XBB.1.22.1 sublineage with S:Q675K (99 seqs in 18 countries)

[HynnSpylor]

Defining mutations: XBB.1.22.1>C925A (ORF1a:D220E), G2265A (ORF1a:C667Y), C23585A (S:Q675K)
GISAID query: Spike_Y200C, Spike_Q675K, G2265A
Earliest seq: 2023-02-20 (Germany, EPI_ISL_17254760)
Most recent seq: 2023-05-29 (Portugal, EPI_ISL_17786191)
Countries detected: Indonesia (11), Germany (3), Portugal (3), India (2), UK (2), Brunei (2), Malaysia (2), France (1), Luxemburg (1), USA (1), Japan (1), Singapore (1)

Usher Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2e1ba_74eb00.json?c=gt-S_675
A mutation near FCS, despite S:Q675H is more common than S:Q675K.

Genomes:
EPI_ISL_17223621, EPI_ISL_17254760, EPI_ISL_17266838, EPI_ISL_17388874, EPI_ISL_17389250-17389251, EPI_ISL_17389319,
EPI_ISL_17406962, EPI_ISL_17469048, EPI_ISL_17503882, EPI_ISL_17503885, EPI_ISL_17521393, EPI_ISL_17630669,
EPI_ISL_17630982, EPI_ISL_17654409, EPI_ISL_17655046, EPI_ISL_17657336, EPI_ISL_17681329, EPI_ISL_17681356,
EPI_ISL_17691900, EPI_ISL_17712546, EPI_ISL_17717567, EPI_ISL_17721796, EPI_ISL_17742266, EPI_ISL_17771926,
EPI_ISL_17786112, EPI_ISL_17786191, EPI_ISL_17788306, EPI_ISL_17788344, EPI_ISL_17788378

[FedeGueli]

Why not on the other page?

[HynnSpylor]

@FedeGueli I'm very sorry but puzzled - do you mean why I didn't propose it in preproposal page?
In my view if a sublineage reaches 30 seqs and emerges in more than two countries, it can be directly proposed in main page.

[FedeGueli]

Yeah of course @HynnSpylor i think there is always time to propose. Here it could be overlooked. with our double scheme we are getting the fast lineages lineages designated before, but that is just my view, of course anyone could urge to propose directly here if there are reasons to .

[FedeGueli]

still 31 viruses last sample from Australia that did not upload a big batch this week. we will see the next week.

[HynnSpylor]

34 seqs now and with a branch of S:S408N (6 seqs)

[FedeGueli]

This now reached 39 seqs with C23585A,A22161G,G2265A and one sublineage counting 7 sequences has got S:R408N

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2a8f_3a240.json?c=userOrOld&label=id:node_6707443

Speaking broadly XBB.1.22.1 seems first lineage to tolerate or promote the emergence of various mutations at 408 (defining in BA.2 with S)
see also the lineage proposed in the other page today:

I would designate this one . cc @corneliusroemer @InfrPopGen

[FedeGueli]

43 as today

[FedeGueli]

C925A , G2265A , C23585A finds 62 as today.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2bf2_dc130.json?c=country&label=id:node_6775589

ping @corneliusroemer i suggest to designate this one.

[HynnSpylor]

81 seqs in 18 countries now
Recently the branch with S:T385A and S:D1118Y is circulating in Europe (latest sample in 2023-08-12), and branch with S:R408G in US (latest sample in 2023-07-18)

[HynnSpylor]

87 seqs now and it seems circulating again.
US branch (with S:R408G) has 2 new seqs with S:N481S

[FedeGueli]

Likely it deserves a designation.

[Memorablea]

94 NOW

[FedeGueli]

Now designated FY.9 via 066dbbb

milestone missing @corneliusroemer