KP.1.1+Orf1b:L2213F+S:N185del, F186I(351 seqs, >10 places, 19 with S:S31F, 9 with further S:K478T rev, further recombinant proposed in #2791)

[aviczhl2]

From sars-cov-2-variants/lineage-proposals#1509

Other than KP.1.1.1(S:K182N), other seqs on the Orf1b:L2213F branch of KP.1.1 have another NTD mutation set that usher doesn't display.

KP.1.1+C20104T(Orf1b:L2213F)+del22115_22117,T22118A(S:N185-, F186I)

GISAID query: T22926C,C7113,T22118A
GISAID query for S:S31F sub-branch: T22926C,C7113,T22118A,C21654T
GISAID query for S:K478T rev further branch:C7113,T22118A,C21654T,-22995

GISAID query for recombinant with additional S:T22N but losing S:K1086R:C25587T, C26195T,A26927G (#2791)

K478T branch--KP.2

Breakpoint between 22119 and 24818

Additional mutations: C21627A,C25587T, C26195T,A26927G
S:T22N
Orf3a:T268M

one of C25587T,C26195T,A26927G from a JN.1.11.1* branch(multiple potential choices)
C21627A and the other 2 of C25587T,C26195T,A26927G are private

No. of seqs: 117(Australia 1 Canada 10 Denmark 2 UK 35 France 14 Germany 1 India 2 Ireland 1 Japan 12 Nepal 2 South Korea 1 Singapore 7 Spain 5 Thailand 1 USA 20(2 from Qatar, 2 from France, 1 from India, 1 from South Africa, 2 from UK))

usher

Usher doesn't display this deletion+mutation and simply put it next to KP.1.1.1. Most seqs on KP.1.1+Orf1b:L2213F branch that is not KP.1.1.1 are in this branch.

Further stepwise S:S31F-S:K478T-recombinant losing S:K1086R but getting S:T22N branch found by @FedeGueli :
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice3_genome_test_50bcb_9e8d40.json?label=id:node_5730247

[FedeGueli]

136 now with 3 samples collected in June , 2 in Hubei. ping @corneliusroemer

[aviczhl2]

167, Netherlands, China, Portugal, Malaysia, New Zealand

[aviczhl2]

186, Iceland

[aviczhl2]

213, Norway, Italy, Mexico

[FedeGueli]

231 ping @corneliusroemer worth a designation this one

[aviczhl2]

240, Belgium,

[aviczhl2]

253, Sweden

[aviczhl2]

276, Luxembourg

[aviczhl2]

284, UAE

[aviczhl2]

289, Israel

[aviczhl2]

309, Poland

[aviczhl2]

@AngieHinrichs This is another example of non-displayed AA change thing.

[aviczhl2]

314, Czech Republic

[DailyCovidCases]

Tree now:
usher
Tracked in Issue 2649

@corneliusroemer This branch should be designated since it's growing rapidly

[aviczhl2]

Edited proposal to include the recombinant described in #2791

KP.1.1+S:N185-,F186I,S:S31F, S:K478T rev, S:T22N, and recombines with a KP* branch to lose S:K1086R, breakpoint between 22119 and 24818

[FedeGueli]

Edited proposal to include the recombinant described in #2791

KP.1.1+S:N185-,F186I,S:S31F, S:K478T rev, S:T22N, and recombines with a KP.2 branch to lose S:K1086R, breakpoint between 22119 and 24818

thx!