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TRIO KP.5 (JN.1.11.1 + S:T572I) with S:R346T (84) #2568

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FedeGueli opened this issue Apr 27, 2024 · 4 comments
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TRIO KP.5 (JN.1.11.1 + S:T572I) with S:R346T (84) #2568

FedeGueli opened this issue Apr 27, 2024 · 4 comments

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@FedeGueli
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FedeGueli commented Apr 27, 2024 •
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Original KP.5 proposal Formerly tracked as Branch 63 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1097 and for FLiRT>Trio branch as Branch 111 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089

JN.1.11.1 >S:T572I (C23277T)
Query:C7113T,C23277T,T3565C, G24872T,-G9010A,-C6070T,-A24819G,T22928C
Samples: 15
EPI_ISL_18989868, EPI_ISL_19012494, EPI_ISL_19022916,
EPI_ISL_19028021, EPI_ISL_19032236, EPI_ISL_19032824,
EPI_ISL_19038709, EPI_ISL_19055484, EPI_ISL_19055680,
EPI_ISL_19058372, EPI_ISL_19070036, EPI_ISL_19070190,
EPI_ISL_19070263, EPI_ISL_19073920, EPI_ISL_19076771

Now with a FLiRT > TRIO Branch:
KP.5 > C3811T > C2197T, C9857T, S:R346T (G22599C) ,A23080G (S:Q506Q)
New query: C3811T, G22599C,C23277T, G17334T by @aviczhl2 from sars-cov-2-variants/lineage-proposals#1724
[former Query:C3811T , C2197T, C9857T,T3565C ]
Samples: 3 (US)

Tree:
Screenshot 2024-04-27 alle 23 36 08
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_150f8_c372a0.json?label=id:node_6971654
This was referenced Apr 27, 2024
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@FedeGueli FedeGueli changed the title JN.1.11.1 acquired S:T572I (15) first and then S:R346T (3) > TRIO JN.1.11.1 acquired S:T572I (25) first and then S:R346T (3) > TRIO May 8, 2024
FedeGueli referenced this issue May 16, 2024
@corneliusroemer
Designate KP.5 (S:T572I), JN.1.39.2 (S:R346T, T111C)
dbfae34
@FedeGueli
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Designated KP.5 via dbfae34

@FedeGueli FedeGueli changed the title JN.1.11.1 acquired S:T572I (25) first and then S:R346T (3) > TRIO KP.5 (JN.1.11.1 + S:T572I) with S:R346T (11) > TRIO Jun 13, 2024
@FedeGueli FedeGueli reopened this Jun 13, 2024
@FedeGueli
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the trio branch has now 11 seqs

@FedeGueli FedeGueli changed the title KP.5 (JN.1.11.1 + S:T572I) with S:R346T (11) > TRIO KP.5 (JN.1.11.1 + S:T572I) with S:R346T (14) > TRIO Jun 20, 2024
@FedeGueli FedeGueli changed the title KP.5 (JN.1.11.1 + S:T572I) with S:R346T (14) > TRIO KP.5 (JN.1.11.1 + S:T572I) with S:R346T (25) > TRIO Jul 1, 2024
@FedeGueli FedeGueli mentioned this issue Jul 10, 2024
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@FedeGueli FedeGueli changed the title KP.5 (JN.1.11.1 + S:T572I) with S:R346T (25) > TRIO TRIO KP.5 (JN.1.11.1 + S:T572I) with S:R346T (49) Jul 10, 2024
@FedeGueli FedeGueli changed the title TRIO KP.5 (JN.1.11.1 + S:T572I) with S:R346T (49) TRIO KP.5 (JN.1.11.1 + S:T572I) with S:R346T (84) Aug 3, 2024
@FedeGueli
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84, only 20 in July tough and with many from Canada, i think this will die off.

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Aug 3, 2024
FedeGueli referenced this issue Oct 22, 2024
@corneliusroemer
Designate KP.2.27 (S:T572I)
986687e 
@AngieHinrichs it's unclear whether it should be KP.5 or KP.2 sublineage
but since KP.2 is more dominant in terms of behaviour I put it there
@FedeGueli
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Dessigntad KP.2.27 via 986687e#diff-ead4244ff49c81bc758e9f068f5ef42156bd985b9c86de8fa4d6fcd7f2829090R1209

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