XBB.1.9.1 + ORF9b:P17L acquired S:L452R and ORF7a:V104L 11 seqs (Wales, ENGLAND, South Korea, Japan, California, Texas, North Carolina, Aus-NSW, Singapore)

[FedeGueli]

Just to take note that one little but interesting node of XBB.1.9.1 is defined by S:L452R and ORF7a:V104L and it has been already found in US and Japan suggesting maybe a wider than seen circulation.

Tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_38201_fd2fa0.json?label=id:node_10149940

Defining mutations: XBB.1.9.1 >> ORF9b:P17L (C28333T) > T3898C > , S:L452R (T22917G), Orf7a:V104L (G27703C)

Gisaid queries: T3898C , G27703C, T22917G, C28333T

Sequences: 3 EPI_ISL_17618728, EPI_ISL_17631093, EPI_ISL_17651262,

Note: EDITED the NSP5_A193Tis just a branch of it more samples came after the first samples not carrying that mutation, so i deleted it from the main proposal

NSP5_A193T was mentioned in this report : https://www.publichealthontario.ca/-/media/Documents/nCoV/ipac/2022/06/sars-cov2-protease-mutations-paxlovid-resistance.pdf?sc_lang=en that didnt find a strong link to Paxlovid Resistance, tough recording its sporadic appearance in the samples analyzed by this report.

[FedeGueli]

2 new sequences Australia and California

[FedeGueli]

One more from Singapore.

[FedeGueli]

One more from South Korea

[FedeGueli]

3 new sample from Wales and one from England not yet on GISAID(England/PHEC-YYE4DU3/2023|2023-05-24)

Quite striking that this keeps popping up here and there without a geographical clear trend if not that it is sequenced in countries with still ongoing good surveillance, this may hint to a good prevalence somewhere in an undersampled region .

cc @corneliusroemer please take a look at this.

Tree: (now it is clear that ORf1a:A3456T (NSP5_A193T) is just a branch of it so i have edited the main proposal: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_12203_1967c0.json?label=id:node_6688471

interestingly the samples from Wales carry S:G184S