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 (6 , 4 places including India )

[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: 5

Places: 3 [India 2, Germany Australia and a GBW pooled sample]
Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice90_genome_test_170b5_7ac650.json?c=userOrOld&label=id:node_7275841

[FedeGueli]

Wrong repo i will leave this open for a while.

[aviczhl2]

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

[aviczhl2]

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.

[aviczhl2]

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

[aviczhl2]

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?

[aviczhl2]

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)