KP.1.1.1 + S:T572I, S:K679N (R), ORF1a:V3091I (14, July 9)

[ryhisner]

Description

Sub-lineage of: KP.1.1.1 (S:K182N, R346T, F456L, V1104L, K1086R)
Earliest sequence: 2024-5-14, USA, NC — EPI_ISL_19175961
Most recent sequence: 2024-6-7, Canada, Ontario — EPI_ISL_19199202
Continents circulating: North America (5), Europe (1)
Countries circulating: Canada (3), USA (2), Finland (1)
Number of Sequences: 6 good sequences + some Ginkgo Bozoworks Garbage
GISAID Nucleotide Query: A22108C, C23277T, T23599C
CovSpectrum Query: Nextcladepangolineage:KP.1* & [2-of: A22108C, C23277T, G23599C]
Substitutions on top of KP.1.1.1:
Spike: T572I, K679N (R)
Nucleotide: G9536A, A22108C, C23277T, G23599C

Phylogenetic Order of Mutations: Unclear due to garbage Ginkgo Bozoworks sequences, including pooled samples

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/KP.1.1.1_T572I_K679N.json?c=gt-S_572&gmax=25384&gmin=21563&label=id:node_7003949

Evidence
The Usher tree for this one is unfortunately a mess with artifactual reversions and "unreversions" due to more Ginkgo Bozoworks tomfoolery, including pooled samples and bad individual samples. We've seen a lot of action around the FCS in JN.1 but nothing that's really caught fire. I doubt if this will either, but there's no doubt that the K679N reversion is real: the reversion is to 23599C when it was originally T23599.

The combination of K182N, R346T, F456L, and T572I is interesting in any case. And the fact that this has been seen in distant states in the US (Colorado and North Carolina), Canada (Ontario), and Finland means it's traveling well. It's apparently been partially present in some of the atrocious GBW sequences, so it could be in some other countries as well.

Genomes

Genomes

EPI_ISL_19175961, EPI_ISL_19186434, EPI_ISL_19193357, EPI_ISL_19199154, EPI_ISL_19199165, EPI_ISL_19199202

[FedeGueli]

@ryhisner i was tracking another KP.1.1.1 with 572I you found in the past as:
Branch 126 of #1089

TRIO found by @ryhisner
KP.1.1.1 > S:T572I (C23277T)
Query:C23277T,A22108C,C20104T
Samples: 11 USA

this seems a different one correct?

[ryhisner]

Is that the one with S:I100L that's mostly in Colorado? That's the other KP.1.1.1 + T572I branch that I see on the KP.1.1.1 tree.

[FedeGueli]

Apparently not that one it is for that reason i was asking, i wonder where did it finish then. let me recheck.

[FedeGueli]

Ok checked right now that one query you flagged weeks ago and i ve tracked in #1089 now finds both the KP.1.1.1 572I branches at least partially:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5afe0_3352b0.json?f_userOrOld=uploaded%20sample&label=id:node_7004502
so i will redirect that to this issue.

Edited now the second KP.1.1.1 trio is tracked as

Branch 149 (ex branch 126)
KP.1.1.1 > C27143T > T9769C,S:T572I (C23277T), G27626T
Query:T9769C, G27626T ,C27143T
Samples:8
in #1089

[FedeGueli]

Designated MG.1 via cov-lineages/pango-designation@f95ef96