KP.1.1+Orf1b:L2213F+S:N185del, F186I(331 seqs, >10 places, 17 with S:S31F, 7 with further S:K478T rev, 6 with further S:F32S, further recombinant proposed in #2791)

[xz-keg]

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,A24819G
GISAID query for S:S31F sub-branch: T22926C,C7113,T22118A,C21654T,A24819G
GISAID query for S:K478T rev further branch:C7113,T22118A,C21654T,-22995,A24819G
GISAID query for S:F32S further branch:C7113,T22118A,C21654T,-22995,T21657C

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

[xz-keg]

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

[xz-keg]

186, Iceland

[xz-keg]

213, Norway, Italy, Mexico

[FedeGueli]

231 ping @corneliusroemer worth a designation this one

[xz-keg]

240, Belgium,

[xz-keg]

253, Sweden

[xz-keg]

276, Luxembourg

[xz-keg]

284, UAE

[xz-keg]

289, Israel

[xz-keg]

309, Poland

[xz-keg]

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

[xz-keg]

314, Czech Republic

[xz-keg]

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!

[xz-keg]

There is a further S:F32S branch after S:S31F and S:K478T rev besides the recombinant, now 6 seqs with C7113,T22118A,C21654T,-22995,T21657C. @FedeGueli

[xz-keg]

355/23/13/6 now

[FedeGueli]

C7113,T22118A,C21654T,-22995,T21657C

wow. thx
No idea why but it doesnt work on covspectrum

[FedeGueli]

@xz-keg some of the new S:F32S branch have 182K (rev) do u think it is real?

[xz-keg]

@xz-keg some of the new S:F32S branch have 182K (rev) do u think it is real?

182N is for KP.1.1.1, this one is not KP.1.1.1, it is KP.1.1+N185-, F186I so it shall have 182K which is not rev( as it never had 182 mutated to anything else)

[FedeGueli]

@xz-keg some of the new S:F32S branch have 182K (rev) do u think it is real?

182N is for KP.1.1.1, this one is not KP.1.1.1, it is KP.1.1+N185-, F186I so it shall have 182K which is not rev( as it never had 182 mutated to anything else)

yeah yeah sorry my bad

[xz-keg]

365-32-22-6

[FedeGueli]

365-32-22-6

@xz-keg i was scratching a bit my head around this but it seems to me that the 478T branch doesnt exist as such: it is the recombinant and the S:F32S branch

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_59dad_ce1a60.json?f_userOrOld=uploaded%20sample&label=id:node_7358966

[xz-keg]

365-32-22-6

@xz-keg i was scratching a bit my head around this but it seems to me that the 478T branch doesnt exist as such: it is the recombinant and the S:F32S branch https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_59dad_ce1a60.json?f_userOrOld=uploaded%20sample&label=id:node_7358966

Yeah I adjust query to exclude the recomb and other similar recombs by forcing it to have S:K1086R. 331-17-7-6 now.

[FedeGueli]

365-32-22-6

@xz-keg i was scratching a bit my head around this but it seems to me that the 478T branch doesnt exist as such: it is the recombinant and the S:F32S branch https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_59dad_ce1a60.json?f_userOrOld=uploaded%20sample&label=id:node_7358966

Yeah I adjust query to exclude the recomb and other similar recombs by forcing it to have S:K1086R. 331-17-7-6 now.

to me being 6/7 with 32S is not useful as of today.

[DailyCovidCases]

Grow advantage now:

[FedeGueli]

Designated KP.1.1.6 and NE.1 via 6637343