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XBB.1.5.15 with S:N185D and S:F456L 5% prevalence in Peru' after July 1 (72) #385

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FedeGueli opened this issue Jul 10, 2023 · 8 comments
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XBB.1.5.15 with S:N185D and S:F456L 5% prevalence in Peru' after July 1 (72) #385

FedeGueli opened this issue Jul 10, 2023 · 8 comments
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designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest S:456
Milestone
FD.5.1

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@FedeGueli
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Defining mutations:
XBB.1.5.15 >> Orf10:A8V (C29580T) > C17304T > S:N185D (A22115G), S:F456L (T22928C)

Gisaid query: C17304T ,A22115G,T22928C

Samples 19 (16 from Peru') :
First :
hCoV-19/Peru/TUM-INS-44609/2023 | Original | EPI_ISL_17715677 | 2023-04-25
Last
hCoV-19/Peru/TUM-INS-45485/2023 | Original | EPI_ISL_17976501 | 2023-06-23
IDs:
EPI_ISL_17715583, EPI_ISL_17715629, EPI_ISL_17715677-17715678,
EPI_ISL_17773104-17773105, EPI_ISL_17773107, EPI_ISL_17773111-17773112,
EPI_ISL_17852693, EPI_ISL_17852706, EPI_ISL_17852722,
EPI_ISL_17852761, EPI_ISL_17952356, EPI_ISL_17976230,
EPI_ISL_17976411, EPI_ISL_17976427, EPI_ISL_17976501,
EPI_ISL_17976524

Tree:
Schermata 2023-07-10 alle 19 14 12
Schermata 2023-07-10 alle 19 14 25
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1436c_c3a6c0.json?c=gt-S_185,456&label=id:node_6761938
@FedeGueli FedeGueli changed the title XBB.1.5.15 with S:N185D and S:F456L may circulate in Peru' (19) XBB.1.5.15 with S:N185D and S:F456L may circulate in Peru' (23) Jul 13, 2023
@FedeGueli
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FedeGueli commented Jul 13, 2023 •
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3 new samples from 3 different region of Peru' and one from California.

It seems to be around 3% of recent samples in Peru'

@FedeGueli FedeGueli changed the title XBB.1.5.15 with S:N185D and S:F456L may circulate in Peru' (23) XBB.1.5.15 with S:N185D and S:F456L may circulate in Peru' (24) Jul 22, 2023
@FedeGueli
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One more from NYC

@FedeGueli FedeGueli changed the title XBB.1.5.15 with S:N185D and S:F456L may circulate in Peru' (24) XBB.1.5.15 with S:N185D and S:F456L may circulate in Peru' (25) Jul 26, 2023
@FedeGueli
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Laat came from Switzerland

@FedeGueli FedeGueli changed the title XBB.1.5.15 with S:N185D and S:F456L may circulate in Peru' (25) XBB.1.5.15 with S:N185D and S:F456L may circulate in Peru' (27) Jul 31, 2023
@FedeGueli
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2 from Peru'

@FedeGueli
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no new upload from peru since so this obviously didnt increase

@FedeGueli FedeGueli added Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest and removed Rapid review needed labels Aug 21, 2023
@FedeGueli FedeGueli changed the title XBB.1.5.15 with S:N185D and S:F456L may circulate in Peru' (27) XBB.1.5.15 with S:N185D and S:F456L may circulate in Peru' (37) Aug 28, 2023
@FedeGueli FedeGueli changed the title XBB.1.5.15 with S:N185D and S:F456L may circulate in Peru' (37) XBB.1.5.15 with S:N185D and S:F456L 5% prevalence in Peru' after July 1 (37) Aug 28, 2023
@FedeGueli
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37 as suspected it was not dead.

@FedeGueli FedeGueli changed the title XBB.1.5.15 with S:N185D and S:F456L 5% prevalence in Peru' after July 1 (37) XBB.1.5.15 with S:N185D and S:F456L 5% prevalence in Peru' after July 1 (40) Sep 4, 2023
@FedeGueli
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still 5 out of 117 samples collected in Peru' after July 1.

@FedeGueli FedeGueli changed the title XBB.1.5.15 with S:N185D and S:F456L 5% prevalence in Peru' after July 1 (40) XBB.1.5.15 with S:N185D and S:F456L 5% prevalence in Peru' after July 1 (42) Sep 6, 2023
@FedeGueli FedeGueli added the Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. label Sep 6, 2023
@FedeGueli FedeGueli changed the title XBB.1.5.15 with S:N185D and S:F456L 5% prevalence in Peru' after July 1 (42) XBB.1.5.15 with S:N185D and S:F456L 5% prevalence in Peru' after July 1 (72) Sep 23, 2023
FedeGueli referenced this issue in cov-lineages/pango-designation Oct 15, 2023
@corneliusroemer
Designate FD.5 (XBB.1.5.15.5, ORF10:A8V, Peru) and FD.5.1 (S:F456L (T…
b14c491 
…22928C), S:N185D, Peru)
@FedeGueli FedeGueli added designated and removed Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. labels Oct 15, 2023
@FedeGueli FedeGueli added this to the FD.5.1 milestone Oct 15, 2023
@FedeGueli
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Desingated FD.5.1 via cov-lineages/pango-designation@b14c491

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