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EB Four LB.1.3 +S:T376S branches with S:H445R in South Africa · Issue #2379 · sars-cov-2-variants/lineage-proposals · GitHub
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Four LB.1.3 +S:T376S branches with S:H445R in South Africa #2379

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FedeGueli opened this issue Jan 22, 2025 · 4 comments
Closed

Four LB.1.3 +S:T376S branches with S:H445R in South Africa #2379

FedeGueli opened this issue Jan 22, 2025 · 4 comments

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@FedeGueli
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FedeGueli commented Jan 22, 2025

Branch 1 LB.1.3.4 + 445R with a R190S + T345S Branch Now designated NZ.1

LB.1.3.4 >> S:H445R (A22896G) > ORF1a:P1207L (C3885T), T12667C, C16092T >
C2710G, G14712A, S:R190S (G22132T), S:T345S (C22596G), ORF3a:L53F (C25549T), A26358G
Query for H445R : 22896G,22688T,-A22753G,-T4054C
Samples: 14 SA
Query for 445R + 190S + 345S: 22896G,C2710G, G14712A
Samples: 2 SA

Branch 2 LB.1.3.4 + 445R + 572I
LB.1.3.4 >> T4054C > Orf3a:T89I (C25658T) >C10228T, ORF1b:I1257V (A17236G), S:H445R (A22896G), S:T572I (C23277T)
Query: A17236G , 22896G, C23277T
Samples: 1 SA

Branch 3 LB.1.3.4 + ORF1a:G4178S + S:H445R
LB.1.3.4 >> A22753G > A397G, C4672A, ORF1a:G4178S (G12797A), ORF3a:L95F (G25677T), ORF3a:P240L (C26111T), ORF8:L4F (C27903T), T29566C > ORF1a:N2768K (T8569G), S:H445R (A22896G)
Query: 25677T,C26111T,T8569G
Samples: 2 (GBW SA)

Branch 4 LB.1.3+S:A376S+ S:H445R
LB.1.3 > Orf1a:T1581M (C5007T)> 6883T, Orf1b:T1599A (A18262G), S:A376S (G22688T), N:G200D (G28872A) > T20799C , ORF7a:T14I > S:H445R (A22896G)
Query for 376S : C5007T,6883T,A18262G
Samples: 10 SA
Query for 376S+ 445R: T20799C ,22896G, C5007T
Samples: 2
SA

tree:

Imagehttps://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice8_genome_test_46610_bca70.json?c=gt-S_445&gmax=25384&gmin=21563&label=id:node_7176314

@HynnSpylor
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the step mutations S:A376S, H445R, R190S and T345S are interesting (and it is a very new sample detected in US international airport). XEC+S:T345S are also growing recently.

@FedeGueli
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the step mutations S:A376S, H445R, R190S and T345S are interesting (and it is a very new sample detected in US international airport). XEC+S:T345S are also growing recently.

yeah T345S was in clusters both on Kp.3.1.1 as XEC the first i remember was in Wales but then also Canada.

@FedeGueli FedeGueli added this to the NZ.1 milestone Jan 29, 2025
@FedeGueli
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BR.1 Designated NZ.1 via cov-lineages/pango-designation@91fc352

FedeGueli referenced this issue in cov-lineages/pango-designation Jan 29, 2025
@xz-keg
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xz-keg commented Feb 17, 2025

other branches not growing

@xz-keg xz-keg closed this as completed Feb 17, 2025
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