KP.2.3 + S:∆S31, T572I [Full Quad] (10 seq, 4 continents, June 13)

[ryhisner]

Description Sub-lineage of: KP.2.3 (JN.1.11.1.2.3 = JN.1 + S:H146Q, R346T, F456L, V1104L, ORF3a:K67N, ORF1a:T2283I) Earliest sequence: 2024-4-24, Mauritius, Grand Port — EPI_ISL_19170222 Most recent sequence: 2024-5-7, Canada, Alberta — EPI_ISL_19163154 Continents circulating: Africa (1), Europe (1), North America (1) Countries circulating: Canada (1), Mauritius (1), Sweden (1) Number of Sequences: 3 GISAID Nucleotide Query: C23277T, G25593T, C28714T,T3565C,C28714T (Edited after @aviczhl2 suggestion to exclude another full quad KP.2.3 lineage) CovSpectrum Query: Nextcladepangolineage:KP.2* & [2-of: C23277T, G25593T] Substitutions on top of KP.2.3: Spike: ∆S31, T572I Nucleotide: ∆21653-21655, C23277T, C28714T

Phylogenetic Order of Mutations: C28714T, ∆21653-21655 (S:∆S31) → C23277T (S:T572I)

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/KP.2.3_S31del_T572I.json?c=gt-S_572&gmax=25384&gmin=21563&label=id:node_2374059

Evidence This is maybe the first branch to have the Full Quad, as I call it: S:∆S31, S:R346T, S:F456L, S:T572I. KP.2.3 also has S:H146Q, famously in BJ.1/XBB. However, the Mauritius sequence does not register S:H146Q, but given the amount of dropout in that sequence, along with the fact that his region of spike is often a troublesome one (with either S:G142D or S:∆Y144 often missing from sequences), and especially the fact that the Mauritius sequence shares the synonymous C28714T with the other two sequences I think it's almost certain that it really has H146Q.

Incidentally, C28714T is one of the three defining mutations of KP.2.3.1, along with S:∆S31. So these sequences have two of the three defining KP.2.3.1 mutations but all lack the third, which is S:A475V.

If the Mauritius sequence really does not have S:H146Q, then it would not technically be part of KP.2.3, even though it contains the other KP.2.3-defining mutation, ORF3a:K67N, and two of the three defining KP.2.3 mutations (S:∆S31 & C28714T). It would constitute a separate KP.2 + S:∆S31 + S:T572I + ORF3a:K67N branch. But that seems extraordinarily unlikely.

Genomes

Genomes

EPI_ISL_19163154, EPI_ISL_19166256, EPI_ISL_19170222

[FedeGueli]

@ryhisner just found another full quad lineage this time on LB.1 Backbone , weirdly it has a Mauritius sample too!:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_4871_707ae0.json?f_userOrOld=uploaded%20sample&label=id:node_7128678

wait wait seems quite bigger than i thought worth ( so i m up proposing it)

[ryhisner]

@FedeGueli, that was the one I talked about the other day, but I don't know if any of those are actually related. There's a huge ORF1b:T1555I branch that all of these should be included in, and it's widespread internationally, though not common in any of the countries with good surveillance.

[FedeGueli]

@FedeGueli, that was the one I talked about the other day, but I don't know if any of those are actually related. There's a huge ORF1b:T1555I branch that all of these should be included in, and it's widespread internationally, though not common in any of the countries with good surveillance.

Thank you Ryan ! i see now that it was that, and weirdly Usher included also the Mauritius one. i ve proposed but i would add an aritfact label.

[FedeGueli]

8 now , also in Asia, Singapore

[aviczhl2]

There is also a KP.2.3+T572I branch without C28714T https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice91_genome_test_3e518_5dbe40.json?label=id:node_5464816

[FedeGueli]

There is also a KP.2.3+T572I branch without C28714T https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice91_genome_test_3e518_5dbe40.json?label=id:node_5464816

thx query changed. please propose this