XBB.1.9.2 with S:V1122L (113 seqs, mainly in Spain, 9 countries), further gained S:T478R (2 seqs, USA)

[NkRMnZr]

Transferred from sars-cov-2-variants/lineage-proposals#463

Defining Mutations: XBB.1.9.2 > C21622T > A14673G > T9508C > C673T, G24926T(S:V1122L) Query: C673T, T9508C, G24926T, -T3576C Earliest seq: 2023-03-22 (EPI_ISL_17482696, Sevilla, Spain) Latest seq: 2023-07-14 (EPI_ISL_18037687, Delaware, USA) Sampled Countries: Spain (50, Mainland/49, Canary Islands/1 ), USA (20), Canada (4), Austria (2), UK (2, England, Scotland), Belgium (1), France (1), Iceland (1)

Genomes:

`EPI_ISL_17482696, EPI_ISL_17482745, EPI_ISL_17482800,`EPI_ISL_17541202, EPI_ISL_17541229, EPI_ISL_17541240,`EPI_ISL_17592159, EPI_ISL_17638016, EPI_ISL_17669025,`EPI_ISL_17669099, EPI_ISL_17669122, EPI_ISL_17669143,`EPI_ISL_17669244, EPI_ISL_17669728, EPI_ISL_17678986-17678987,`EPI_ISL_17679198, EPI_ISL_17679245, EPI_ISL_17679377-17679378,`EPI_ISL_17679443, EPI_ISL_17679445, EPI_ISL_17679519,`EPI_ISL_17679529, EPI_ISL_17679544, EPI_ISL_17679546,`EPI_ISL_17679688, EPI_ISL_17679691, EPI_ISL_17719463,`EPI_ISL_17731340, EPI_ISL_17731355, EPI_ISL_17731371,`EPI_ISL_17731418-17731419, EPI_ISL_17731424-17731425, EPI_ISL_17731429,`EPI_ISL_17731431, EPI_ISL_17732319, EPI_ISL_17735006,`EPI_ISL_17743015, EPI_ISL_17781607, EPI_ISL_17782295,`EPI_ISL_17795927, EPI_ISL_17795966, EPI_ISL_17804456,`EPI_ISL_17809741, EPI_ISL_17812691, EPI_ISL_17814775,`EPI_ISL_17817615, EPI_ISL_17817706, EPI_ISL_17817892,`EPI_ISL_17830861, EPI_ISL_17849282, EPI_ISL_17850570,`EPI_ISL_17854250, EPI_ISL_17948633, EPI_ISL_17948642,`EPI_ISL_17948671, EPI_ISL_17949014, EPI_ISL_17949027,`EPI_ISL_17949089, EPI_ISL_17949195, EPI_ISL_17971523,`EPI_ISL_17972054, EPI_ISL_17976686, EPI_ISL_17978961,`EPI_ISL_17979120, EPI_ISL_17979266, EPI_ISL_17989504,`EPI_ISL_17995465, EPI_ISL_18001506, EPI_ISL_18011160-18011161,`EPI_ISL_18012810, EPI_ISL_18030073, EPI_ISL_18037687,`EPI_ISL_18043050, EPI_ISL_18053907, EPI_ISL_18054668,`EPI_ISL_18054681`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_36c95_a02600.json?f_userOrOld=uploaded%20sample

Trivia:

• Spain/CT-LabRefCat-4864840/2023|EPI_ISL_17806705|2023-05-24 seems to be a recombination with XBB.1.5, placed under a weird flip-flop sub-branch of it, the query is already using -T3576C to filter it out.

[NkRMnZr]

Tracking updates:

08-08, 6 seqs from Spain and USA

`EPI_ISL_18060942, EPI_ISL_18070169, EPI_ISL_18075201, EPI_ISL_18075211, EPI_ISL_18075489, EPI_ISL_18075534`

08-13, 4 seqs from Spain and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_b839_8d2ba0.json?f_userOrOld=uploaded%20sample  `EPI_ISL_18090697, EPI_ISL_18093504, EPI_ISL_18094601, EPI_ISL_18094821`

08-22, 6 seqs from Spain, UK and USA

`EPI_ISL_18113881, EPI_ISL_18118144, EPI_ISL_18119121, EPI_ISL_18119843, EPI_ISL_18120462, EPI_ISL_18122216`

08-24, 3 seqs from USA and Canada

`EPI_ISL_18124344, EPI_ISL_18126360, EPI_ISL_18129892`

08-30, 2 seqs from Denmark

`EPI_ISL_18159862, EPI_ISL_18160045`

09-08, 8 seqs from Spain, UK, USA. A branch of S:T478R emerges

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3df2e_c16040.json?f_userOrOld=uploaded%20sample&label=id:node_6967374  `EPI_ISL_18167896, EPI_ISL_18168064, EPI_ISL_18222782, EPI_ISL_18227931, EPI_ISL_18227991, EPI_ISL_18229896, EPI_ISL_18229907, EPI_ISL_18234018` sub-branch of `S:T478R` follows: _main proposal_ > `A5401G` > `T19980G` > `T4909C` > `G12694A` > `C22995G(S:T478R), T27905A` , Query: `T4909C, G12694A, C22995G` finds 2 as of 09/09.

09-23, 3 seqs from USA

`EPI_ISL_18270869, EPI_ISL_18291115, EPI_ISL_18296787`

[NkRMnZr]

Seems slow.