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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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KP.1.1.1 + S:T572I, S:K679N (R), ORF1a:V3091I (14, July 9) #1623

Closed ryhisner closed 2 months ago

ryhisner commented 3 months ago

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

image

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 commented 3 months ago

@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 commented 3 months ago

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.

image
FedeGueli commented 3 months ago

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

FedeGueli commented 3 months ago

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:

Screenshot 2024-06-19 alle 21 47 23

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 commented 2 months ago

Designated MG.1 via https://github.com/cov-lineages/pango-designation/commit/f95ef962a259317a268b0b4a9c9ea2ba9e087f7f