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XBB.2 + S:F486P+Orf1a:V2027I (NSP3_V1209I )sublineage circulating in Russia (81 seqs) #1877

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FedeGueli opened this issue Apr 11, 2023 · 11 comments
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designated recommended Recommended for designation by pango team member XBB proposed sublineage of XBB
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@FedeGueli
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FedeGueli commented Apr 11, 2023

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:
Schermata 2023-04-12 alle 00 27 44

Schermata 2023-04-12 alle 00 27 02

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

@thomasppeacock thomasppeacock added the XBB proposed sublineage of XBB label Apr 12, 2023
@FedeGueli FedeGueli changed the title XBB.2 + S:F486P+ NSP3_V1209I sublineage circulating in Russia (40seqs) XBB.2 + S:F486P+ NSP3_V1209I sublineage circulating in Russia (47 seqs) Apr 16, 2023
@FedeGueli
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FedeGueli commented Apr 16, 2023

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
Screenshot 2023-04-16 alle 08 33 57

And the two thailandese samples seem unrelated.

@thomasppeacock thomasppeacock added the recommended Recommended for designation by pango team member label Apr 16, 2023
@FedeGueli FedeGueli changed the title XBB.2 + S:F486P+ NSP3_V1209I sublineage circulating in Russia (47 seqs) XBB.2 + S:F486P+ NSP3_V1209I sublineage circulating in Russia (57 seqs) Apr 18, 2023
@FedeGueli
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57 sequences as today all new samples from Moscow.

@FedeGueli FedeGueli changed the title XBB.2 + S:F486P+ NSP3_V1209I sublineage circulating in Russia (57 seqs) XBB.2 + S:F486P+ NSP3_V1209I sublineage circulating in Russia (58 seqs) Apr 22, 2023
@FedeGueli
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58 last one from Austria

@corneliusroemer
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Ping me when this reaches 100 sequences

@FedeGueli
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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 FedeGueli changed the title XBB.2 + S:F486P+ NSP3_V1209I sublineage circulating in Russia (58 seqs) XBB.2 + S:F486P+ NSP3_V1209I sublineage circulating in Russia (59 seqs) Apr 24, 2023
@FedeGueli
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New seq from Thailand

@FedeGueli
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FedeGueli commented Apr 26, 2023

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
Schermata 2023-04-26 alle 11 42 56

@FedeGueli FedeGueli changed the title XBB.2 + S:F486P+ NSP3_V1209I sublineage circulating in Russia (59 seqs) XBB.2 + S:F486P+Orf1a:V2027I (NSP3_V1209I )sublineage circulating in Russia (60 seqs) Apr 26, 2023
@FedeGueli FedeGueli changed the title XBB.2 + S:F486P+Orf1a:V2027I (NSP3_V1209I )sublineage circulating in Russia (60 seqs) XBB.2 + S:F486P+Orf1a:V2027I (NSP3_V1209I )sublineage circulating in Russia (61 seqs) Apr 27, 2023
@FedeGueli
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One more sample from Germany

@FedeGueli
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FedeGueli commented Apr 29, 2023

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.

@FedeGueli FedeGueli changed the title XBB.2 + S:F486P+Orf1a:V2027I (NSP3_V1209I )sublineage circulating in Russia (61 seqs) XBB.2 + S:F486P+Orf1a:V2027I (NSP3_V1209I )sublineage circulating in Russia (81 seqs) Apr 29, 2023
@InfrPopGen InfrPopGen self-assigned this May 11, 2023
InfrPopGen pushed a commit to InfrPopGen/pango-designation that referenced this issue May 11, 2023
… designations, and 6 updated from XBB.2
InfrPopGen added a commit that referenced this issue May 11, 2023
Added new lineage XBB.2.9 from #1877 with 40 new sequence designations, and 6 updated from XBB.2
@InfrPopGen InfrPopGen added this to the XBB.2.9 milestone May 11, 2023
@InfrPopGen
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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
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Thz @InfrPopGen

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