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EG.5.1.1/XBB.1.16.6 Recombinant (US, Spain, England, 15 seq, Oct 20) #777

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ryhisner opened this issue Sep 9, 2023 · 5 comments
Closed

EG.5.1.1/XBB.1.16.6 Recombinant (US, Spain, England, 15 seq, Oct 20) #777

ryhisner opened this issue Sep 9, 2023 · 5 comments
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. recombinant S:456 S:478

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@ryhisner
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ryhisner commented Sep 9, 2023

Description

Recombinant of: EG.5.1.1 / XBB.1.16.6
Breakpoint: 14856-16878 (Before 14856 = EG.5.1.1, After 16878 = XBB.1.16.6)
Earliest sequence: 2023-8-17, Spain, Basque Country — EPI_ISL_18241651
Most recent sequence: 2023-8-29, England — EPI_ISL_18237603
Countries circulating: England (4), Spain (1)
Number of Sequences: 5
GISAID Nucleotide Query: C1875T, T17454A
CovSpectrum Query: [2-of: G393A, C1875T, T17454A]
(possible) Private Substitutions:
ORF1a: R43H, A537V
Nucleotide: G393A, C1875T, T17454A

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.16.6_EG.5.1.1_Recomb.json?c=gt-nuc_17454&gmax=18454&gmin=16454&label=id:node_6821120
image

Notes
None for now.

Genomes

Genomes EPI_ISL_18227047, EPI_ISL_18227118, EPI_ISL_18227645, EPI_ISL_18237603, EPI_ISL_18241651
@NkRMnZr NkRMnZr mentioned this issue Sep 11, 2023
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@FedeGueli FedeGueli changed the title EG.5.1.1/XBB.1.16.6 Recombinant (Spain, England, 5 seq, Sept 9) EG.5.1.1/XBB.1.16.6 Recombinant (US, Spain, England, 10 seq, Sept 29) Sep 29, 2023
@FedeGueli
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10 now sampled in California too.

@FedeGueli
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it seems slowing down

@FedeGueli FedeGueli added Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. and removed Rapid review needed labels Oct 3, 2023
@FedeGueli FedeGueli changed the title EG.5.1.1/XBB.1.16.6 Recombinant (US, Spain, England, 10 seq, Sept 29) EG.5.1.1/XBB.1.16.6 Recombinant (US, Spain, England, 15 seq, Oct 20) Oct 20, 2023
@FedeGueli
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FedeGueli commented Oct 20, 2023 •
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It appear to spread very limitedly in Uk closing it now ping @corneliusroemer for his recombinant search.

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Oct 20, 2023
@xz-keg
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xz-keg commented Nov 1, 2023

23 now

@NkRMnZr
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NkRMnZr commented Nov 20, 2023

new countries: France and Sweden

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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. recombinant S:456 S:478
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@xz-keg @ryhisner @FedeGueli @NkRMnZr