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LF.7.1 + S:T572I (39, >10 Places) #2873

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FedeGueli opened this issue Jan 20, 2025 · 7 comments
Open

LF.7.1 + S:T572I (39, >10 Places) #2873

FedeGueli opened this issue Jan 20, 2025 · 7 comments

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@FedeGueli
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FedeGueli commented Jan 20, 2025 •
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This was fromerly known as Branch 4 of sars-cov-2-variants/lineage-proposals#2215
Initially we tracked just the T493C branch , then Usher added some recent sample without it starting directly from the S:T572I node ,as @xz-keg analyzed. this creates unfortunately the need to use a double query for this lineage one excluding the 493C samples and all the convergent appearance of LF.71. and the other the original T493C+ T572i query

LF.7.1 >> S:T572I (C23277T) > T493C
Double Query:
C6310T,C23277T,C8818T,-T493C,-A3398G, -C4068T,-C25006T,-C25671T,-G4354A,-A798G,-T20040C,-C2048T,-A3008G,-C583T,-C3828T
PLUS
T493C,C23277T, C7869T
Samples:17
Places: 9 [ Slovenia, US, Sweden, England,Poland,France, Finland, Netherlands, Singapore]
Tree:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_2a2d2_e06440.json?label=id:node_7183519
Image

IDs List ( with both 493C and 493T to avoid issues during designation eventually):
EPI_ISL_19658646, EPI_ISL_19664058, EPI_ISL_19666744,
EPI_ISL_19485019, EPI_ISL_19485035, EPI_ISL_19527136,
EPI_ISL_19550733, EPI_ISL_19575726, EPI_ISL_19624325,
EPI_ISL_19631425, EPI_ISL_19632487, EPI_ISL_19633180,
EPI_ISL_19646294, EPI_ISL_19646548, EPI_ISL_19650840,
EPI_ISL_19669981, EPI_ISL_19671470
@FedeGueli FedeGueli mentioned this issue Jan 20, 2025
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@FedeGueli FedeGueli changed the title LF.7.1 + S:T572I (17, 9 Places) LF.7.1 + S:T572I (19, 10 Places) Jan 20, 2025
@FedeGueli
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+2 in the non 493C branch one from Singapore the other from Portugal new country

@FedeGueli FedeGueli changed the title LF.7.1 + S:T572I (19, 10 Places) LF.7.1 + S:T572I (20, 10 Places) Jan 23, 2025
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+1 NY

@FedeGueli FedeGueli changed the title LF.7.1 + S:T572I (20, 10 Places) LF.7.1 + S:T572I (21, 10 Places) Jan 28, 2025
@FedeGueli FedeGueli changed the title LF.7.1 + S:T572I (21, 10 Places) LF.7.1 + S:T572I (27, 10 Places) Feb 12, 2025
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10+17 gives 27 with new samples from Slovenia and Finland

@FedeGueli FedeGueli changed the title LF.7.1 + S:T572I (27, 10 Places) LF.7.1 + S:T572I (29, >10 Places) Feb 15, 2025
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+2 IL

@FedeGueli FedeGueli changed the title LF.7.1 + S:T572I (29, >10 Places) LF.7.1 + S:T572I (27, >10 Places) Feb 15, 2025
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27 total with new query with more -s

@FedeGueli FedeGueli changed the title LF.7.1 + S:T572I (27, >10 Places) LF.7.1 + S:T572I (33, >10 Places) Feb 21, 2025
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FedeGueli commented Feb 21, 2025 •
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33 now France Chile and a cluster with S:Q690P in Us

ping @corneliusroemer it seems 572I workjs very well with LF.7 backbone (without 475V though)

@FedeGueli FedeGueli changed the title LF.7.1 + S:T572I (33, >10 Places) LF.7.1 + S:T572I (39, >10 Places) Mar 1, 2025
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39 now

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