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LB.1.3 + S:T>A376S circulating in South Africa (53, 5 places, 40% South Africa after OCT 15 with a sublineage with S:H445R (7) #2825

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FedeGueli opened this issue Nov 9, 2024 · 8 comments
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LB.1.3 + S:T>A376S circulating in South Africa (53, 5 places, 40% South Africa after OCT 15 with a sublineage with S:H445R (7) #2825

FedeGueli opened this issue Nov 9, 2024 · 8 comments

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@FedeGueli
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FedeGueli commented Nov 9, 2024 •
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LB.1.3>> Orf1a:G432S (G1559A) > S:A376S (G22688T) > S:k147R (A22002G)
Query:22688T,G1559A
Samples: 38 (South Africa 34, Denmark 2, Canada 1,Portugal 1,Spain, US)
First sampled on 2024-08-06 in a traveler from SA

Query for S:H445R branch: 22688T,G1559A,22896G
Samples: 4 ( splitted as the whole lineage in two on Usher)
Places: South Africa, Spain, Colorado
Last sampled on 2024-11-04 Colorado

K147R branch likely dead Query for S:K147R branch: A22002G,22688T Samples: 6

The tree as November 24 is split in two with one branch belonging to a South African LB.1.3 branch with ORF1a:T1581M (C5007T):
Screenshot 2024-11-24 alle 23 03 19
Screenshot 2024-11-24 alle 23 03 48
Screenshot 2024-11-24 alle 23 04 02
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_599c0_39fba0.json?c=gt-S_376&label=id:node_7210934

IDs:
EPI_ISL_19339131, EPI_ISL_19438359, EPI_ISL_19453873-19453874,
EPI_ISL_19453879, EPI_ISL_19453891, EPI_ISL_19463191,
EPI_ISL_19463196-19463197, EPI_ISL_19463199, EPI_ISL_19467580,
EPI_ISL_19467656, EPI_ISL_19485379, EPI_ISL_19485390,
EPI_ISL_19522660, EPI_ISL_19531084, EPI_ISL_19531086,
EPI_ISL_19546684, EPI_ISL_19546686-19546687, EPI_ISL_19546690-19546691,
EPI_ISL_19546694-19546699, EPI_ISL_19546701-19546704, EPI_ISL_19546706,
EPI_ISL_19546708-19546710, EPI_ISL_19546714, EPI_ISL_19546718,
@FedeGueli FedeGueli mentioned this issue Nov 9, 2024
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@FedeGueli FedeGueli changed the title LB.1.3 + S:T>A376S circulating in South Africa (17, 4 places, 20% South Africa after Sept 1) LB.1.3 + S:T>A376S circulating in South Africa (38, 4 places, 40% South Africa after OCT 1) Nov 15, 2024
@FedeGueli
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38 now, 14/33 after OCT.1 in South Africa, @corneliusroemer this needs a rapid designation.

@FedeGueli FedeGueli changed the title LB.1.3 + S:T>A376S circulating in South Africa (38, 4 places, 40% South Africa after OCT 1) LB.1.3 + S:T>A376S circulating in South Africa (38, 4 places, 40% South Africa after OCT 1) with a sublineage with S:K147R Nov 15, 2024
@FedeGueli
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FedeGueli commented Nov 15, 2024 •
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Re updating the tree, there is also a K147R branch of it

@FedeGueli FedeGueli changed the title LB.1.3 + S:T>A376S circulating in South Africa (38, 4 places, 40% South Africa after OCT 1) with a sublineage with S:K147R LB.1.3 + S:T>A376S circulating in South Africa (39, 5 places, 40% South Africa after OCT 1) with a sublineage with S:K147R Nov 20, 2024
@FedeGueli
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+1 Spain, @corneliusroemer this could be something to designate soon.

@FedeGueli FedeGueli changed the title LB.1.3 + S:T>A376S circulating in South Africa (39, 5 places, 40% South Africa after OCT 1) with a sublineage with S:K147R LB.1.3 + S:T>A376S circulating in South Africa (40, 5 places, 40% South Africa after OCT 1 with a sublineage with S:H445R (4) Nov 24, 2024
@FedeGueli
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40 with a new sample from Colorado it belongs to a S:H445R branch counting 4 samples 2 South Africa, 1 Spain and the most recent one from November collected in Colorado
Query added for 445R : 22688T,G1559A,22896G
I strongly suggest to designate this one.
cc @corneliusroemer

@FedeGueli FedeGueli changed the title LB.1.3 + S:T>A376S circulating in South Africa (40, 5 places, 40% South Africa after OCT 1 with a sublineage with S:H445R (4) LB.1.3 + S:T>A376S circulating in South Africa (41, 5 places, 40% South Africa after OCT 1 with a sublineage with S:H445R (4) Dec 3, 2024
@FedeGueli
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one old one from South Africa

@FedeGueli FedeGueli changed the title LB.1.3 + S:T>A376S circulating in South Africa (41, 5 places, 40% South Africa after OCT 1 with a sublineage with S:H445R (4) LB.1.3 + S:T>A376S circulating in South Africa (43, 5 places, 40% South Africa after OCT 1 with a sublineage with S:H445R (5) Dec 6, 2024
@FedeGueli FedeGueli changed the title LB.1.3 + S:T>A376S circulating in South Africa (43, 5 places, 40% South Africa after OCT 1 with a sublineage with S:H445R (5) LB.1.3 + S:T>A376S circulating in South Africa (43, 5 places, 40% South Africa after OCT 15 with a sublineage with S:H445R (5) Dec 6, 2024
@FedeGueli
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43 now with two samples from South Africa one of them with H445R. It keeps a share of 40% of genomes in South Africa after October 15. ping @corneliusroemer this should get a designation

@xz-keg
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xz-keg commented Dec 11, 2024

designated LB.1.3.4

@FedeGueli
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designated LB.1.3.4

via 16205e7

@FedeGueli FedeGueli changed the title LB.1.3 + S:T>A376S circulating in South Africa (43, 5 places, 40% South Africa after OCT 15 with a sublineage with S:H445R (5) LB.1.3 + S:T>A376S circulating in South Africa (53, 5 places, 40% South Africa after OCT 15 with a sublineage with S:H445R (7) Dec 27, 2024
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