KP.1.1+Orf1b:L2213F+S:N185del, F186I(114 seqs) DONOR OF XEN

[xz-keg]

It seems that 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,C7113T,T22118A
No. of seqs: 14(UK 4 Canada 1 India 1 Thailand 1 Ireland 1 USA 6(1 from South Africa 2 from Qatar))

First:EPI_ISL_19025542, 2024-2-11, Thailand
Latest: EPI_ISL_19038720, 2024-3-26, USA(GBW baseline)

Usher doesn't display both mutations @AngieHinrichs, I think it shall at least display S:F186I, reading frame issue?
usher

Top is KP.1.1.1, all others belong to this branch.

[AngieHinrichs]

Looking at the reference sequence at 22111-22120, it looks like that deletion could be placed one base to the right without a substitution:

1234567890
GGGT---ATC  left-aligned:  del22115_22117(AAT),T22118A
GGGTAATTTC  reference
GGGTA---TC  right-aligned: del22116_22118(ATT)

(The uploaded sequence is "GGGTATC" with either alignment.)

The child of this branch with A22108C (S:K182N) has been designated KP.1.1.1.

[xz-keg]

Looking at the reference sequence at 22111-22120, it looks like that deletion could be placed one base to the right without a substitution:

1234567890
GGGT---ATC  left-aligned:  del22115_22117(AAT),T22118A
GGGTAATTTC  reference
GGGTA---TC  right-aligned: del22116_22118(ATT)

(The uploaded sequence is "GGGTATC" with either alignment.)

The child of this branch with A22108C (S:K182N) has been designated KP.1.1.1.

KP.1.1.1 doesn't have this deletion. They seem to be different branches.

[xz-keg]

22, Denmark, Singapore, Spain

[xz-keg]

71, France, Nepal,Germany, Japan, South Korea

[FedeGueli]

114

[FedeGueli]

Please propose it

[FedeGueli]

Designated KP.1.1.6 starting with S:S31F via cov-lineages/pango-designation@6637343

[FedeGueli]

XEN has this as parental of the sub branch(NE.1) that recombined then to give XEN (see: cov-lineages/pango-designation#2791)