KS.1.1.2/KP.3 recombinant(45 seqs, 10 places)

[xz-keg]

From sars-cov-2-variants/lineage-proposals#2017

It seems that there's another KS.1.1/KP.3 recombinant result in the XEC spike of S:T22N,F59S,F456L,Q493E,V1104L.
It has a slightly different breakpoint that allows it to keep an additional S:R346T.

KS.1.1.2--KP.3

Breakpoint between 22600 and 23038 (S:346 and S:493)

Additional mutations: T12418C, G16943T

Orf1b:S1159I

T12418C from a KS.1.1.2 branch.
G16943T is private

GISAID query: C6701,T12418C, G24872T,-del21653
Supplementary query: 16943T, C16887T, C19716T,-6701
No. of seqs: 10(USA 9(Puerto Rico,TX,CO,AZ) Italy 1)

First: EPI_ISL_19391597, Puerto Rico, 2024-8-26
Latest: EPI_ISL_19499799, TX, 2024-10-2

usher

[NkRMnZr]

it seems to be placed as a sibling branch to XEL now

[FedeGueli]

13 Rhode Island, Alberta

[Over-There-Is]

25 now, US-CO+12

[xz-keg]

25 now, US-CO+12

@corneliusroemer

[Over-There-Is]

29 now

[xz-keg]

also in DE

[xz-keg]

+1 NV

[xz-keg]

Add a supplementary query that catches 6 more thanks to @JosetteSchoenma

@corneliusroemer , suggests to designate this.

[FedeGueli]

Add a supplementary query

i think T12418C, G24872T,G16943T catches 35/36 so quite all of them

[JosetteSchoenma]

Add a supplementary query

i think T12418C, G24872T,G16943T catches 35/36 so quite all of them

No, it catches a KP.3 that doesn't belong, so C16887T, C19716T, G16943T that catches 35 real ones is still better (but not perfect).

[JosetteSchoenma]

Add a supplementary query

i think T12418C, G24872T,G16943T catches 35/36 so quite all of them

No, it catches a KP.3 that doesn't belong, so C16887T, C19716T, G16943T that catches 35 real ones is still better (but not perfect).

Looks like @xz-keg 's query actually catches that KP.3 as well.

[FedeGueli]

Add a supplementary query

i think T12418C, G24872T,G16943T catches 35/36 so quite all of them

No, it catches a KP.3 that doesn't belong, so C16887T, C19716T, G16943T that catches 35 real ones is still better (but not perfect).

Looks like @xz-keg 's query actually catches that KP.3 as well.

the one from Texas?
anyway that query i linked catches the 30 from the query by XZ and 5/6 of the additonal query

[JosetteSchoenma]

Add a supplementary query

i think T12418C, G24872T,G16943T catches 35/36 so quite all of them

No, it catches a KP.3 that doesn't belong, so C16887T, C19716T, G16943T that catches 35 real ones is still better (but not perfect).

Looks like @xz-keg 's query actually catches that KP.3 as well.

the one from Texas?
anyway that query i linked catches the 30 from the query by XZ and 5/6 of the additonal query

Yes, the one from Texas. Like the query from XZ. But I think mine catches all and no extra ones.

[FedeGueli]

Add a supplementary query

i think T12418C, G24872T,G16943T catches 35/36 so quite all of them

No, it catches a KP.3 that doesn't belong, so C16887T, C19716T, G16943T that catches 35 real ones is still better (but not perfect).

oh that is perfect i was referring to the additional one!

[FedeGueli]

38 , +2 TX

[xz-keg]

36+8=44. Also in RI.

[corneliusroemer]

2 doublings in 3 weaks, not super fast but also not slow. I'll designate when I have a minute!

[xz-keg]

No, it catches a KP.3 that doesn't belong, so C16887T, C19716T, G16943T that catches 35 real ones is still better (but not perfe
ct).

Are you referring to EPI_ISL_19499799? I check it and it shall belong to this recombinant despite usher places it elsewhere. Texas seqs are usually of low quality and it may miss some mutations uncovered so that usher doesn't place it together with other seqs. @AngieHinrichs

[JosetteSchoenma]

No, it catches a KP.3 that doesn't belong, so C16887T, C19716T, G16943T that catches 35 real ones is still better (but not perfe
ct).

Are you referring to EPI_ISL_19499799? I check it and it shall belong to this recombinant despite usher places it elsewhere. Texas seqs are usually of low quality and it may miss some mutations uncovered so that usher doesn't place it together with other seqs. @AngieHinrichs

Yes, that's the one I mean. It is not of low quality. In the Spike it has no T22N, no F59S, no R346T, none of which are close to an area with missing nucleotides. Plus, it does have S:S31del!

[xz-keg]

Yes, that's the one I mean. It is not of low quality. In the Spike it has no T22N, no F59S, no R346T, none of which are close to an area with missing nucleotides. Plus, it does have S:S31del!

oh I see, that one shall be a 2nd level recombinant of this recomb and a 31del branch. It has the signature private mutations of this lineage. Thanks for informing. I've edited query accordingly. Now 45 seqs total.

[JosetteSchoenma]

Yes, that's the one I mean. It is not of low quality. In the Spike it has no T22N, no F59S, no R346T, none of which are close to an area with missing nucleotides. Plus, it does have S:S31del!

oh I see, that one shall be a 2nd level recombinant of this recomb and a 31del branch. It has the signature private mutations of this lineage. Thanks for informing. I've edited query accordingly. Now 45 seqs total.

Yes. That's what I thought was well.