XBB.2.3.3 (S:K182N) acquired S:T478R in Thailand (3% prevalence in August) and it is spreading internationally (158 seq - 13 countries)

[FedeGueli]

Originally discussed in sars-cov-2-variants/lineage-proposals#429 (comment)

XBB.2.3.3 recently acquired S:T478R as several siblings of it did before.

Defining mutations: XBB.2.3.3 >> C19884T, C13138T> A11794G, S:T478R (A22995G)

Gisaid query: C19884T, C13138T,A11794G

Samples: 35
First:
hCoV-19/Thailand/TROPMED-0179/2023 | Original | EPI_ISL_17952206 | 2023-04-20
Last:
hCoV-19/USA/NY-GBW-H20-332-9576/2023 | Original | EPI_ISL_18094979 | 2023-08-03 (From Uk)

IDs

EPI_ISL_17622144, EPI_ISL_17624077, EPI_ISL_17683098, EPI_ISL_17692219, EPI_ISL_17696820, EPI_ISL_17816161, EPI_ISL_17835426, EPI_ISL_17952206, EPI_ISL_17956877, EPI_ISL_17980180, EPI_ISL_17984544, EPI_ISL_17984546, EPI_ISL_17987920, EPI_ISL_17994632, EPI_ISL_17994656, EPI_ISL_17994683, EPI_ISL_18042024, EPI_ISL_18042029, EPI_ISL_18042074-18042075, EPI_ISL_18056679, EPI_ISL_18056691, EPI_ISL_18057066, EPI_ISL_18059124, EPI_ISL_18062445, EPI_ISL_18062508, EPI_ISL_18062923, EPI_ISL_18063001, EPI_ISL_18064544, EPI_ISL_18072098, EPI_ISL_18078449, EPI_ISL_18080164, EPI_ISL_18094249, EPI_ISL_18094931, EPI_ISL_18094979

tree:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_4180e_8f9750.json?c=gt-S_478&label=id:node_7222026

Countries:

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EDITED
During the night of 28th august i spotted a sequence of this lineage uploaded by GBW US airport surveillance.
Re-ushering it to check it was clear that a new sublineage of this is spreading quite quickly in Europe with additional spike mutation S:S255F

So i want to propose it suggest a quick coupled designation of these lineages.

Defining mutations of sublineage:
XBB.2.3.3 (>> C19884T, C13138T> A11794G, S:T478R (A22995G) = #2181 original issue) >>
ORF1a:A540V (C1884T ), Orf1a:A3963V (C12153T ) , S:S255F (C22326T)

Gisaid query NEW sublineage: C1884T, C12153T, C22326T consider that finds just 13 seqs the remaining ones are still only on CLIMB UK database

Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_616d_d35a10.json?c=userOrOld&label=id:node_7367025
The lineage is already showing interesting diversity in the spike and outside:

[FedeGueli]

This is accelerating now reached 51 seqs last doubling in 16 days just stuck to the back of the leading pack

[FedeGueli]

South Korea and Texas origin mostly for the last samples

[FedeGueli]

cc @AngieHinrichs @corneliusroemer @InfrPopGen i have edited the proposal cause i spotted that this already has a sublineage defined by spike_S255F spreading fast in Europe (many sequences are only on CLimb-UK, so the following query catches just a bit more than the half of them >C1884T, C12153T, C22326T) i think this should be designated as happened for XBB.2.3.8,GE.1 and XBB.2.3.11

[FedeGueli]

89 now. this reached around 3% in thailand in August and it spread widely now to Texas , South Korea , Scotland

[FedeGueli]

@corneliusroemer this is going up doubling in 16 days close to current dominant lineages ( not to flips)

[FedeGueli]

100 as today.

[FedeGueli]

105

[FedeGueli]

Big jump to 158 mainly due Texas (55/158) and Thailand sequences

[FedeGueli]

Designated GJ.5 and GJ.5.1 via 897f423 and 7122242