XEN: Recombinant of KP.1.1 + Orf1b:L2213F + S:N185del+S:F186I (#2649) that acquired in a stepwise manner S:S31F S:K478T (rev) before recombination. Then with recombination it lost S:K1086R and acquired S:T22N (20, 9 places including India,Hawaii,Singapore)

[FedeGueli]

This a sub branch of #2649 that got 31F 478T then recombined with KP.2* losing S:K1086R (defining of KP.1.1) and acquiring then S:T22N . Full credit for the analysis by @aviczhl2 that had proposed the parental branch long ago.

Recombinant of #2649 [KP.1.1> Orf1b:L2213F (C20104T)> S:N185Del/S:F186I >> S:S31F (C21654T) > S:K478T (A22995C rev) ] >> recombination: >S:R1086K (G24819A rev), C25587T, Orf3a:T268M (C26195T), A26927G > T10093G, S:T22N (C21627A), Orf3a:V13L (G25429T)
Query for the recombinant branch: C25587T, C26195T,A26927G (by @aviczhl2 )
Samples: 8

Places: 5 [India 2, Germany Australia and a GBW pooled sample]
Tree updated on Oct 10:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_42d49_7a15c0.json?label=id:node_7351958

Singlet from Pa,Us with three spike mutations S:A263S, S:D428H ,S:T500N
Query: T8902C, G17035A

[FedeGueli]

Wrong repo i will leave this open for a while.

[xz-keg]

This is sub-branch of #2649, and have S:185del, S:F186I.

[xz-keg]

I think it shall be recombinant with other KP* as S:1086 is reverted. (breakpoint shall be after S:186 as it inherits the S:185del, F186I from #2649.)

[FedeGueli]

I think it shall be recombinant with other KP* as S:1086 is reverted. (breakpoint shall be after S:186 as it inherits the S:185del, F186I from #2649.)

Very good spot for some reason i didn't notice that del so no light turned on my mind and also i didnt found any KP.1.1 matching with this, my bad! likely i was focusing on S:S31F.
As this point it is better to broaden the original proposal with this and i will close this. let me know.

[xz-keg]

All 3 on the recomb branch shall have S:T22N(the Germany one has S:22 missing coverage), actually we get 5 using query C25587T, C26195T,A26927G. The other 2 India seqs are removed by usher due to too many reversions.

See analyse on #2649

[xz-keg]

Maybe better keep this open for a 5-seq recomb branch with 2 from India? It deserves a separate proposal.

[FedeGueli]

Maybe better keep this open for a 5-seq recomb branch with 2 from India? It deserves a separate proposal.

Ah so u want to keep it in both ok! i was thinking it was absorbed. So what it the query for the recombinant ?
C25587T, C26195T,A26927G
3/5 with 22N right?

[xz-keg]

Ah so u want to keep it in both ok! i was thinking it was absorbed. So what it the query for the recombinant ? C25587T, C26195T,A26927G 3/5 with 22N right?

All shall have S:T22N, the other 2 has S:22 missing coverage I think?

[FedeGueli]

Ah so u want to keep it in both ok! i was thinking it was absorbed. So what it the query for the recombinant ? C25587T, C26195T,A26927G 3/5 with 22N right?

All shall have S:T22N, the other 2 has S:22 missing coverage I think?

let me check i ve edited the proposal please check if i got your analysis right)

[FedeGueli]

C25587T, C26195T,A26927G

Ok one from India has coverage but i assume can be just base calling. so i will modify further

[FedeGueli]

Ping: @corneliusroemer if interested this should be designated with a chain of designations involving #2649 its sublineage with 31F adn 478T and its recombinant proposed here. not designating all of them but just one could be very messy then

[FedeGueli]

6 , new place Penn.(US)

[FedeGueli]

+1 Hawaii

[FedeGueli]

8, Utah

[xz-keg]

+4 Singapore, 12 seqs now

[FedeGueli]

The sample from Pennsylvania has three additional spike mutations: S:A263S, D428H,T500N

[xz-keg]

+1 Qatar, 13 seqs now

[FedeGueli]

+1 Qatar, 13 seqs now

boom quit e a thing this one too! i have the feeling that we are now facing the heavy weights of Jn.1 evolution and timing for them is quite perfect

[xz-keg]

+1 USA-NJ, 14 total

[xz-keg]

one more from Qatar

[FedeGueli]

The club of little fast lineages stil undesignated is going at fast pace. Hope they wil be designated soon. Most of people is not even aware of all of them.

[xz-keg]

More seq from Qatar, 16 now.

[xz-keg]

One more of this from Taiwan

[FedeGueli]

Taiwan but infected elsewhere, this is fast.

[xz-keg]

+1 Canada-SK, 18 seqs now

[xz-keg]

+1 Singapore

[xz-keg]

+! Japan, 20 now.

[FedeGueli]

Designated XEN via 6637343

[FedeGueli]

4 new sequences from Indonesia (one from an airport in Japan) , i suiggest to change the query: T10093G ,C20104T

[xz-keg]

@AngieHinrichs @corneliusroemer usher has moved the placement of XEN and there seems to be a new bug of its placement.

Everything on the image shall be XEN, instead of only the top branch.

Please fix it.

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice189_genome_test_29969_21df80.json?label=id:node_5873219