EPI_ISL_18564533, EPI_ISL_18564565, EPI_ISL_18564603, EPI_ISL_18564701, EPI_ISL_18564813, EPI_ISL_18564892, EPI_ISL_18564897, EPI_ISL_18565136

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_356f8_c1a890.json?label=id:node_3518019

Trivia:

• Note by @ryhisner:

To me, branch 28 deserves to be moved to the main Pango page. There are lots of interesting branches there, and a really interesting sequence from Shanghai just showed up as well—EPI_ISL_18518361. The one branch has C26681T, the synonymous mutation in M that is also in BA.2.86 and many other sequences/lineages of interest.

M:K15Q is an A->C nuc mutation and N:T166R is C->G. These are rare nuc mutations, and I don't think they happened by accident.

[NkRMnZr]

Tracking updates

23-12-14, 12 seqs from South Korea, Singapore, Sweden and USA

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3f48b_c0c420.json?f_userOrOld=uploaded%20sample&label=id:node_3473805

EPI_ISL_18586988, EPI_ISL_18586991, EPI_ISL_18592629, EPI_ISL_18597058, EPI_ISL_18597161, EPI_ISL_18597495, EPI_ISL_18597630, EPI_ISL_18597861, EPI_ISL_18597964, EPI_ISL_18604614, EPI_ISL_18607189, EPI_ISL_18621188

24-01-13, 65 seqs from Australia, China, S. Korea and USA

EPI_ISL_18639334, EPI_ISL_18639578, EPI_ISL_18639618, EPI_ISL_18639950, EPI_ISL_18639977, EPI_ISL_18651626, EPI_ISL_18651641, EPI_ISL_18651643, EPI_ISL_18651645, EPI_ISL_18667547, EPI_ISL_18679518, EPI_ISL_18686689, EPI_ISL_18686862, EPI_ISL_18686867, EPI_ISL_18686947, EPI_ISL_18686950, EPI_ISL_18687264, EPI_ISL_18687440, EPI_ISL_18687550, EPI_ISL_18687555-18687557, EPI_ISL_18687559, EPI_ISL_18687610-18687611, EPI_ISL_18691001, EPI_ISL_18693135, EPI_ISL_18699477, EPI_ISL_18699750, EPI_ISL_18703813, EPI_ISL_18706576-18706579, EPI_ISL_18706596, EPI_ISL_18711463, EPI_ISL_18711466, EPI_ISL_18711474, EPI_ISL_18711476, EPI_ISL_18711487-18711488, EPI_ISL_18711492, EPI_ISL_18711494, EPI_ISL_18711563, EPI_ISL_18711692, EPI_ISL_18711773, EPI_ISL_18712018, EPI_ISL_18712169, EPI_ISL_18712253, EPI_ISL_18712259, EPI_ISL_18712321, EPI_ISL_18712333, EPI_ISL_18733013, EPI_ISL_18733087, EPI_ISL_18733584-18733586, EPI_ISL_18733662, EPI_ISL_18733688, EPI_ISL_18733883, EPI_ISL_18751383, EPI_ISL_18751534, EPI_ISL_18752139, EPI_ISL_18752971, EPI_ISL_18756394

[FedeGueli]

475V branch now 59 no January sample yet

[DailyCovidCases]

Please close this issue

[Over-There-Is]

194 now, 11 dropped 22927 out, suggest using C5812T, C28770G instead