XBB.1.17.1 with ORF1a:N1080D (nsp3_N262D), ORF1a:S2553F (nsp3_S1735F) and S:K356T (18 seqs, 6 countries)

NkRMnZr commented 1 year ago

Defining Mutations: [on top of XBB.1.17.1's G22205C > T23018C > G20173A/ORF1b:V2236I branch, that is, sibling to GA.2/3] > A3503G(ORF1a:N1080D), C7923T(ORF1a:S2553F) > A22629C(S:K356T) >

Query: G20173A, C7923T, A22629C Earliest seq: 2023-03-21 (EPI_ISL_17464855, Spain) Latest seq: 2023-06-07 (EPI_ISL_17817102, Italy) Sampled Countries: Spain (4), UK (3, England/2, Wales/1), France (1), Italy (1), USA (1, Florida)

Genomes:

EPI_ISL_17464855, EPI_ISL_17535624, EPI_ISL_17535628, EPI_ISL_17589733, EPI_ISL_17607286, EPI_ISL_17721637, EPI_ISL_17721668, EPI_ISL_17762293, EPI_ISL_17786030, EPI_ISL_17817102

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_dff_ab0a20.json?f_userOrOld=uploaded%20sample&label=id:node_6977892

Overview from XBB.1.17.1 polytomy

Details: Details

Trivia:

A few seqs placed in UShER have Ns near 22629, so they are not caught by query:
Genomes:
Luxembourg/LNS3117480/2023|EPI_ISL_17633308|2023-04-22

Those seqs with Ns may suggest this branch came from Nigeria, but it's almost impossible to find out whether K356T evolved earlier date in Nigeria or later date in Spain.
Despite K356T being quite successful on many variants, it is not quite often seen on XBB's backbone, with some exceptions like XBB.1.28 and XBB.1.5.44.
Credit to @Sinickle to spot it first #17 , what confused me is another branch: C2189T(ORF1a:L642F), A5101G, A14199G > A22629C(S:K356T), C28000T(ORF8:P36L) [query: A22629C, C28000T, C2189T, finds 3], I thought that was the other proposal, but in fact this one is a duplication, just different look on UShER.

FedeGueli commented 1 year ago

This was noticed first by @Sinickle in https://github.com/sars-cov-2-variants/lineage-proposals/issues/17, but he proposed it starting deeper in the tree

FedeGueli commented 1 year ago

It seems slow to me looking at collection dates but good to monitor it.

NkRMnZr commented 1 year ago

oops seems I'm late again, should I close this one and keep #17 on?

FedeGueli commented 1 year ago

@Sinickle if you agree i would keep this one that is broader one open maybe adding explicit credits to you at the start of the main post.

NkRMnZr commented 1 year ago

Tracking updates:

Update 1: 23-07-03, 2 seqs from 2 countries

1 from Texax, USA:EPI_ISL_17955966 Note this one is a mini-saltation, which got futher S:T478R new entry: 1 from Belgium: EPI_ISL_17950428

Update 2: 23-07-07, 4 seqs from Italy & USA

2 from Italy: EPI_ISL_17963425, EPI_ISL_17963428 2 from California: EPI_ISL_17965284, EPI_ISL_17972496

Update 3: 23-07-19, 2 seqs from New York, with Travel history to: Qatar

EPI_ISL_17996097, EPI_ISL_17996116

FedeGueli commented 1 year ago

https://github.com/cov-lineages/pango-designation/commit/32f5f23e371d39b1fac054c805817de0e036a697

sars-cov-2-variants / lineage-proposals

XBB.1.17.1 with ORF1a:N1080D (nsp3_N262D), ORF1a:S2553F (nsp3_S1735F) and S:K356T (18 seqs, 6 countries) #265