XBB.2.3.6 with ORF1a:R4017K (nsp8_R75K), ORF1a:S3099L (nsp4_S336L) and S:N388K (33 seqs, Japan), follows a sub-lineage with S:Y453H (4 seqs, Japan)

[NkRMnZr]

Defining Mutations: On top of XBB.2.3.6's [T22843C > C7105T > C1063T] > G12315A(ORF1a:R4017K) > G26834T > C9561T(ORF1a:S3099L) > T22726A(S:N388K) Query: C9561T, T22726A Earliest seq: 2023-05-15 (EPI_ISL_17881889, Tokyo, Japan) Latest seq: 2023-07-03 (EPI_ISL_17994250, Kumamoto, Japan) Sampled Countries: Japan (10), USA (3, Virginia, Travel history to Japan)

Genomes:

EPI_ISL_17881889, EPI_ISL_17884007, EPI_ISL_17960078, EPI_ISL_17971830, EPI_ISL_17971864, EPI_ISL_17971891, EPI_ISL_17973271, EPI_ISL_17985853, EPI_ISL_17994250, EPI_ISL_17996449, EPI_ISL_17996453, EPI_ISL_18006463, EPI_ISL_18006974

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_5ff1_be5620.json?f_userOrOld=uploaded%20sample

view from XBB.2.3 polytomy

details

Trivia:

• No idea what S:N388K does, it seems to be deleterious by all predictions, but all those calculators are made on XBB.1.5 backbone, maybe slightly different on XBB.2*? Or simply a super-spreader event?

[NkRMnZr]

Tracking updates:

07-28, 3 seqs from Japan: EPI_ISL_18041378, EPI_ISL_18041462, EPI_ISL_18044092 07-31, 2 seqs from Japan, plus 17 more cannot be caught by query due to Ns around 388 08-05, 6 seqs from Japan, with S:F490S>Y and S:Y453H branches emerged, query for follow-up S:Y453H: C11235T, T22919C 08-15, 6 from Japan: EPI_ISL_18097512, EPI_ISL_18097515, EPI_ISL_18100589, EPI_ISL_18100805, EPI_ISL_18101073, EPI_ISL_18101251

[NkRMnZr]

07-31: 2 seqs from Japan: EPI_ISL_18051463, EPI_ISL_18051683

and 17 more failed to catch by query due to quality issues, but UShER somehow place them under this branch:

Genomes:

`EPI_ISL_18051364, EPI_ISL_18051404, EPI_ISL_18051428, EPI_ISL_17978131, EPI_ISL_17978132, EPI_ISL_18013017, EPI_ISL_17982075, EPI_ISL_17978139, EPI_ISL_18041334, EPI_ISL_18012714, EPI_ISL_17978086, EPI_ISL_17978127, EPI_ISL_18041321, EPI_ISL_18041450, EPI_ISL_18041498, EPI_ISL_18041413, EPI_ISL_18041448`

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3aefd_7b4060.json?f_userOrOld=uploaded%20sample

[ryhisner]

There are now three sequences in this lineage with S:Y453H from Japan, a very interesting development. Two from Chiba, one from Tokyo. EPI_ISL_18044092, EPI_ISL_18065162, EPI_ISL_18065176

[NkRMnZr]

08-05, 6 seqs from Japan: EPI_ISL_18051463, EPI_ISL_18051683, EPI_ISL_18056423, EPI_ISL_18060285, EPI_ISL_18065162, EPI_ISL_18065176

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2a33f_e259f0.json?f_userOrOld=uploaded%20sample

Note that there's branch with S:F490S>Y (T23031C>A), and branch with S:Y453H (T22919C) spotted by @ryhisner

follows: main proposal > T1294C, A27655G (ORF7a:I88V) > C11235T(ORF1a:A3657V), T22919C(S:Y453H)

Query for follow-up S:Y453H: C11235T, T22919C

[FedeGueli]

propose it when reaches 35, please.

[NkRMnZr]

08-13, 4 seqs from Japan: EPI_ISL_18071583, EPI_ISL_18071623, EPI_ISL_18081987, EPI_ISL_18082738

[FedeGueli]

6 + from jap

[FedeGueli]

Designated GM.3.1 via https://github.com/cov-lineages/pango-designation/commit/56e3ad0411769d342772935635f611dfaa29da79