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Repository for suggesting new lineages that should be added to the current scheme
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XBB.1.16 with S:K304Q (100 seqs, 9 countries) #2187

Closed NkRMnZr closed 12 months ago

NkRMnZr commented 1 year ago

Taken from Branch 1 of multitsak sars-cov-2-variants/lineage-proposals#517

Defining Mutations: XBB.1.16 > A22472C(S:K304Q) Query: A22101T, A22472C, C29386T, -T16209C Earliest seq: 2023-04-06 (EPI_ISL_17496355, Singapore) Latest seq: 2023-07-26 (EPI_ISL_18098984, Texas, USA) Sampled Countries: Japan (16), USA (10), South Korea (7), Singapore (6), Canada (3), India (2)

Genomes: `EPI_ISL_17496355, EPI_ISL_17539792, EPI_ISL_17596417, EPI_ISL_17631385, EPI_ISL_17695054, EPI_ISL_17777161, EPI_ISL_17807332, EPI_ISL_17837583, EPI_ISL_17856816, EPI_ISL_17884028, EPI_ISL_17927867, EPI_ISL_17927876, EPI_ISL_17930453, EPI_ISL_17949711, EPI_ISL_17956589, EPI_ISL_17984091, EPI_ISL_17996307, EPI_ISL_18006528, EPI_ISL_18006550, EPI_ISL_18008936, EPI_ISL_18009151, EPI_ISL_18038978, EPI_ISL_18044135, EPI_ISL_18045251, EPI_ISL_18045294, EPI_ISL_18050922, EPI_ISL_18050961, EPI_ISL_18051952, EPI_ISL_18055280, EPI_ISL_18058363, EPI_ISL_18063130, EPI_ISL_18067271, EPI_ISL_18071590, EPI_ISL_18073723, EPI_ISL_18073893, EPI_ISL_18081404, EPI_ISL_18081957, EPI_ISL_18082731, EPI_ISL_18095875, EPI_ISL_18096954, EPI_ISL_18096982, EPI_ISL_18097380, EPI_ISL_18098984, EPI_ISL_18099985`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3c709_a67100.json?f_userOrOld=uploaded%20sample Branch1

NkRMnZr commented 1 year ago

Tracking updates:

08-18, 6 seqs from China, Japan and USA 1 from Shanghai, China: `EPI_ISL_18105658`, travel history: Japan 2 from Japan: `EPI_ISL_18101000, EPI_ISL_18106231` 3 from USA (AK, AZ, NY): `EPI_ISL_18104291, EPI_ISL_18104556, EPI_ISL_18106371`
08-22, 13 seqs from Israel, Japan, South Korea and USA https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_6cef_4bc0e0.json?f_userOrOld=uploaded%20sample&label=id:node_6836300 ![image](https://github.com/cov-lineages/pango-designation/assets/125747944/adc9a3e4-b782-4ec4-b6b2-6a42e44f5ce7) `EPI_ISL_18115854, EPI_ISL_18115925, EPI_ISL_18115931, EPI_ISL_18115946, EPI_ISL_18116762, EPI_ISL_18120131, EPI_ISL_18121096, EPI_ISL_18121187, EPI_ISL_18122981, EPI_ISL_18123077, EPI_ISL_18123089, EPI_ISL_18123096, EPI_ISL_18123111`
08-25, 6 seqs from Canada, Japan and USA `EPI_ISL_18126206, EPI_ISL_18127315-18127316, EPI_ISL_18127559, EPI_ISL_18129164, EPI_ISL_18131585`
08-30, 31 seqs from Australia, Denmark, Japan and USA https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_15932_f6ffe0.json?f_userOrOld=uploaded%20sample&label=id:node_6839891 ![image](https://github.com/cov-lineages/pango-designation/assets/125747944/6ae959cf-bfae-478a-93b3-17ae202d2ef7) `EPI_ISL_18137910, EPI_ISL_18139532, EPI_ISL_18139549, EPI_ISL_18140894, EPI_ISL_18140930, EPI_ISL_18143983, EPI_ISL_18144025, EPI_ISL_18144186, EPI_ISL_18144509, EPI_ISL_18144568, EPI_ISL_18144601, EPI_ISL_18144833, EPI_ISL_18144935, EPI_ISL_18145372, EPI_ISL_18145425, EPI_ISL_18145728, EPI_ISL_18146228, EPI_ISL_18147532, EPI_ISL_18158963, EPI_ISL_18160487, EPI_ISL_18161172, EPI_ISL_18162481, EPI_ISL_18162490-18162493, EPI_ISL_18162495-18162497, EPI_ISL_18162938, EPI_ISL_18163111`
FedeGueli commented 12 months ago

This is quite fast last doubling went down to interesting levels

FedeGueli commented 12 months ago

Designated XBB.1.16.23 via https://github.com/cov-lineages/pango-designation/commit/9f68787c3a28d8a26a6366c354408f0ed8517227

Milestone in the original issue.