XBB.2 + S:F486P+Orf1a:V2027I (NSP3_V1209I )sublineage circulating in Russia (81 seqs)

[FedeGueli]

XBB.2 sublinege sampled in many different regions of Russia (Bryansk, Omsk, Mordova, Penza, Saint Petersburg, Kovrov, Moscow)
and exported successfully to Singapore, Israel and Germany.

Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_22b8f_5dd7c0.json?f_userOrOld=uploaded%20sample&label=id:node_6037818

Defining mutations:
XBB.2 >> A21231G >> ORF1a:V2027I (G6344A),S:F486P (T23018C)

Gisaid query: A21231G ,G6344A, T23018C

Sequences : 40
EPI_ISL_16504361, EPI_ISL_16807781, EPI_ISL_16832523,
EPI_ISL_16847539, EPI_ISL_16975273, EPI_ISL_17105872,
EPI_ISL_17105927, EPI_ISL_17106038, EPI_ISL_17106092,
EPI_ISL_17106126, EPI_ISL_17106132-17106133, EPI_ISL_17106268,
EPI_ISL_17106314, EPI_ISL_17106328, EPI_ISL_17106384,
EPI_ISL_17106426, EPI_ISL_17106483, EPI_ISL_17106497,
EPI_ISL_17264407, EPI_ISL_17317850, EPI_ISL_17317954,
EPI_ISL_17317956, EPI_ISL_17318115, EPI_ISL_17318149,
EPI_ISL_17318250-17318251, EPI_ISL_17318257, EPI_ISL_17318335,
EPI_ISL_17318339, EPI_ISL_17318379, EPI_ISL_17318397,
EPI_ISL_17318443, EPI_ISL_17318471, EPI_ISL_17318482,
EPI_ISL_17318521, EPI_ISL_17318530, EPI_ISL_17318562,
EPI_ISL_17318580, EPI_ISL_17318585

[FedeGueli]

47 sequences as today. This week 4 more samples came from Russia (Moscow) 1 from Austria-Tyrol and 2 from Thailand one of them labeled as "foreigner".

@thomasppeacock @corneliusroemer @InfrPopGen I would designate this one for its geographical relevance and further international spread beyond the known fit of its 486P mutation in the XBB.2 background.

Notably the Austrian sample gained S:T478R:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2fb8c_b96240.json?c=userOrOld&label=id:node_6035499

And the two thailandese samples seem unrelated.

[FedeGueli]

57 sequences as today all new samples from Moscow.

[FedeGueli]

58 last one from Austria

[corneliusroemer]

Ping me when this reaches 100 sequences

[FedeGueli]

Thx @corneliusroemer for your great work
I think both this one and the other russian xbb.2 +486P have to be tracked for a while and i will be happy to do. I will ping you at 100seqs.

[FedeGueli]

New seq from Thailand

[FedeGueli]

Interestingly basal to this lineage, lacking defining Orf1a:V2027I there is a sequence from Belgium defined by S:G482S maybe just misplaced: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice3_genome_296e8_8e52a0.json?c=gt-S_482&label=id:node_10054482

[FedeGueli]

One more sample from Germany

[FedeGueli]

Big Jump to 81 sequences for this one. Samples came in from 5 different Russian regions and Austria.
I think it deserves a rapid designation . @InfrPopGen @thomasppeacock @corneliusroemer

6 out of 166 samples collected after 20th of March in Russia belongs to this sublineage.

[InfrPopGen]

Thanks for submitting. We've added lineage XBB.2.9 with 40 newly designated sequences, and 6 updated. Defining mutations G6344A (ORF1a:V2027I), T23018C (S:S486P) (following A21231G).

[FedeGueli]

Thz @InfrPopGen