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JQ.2 (BA.2.86.3 + S:R346T ) got S:L455S in South Africa - 3% prevalence in February (18 Samples) #2505

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FedeGueli opened this issue Feb 28, 2024 · 11 comments
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JQ.2 (BA.2.86.3 + S:R346T ) got S:L455S in South Africa - 3% prevalence in February (18 Samples) #2505

FedeGueli opened this issue Feb 28, 2024 · 11 comments
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@FedeGueli
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FedeGueli commented Feb 28, 2024 •
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Transferred from sars-cov-2-variants/lineage-proposals#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):
Screenshot 2024-02-28 alle 23 38 30
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
@FedeGueli FedeGueli mentioned this issue Feb 28, 2024
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@Mydtlwn
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Mydtlwn commented Feb 29, 2024

@corneliusroemer

@FedeGueli FedeGueli changed the title BA.2.86.3 got S:R346T (13) and then S:L455S in South Africa - 5% prevalence in January (10 Samples) BA.2.86.3 got S:R346T (15) and then S:L455S in South Africa - 5% prevalence in January (12 Samples) Mar 4, 2024
@FedeGueli
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+2 samples with S:L455S from Canada .
@corneliusroemer This seems another to watch for a potential designation

corneliusroemer added a commit that referenced this issue Mar 5, 2024
@corneliusroemer
Designate JQ.2 (S:R346T, G2944A, South Africa, from #2505)
c93fc79
@FedeGueli FedeGueli changed the title BA.2.86.3 got S:R346T (15) and then S:L455S in South Africa - 5% prevalence in January (12 Samples) JQ.2 (BA.2.86.3 + S:R346T ) got S:L455S in South Africa - 5% prevalence in January (12 Samples) Mar 6, 2024
@FedeGueli FedeGueli reopened this Mar 6, 2024
@FedeGueli
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i keep this open to track the 455S sublineage

@FedeGueli FedeGueli reopened this Mar 6, 2024
@FedeGueli FedeGueli changed the title JQ.2 (BA.2.86.3 + S:R346T ) got S:L455S in South Africa - 5% prevalence in January (12 Samples) JQ.2 (BA.2.86.3 + S:R346T ) got S:L455S in South Africa - 5% prevalence in January (13 Samples) Mar 12, 2024
@FedeGueli
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+1 Canada

@FedeGueli FedeGueli changed the title JQ.2 (BA.2.86.3 + S:R346T ) got S:L455S in South Africa - 5% prevalence in January (13 Samples) JQ.2 (BA.2.86.3 + S:R346T ) got S:L455S in South Africa - 5% prevalence in January (14 Samples) Mar 17, 2024
@FedeGueli
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+1 Scotland

@FedeGueli FedeGueli changed the title JQ.2 (BA.2.86.3 + S:R346T ) got S:L455S in South Africa - 5% prevalence in January (14 Samples) JQ.2 (BA.2.86.3 + S:R346T ) got S:L455S in South Africa - 5% prevalence in January (18 Samples) Mar 19, 2024
@FedeGueli FedeGueli changed the title JQ.2 (BA.2.86.3 + S:R346T ) got S:L455S in South Africa - 5% prevalence in January (18 Samples) JQ.2 (BA.2.86.3 + S:R346T ) got S:L455S in South Africa - 3% prevalence in February (18 Samples) Mar 19, 2024
@FedeGueli
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18, but prevalence in SA declining

@xz-keg
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xz-keg commented Mar 20, 2024

Designated JQ.2.1

@corneliusroemer corneliusroemer added this to the JN.2.1 milestone Mar 20, 2024
@FedeGueli
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@corneliusroemer wrong milestone it is JQ.2.1 @AngieHinrichs

@FedeGueli
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JQ.2.1 via 617afbf

FedeGueli referenced this issue Mar 20, 2024
@corneliusroemer
Designate JQ.2.1 (S:L455S, South Africa)
617afbf
@corneliusroemer corneliusroemer removed this from the JN.2.1 milestone Mar 20, 2024
@Mydtlwn
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Mydtlwn commented Mar 21, 2024

Thank.

@FedeGueli
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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
Screenshot 2024-04-30 alle 19 28 27
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_33049_129030.json?label=id:node_6906408

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@xz-keg @corneliusroemer @Mydtlwn @FedeGueli