JQ.2 (BA.2.86.3 + S:R346T ) got S:L455S in South Africa - 3% prevalence in February (18 Samples)

[FedeGueli]

Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/1373

Defining mutations BA.2.86.3 (T12775C) > S:R346T (G22599C) > G2944A > Orf1a:L3711F (C11396T) > S:L455S (T22926C)

JQ.2 Query

NEW QUERY ( 29/02/2024): Fro the main S:R346T branch : _G2944A, T12775C, G22599C, T12775C, C897A_ = 13 Samples

S:L455S branch: G2944A, T12775C, G22599C, C11396T = 10 Samples (6 SA, 4 Can)

EPI_ISL_18871078, EPI_ISL_18933515, EPI_ISL_18933635, EPI_ISL_18933642, EPI_ISL_18933692, EPI_ISL_18939867, EPI_ISL_18939872, EPI_ISL_18939880, EPI_ISL_18939888,

New Tree (Edited):

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_10e2f_fb42b0.json?c=gt-S_346,455&gmax=25384&gmin=21563&label=id:node_6875571

[Mydtlwn]

@corneliusroemer

[FedeGueli]

+2 samples with S:L455S from Canada . @corneliusroemer This seems another to watch for a potential designation

[FedeGueli]

i keep this open to track the 455S sublineage

[FedeGueli]

+1 Canada

[FedeGueli]

+1 Scotland

[FedeGueli]

18, but prevalence in SA declining

[aviczhl2]

Designated JQ.2.1

[FedeGueli]

@corneliusroemer wrong milestone it is JQ.2.1 @AngieHinrichs

[FedeGueli]

JQ.2.1 via https://github.com/cov-lineages/pango-designation/commit/617afbf50b158be78886097af6c5919debe95afd

[Mydtlwn]

Thank.

[FedeGueli]

JQ.2.1 seems to have acquired S:S71F in the only lineage currently sampled outside South Africa: JQ.2.1> Orf1a:T2777I (C8595T) >C10228T,C12043T,S:S71F (C21774T) Query: C8595T,C10228T,C12043T Samples:6 Countries: 2 Uk , NZL

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_33049_129030.json?label=id:node_6906408