XEC/24F: Potential KS.1.1/KP.3.3 recombinant (35 sequences, 9 countries)

[Walde1nsamkeit]

Transferred from sars-cov-2-variants/lineage-proposals#1827
Thx @aviczhl2 .

Mutations based on JN.1: C18657T, C19716T, C21627A(S:T22N), T21738C(S:F59S) / T22928C(S:F456L), C23039G(S:Q493E), G24872T(S:V1104L), C25006T, C28291A(Orf9b:P3H), G28884C(N:R204P)
The 5' donor could be from a pre-C6701T KS.1.1 branch with C18657T.
Breakpoint: 21738~22599
Query: C18657T, C19716T, C25006T
Query for sequences without 19716 mutation: -G9130T, C18657T, -C19716T, G24872T, C25006T

Earliest sequence: 06-24 Berlin, Germany EPI_ISL_19283881
Latest sequence: 07-28 Stockholm, Sweden EPI_ISL_19310587
Regions detected:
Germany 15(Bayern 6, Berlin 4, Nordrhein-Westfalen 4, Rheinland-Pfalz 1), Netherlands 4(Noord-Brabant 1, Noord-Holland 1, Utrecht 1, Zuid-Holland 1), Sweden 3(Stockholm 2, Örebro 1), France 1(ARA), Spain 1(Asturias), UK 1(Scotland)
US 8(Virginia 4, Washington 2[1 from airport screening, 1 from Germany], Ohio 1, Pennsylvania), Canada 1(Alberta);
South Korea 1.

https://nextstrain.org/fetch/raw.githubusercontent.com/Over-There-Is/subtreeAuspice/main/XEC.json?c=country&label=id:node_7040630

Sequences:

EPI_ISL_19270230, EPI_ISL_19283843, EPI_ISL_19283881,
EPI_ISL_19283891, EPI_ISL_19283905, EPI_ISL_19288354,
EPI_ISL_19292873, EPI_ISL_19299882, EPI_ISL_19300184,
EPI_ISL_19304941, EPI_ISL_19308953, EPI_ISL_19308959,
EPI_ISL_19308971, EPI_ISL_19308982, EPI_ISL_19308990,
EPI_ISL_19309895, EPI_ISL_19309916, EPI_ISL_19310160,
EPI_ISL_19310201, EPI_ISL_19310562, EPI_ISL_19310587,
EPI_ISL_19310626, EPI_ISL_19310656, EPI_ISL_19310662,
EPI_ISL_19312373, EPI_ISL_19313844, EPI_ISL_19313900,
EPI_ISL_19314468, EPI_ISL_19316511, EPI_ISL_19316527,
EPI_ISL_19316531, EPI_ISL_19316606, EPI_ISL_19317075,
EPI_ISL_19317285, EPI_ISL_19319036

[FedeGueli]

cc @corneliusroemer @AngieHinrichs @thomasppeacock initial growth pretty impressive i suggest direct designation for this.

[FedeGueli]

Wait wait the bottom branch has Orf1a:I1367L that is the defining of #2707 and its sublineage #2704 both growing fast too , could be another recombination? or convergence?
@ryhisner (many thx for his neverending effort!) has identified that mutation as a marker in chronic infections that until today has not spread easily in general population, so how many chances it is a second appearance instead of a further recombination?

[xz-keg]

Wait wait the bottom branch has Orf1a:I1367L that is the defining of #2707 and its sublineage #2704 both growing fast too , could be another recombination? or convergence? @ryhisner (many thx for his neverending effort!) has identified that mutation as a marker in chronic infections that until today has not spread easily in general population, so how many chances it is a second appearance instead of a further recombination?

This is interesting. If the recomb hypothesis holds, then it is like XDP and XEB pair, a 1-BP recomb and a 2-BP recomb of same lineages occur at the same time.

[FedeGueli]

33

[corneliusroemer]

I'm having a look! At a high level, this one is interesting because it has the somewhat beneficial N/ORF9b of KP.3.3 and S:59 and S:22, right?

22 on its own seems to be less beneficial than 31del, am I right? Have we ever seen 22 and 31del together? Are they additively beneficial?

KS is JN.1.13.1 off the top of my head, correct?

[corneliusroemer]

Designated as XEC - thanks for the issue, characterisation and ping everyone!

[FedeGueli]

I'm having a look! At a high level, this one is interesting because it has the somewhat beneficial N/ORF9b of KP.3.3 and S:59 and S:22, right?

Right!

22 on its own seems to be less beneficial than 31del, am I right? Have we ever seen 22 and 31del together? Are they additively beneficial?

Not yet just a dozen and half of sequences with that combo but all recent so it could be the next development but we saw 22N working quite well with S:31X i think in MB.1.1

KS is JN.1.13.1 off the top of my head, correct?

yeah exactly!

Thx for designating

[Walde1nsamkeit]

It's also detected in Canada now.

[xz-keg]

I'm having a look! At a high level, this one is interesting because it has the somewhat beneficial N/ORF9b of KP.3.3 and S:59 and S:22, right?

22 on its own seems to be less beneficial than 31del, am I right? Have we ever seen 22 and 31del together? Are they additively beneficial?

S:T22N is slightly more beneficial than S:S31-. on both FLiRT and FLuQE (KP.2 and KP.3) backbone.