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XDR.1: XDR + S:F59S(7 seq, 4 countries) + S:R346T(6 seq) #1542

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DoropFan opened this issue May 3, 2024 · 5 comments
Closed

XDR.1: XDR + S:F59S(7 seq, 4 countries) + S:R346T(6 seq) #1542

DoropFan opened this issue May 3, 2024 · 5 comments
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designated S:59 S:346 XDR
Milestone
XDR.1

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@DoropFan
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DoropFan commented May 3, 2024 •
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Sub-lineage of:XDR
Earliest sequence:2024-02-08(Brazil)EPI_ISL_18970545
Most recent sequence:2024-04-03(England)EPI_ISL_19055525
Countries circulating:Peru(2), Brazil(1), United States(1), United Kingdom(1)
Sequences:5

UShER Tree
XDR>C5005T>ORF1a:A1938S(G6077T), A14031G, S:F59S(T21738C), C26801T
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1cc89_4656e0.json?c=gt-S_346&gmax=25384&gmin=21563&label=id:node_7012477
XDR+59S+346T

Query:C2668T, G6077T, T21738C
CovSpectrum

Genomes
EPI_ISL_19084464
EPI_ISL_19084465
EPI_ISL_18970545
EPI_ISL_18960074
EPI_ISL_19055525
@FedeGueli FedeGueli changed the title XDR + S:F59S(5 seq, 4 countries) + S:R346T(4 seq) XDR + S:F59S(7 seq, 4 countries) + S:R346T(6 seq) May 15, 2024
@FedeGueli
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7 seqs now (6 346T)

FedeGueli referenced this issue in cov-lineages/pango-designation May 15, 2024
@corneliusroemer
Designate XDR.1 (S:F59S, G6077T, A14031G, C26801T, Brazil/Peru)
acd0f55
@FedeGueli FedeGueli added this to the XDR.1 milestone May 15, 2024
@FedeGueli
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XDR.1 designated starting from S:F59S
cov-lineages/pango-designation@acd0f55

@FedeGueli FedeGueli changed the title XDR + S:F59S(7 seq, 4 countries) + S:R346T(6 seq) XDR.1: XDR + S:F59S(7 seq, 4 countries) + S:R346T(6 seq) May 15, 2024
@FedeGueli
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Lets see if all the sequences have 346T it could be don and dusted here.

@xz-keg
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xz-keg commented Jun 23, 2024 •
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image

Usher tree changes and it seems not recognizing XDR.1 now.

usher

@AngieHinrichs

@AngieHinrichs
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Thanks @aviczhl2! It will be fixed in the 2024-06-27 tree later today.

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designated S:59 S:346 XDR
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@AngieHinrichs @xz-keg @FedeGueli @DoropFan