KP.1.1.1+S:T22N,N30-,S31-,F32I,K478T rev(21 seqs, 10 places including GBW from India and UAE, 4 with S:A688S)

[xz-keg]

First highlighted in #1920 (comment)

There seems to be a KP.1.1.1 branch that shares the S:N30-,S31-,F32I with XDV.1.9.1 as well as S:T22N,K182N,K478T with MV.1 that is misplaced in an F59S flip-flop branch on usher.

KP.1.1.1+A6124G, C21627A, del21650_21655, T21656A, A22995C( S:T22N,N30-,S31-,F32I,K478T)

GISAID query: A6124G , A22108C ,C20104T, -C6500T(by @FedeGueli )
No. of seqs: 8(USA 5(CA, GBW from India and UK), Ireland 1 Canada 1 UK 1)
GISAID query for S:A688S sub-branch: A6124G, C20104T,A22108C,-22995,G23624T

First: EPI_ISL_19439491, USA-CA, 2024-8-12
Latest:EPI_ISL_19461123, GBW from UK, 2024-9-26

usher

Everything on the A6124G branch belongs to this and no seq actually have S:F59S. @AngieHinrichs

[FedeGueli]

Thank you for proposing i noticed it the last week. it seems growing fast so very good to be proposed separately from the branch where uSher places it.

[xz-keg]

Change query to exclude the recombinant in #2134

[FedeGueli]

+1 France

[xz-keg]

+1 GBW from UAE

[FedeGueli]

PING @corneliusroemer this seems fast

[FedeGueli]

9 California

[FedeGueli]

+1 Japan

[xz-keg]

+1 Germany

[xz-keg]

+1 USA-NY

[FedeGueli]

+1 USA-NY

still one only since october 1

[xz-keg]

There is also an S:A688S sub-branch of this now.

[FedeGueli]

Now 15 with the Utah sample, looking for a query that catches it too.

[FedeGueli]

Now 15 with the Utah sample, looking for a query that catches it too.

this one should catch all : A6124G , A22108C ,C20104T, -C6500T
excludint the KP.2.2 recombinant, also the last from Utah is likely a recent recombinant but i. would keep tracked here maybe specifying it in the proposal cc @xz-keg

[corneliusroemer]

You guys are so early with stuff! Just came across this when cleaning up tree for Nextclade release - there was a bunch of stuff wrong with KP.1.1.1 and KP.1.1.6.

[corneliusroemer]

MG.3 via cov-lineages/pango-designation@36e8c56

[xz-keg]

You guys are so early with stuff! Just came across this when cleaning up tree for Nextclade release - there was a bunch of stuff wrong with KP.1.1.1 and KP.1.1.6.

Thanks to the tool that can catch almost everything at early stage as long as they gather on usher.
https://github.com/xz-keg/Lineage-Detector

[corneliusroemer]

Thanks to the tool that can catch almost everything at early stage as long as they gather on usher.
https://github.com/xz-keg/Lineage-Detector

Looks interesting, I don't know what it does but I guess it calculates collection date based growth rates for each Usher branch, or maybe submission date based growth rates? I'll have a look at it when I have time.

[xz-keg]

Looks interesting, I don't know what it does but I guess it calculates collection date based growth rates for each Usher branch, or maybe submission date based growth rates? I'll have a look at it when I have time.

It doesn't. I may do this if I develop this tool in 2021 or 2022, however now sequencing has largely reduced. When new lineages emerge it is hard to compute growth advantage with very few seqs. What I'm doing is just highlighting undesignated branches that appears in different regions in recent times(which is sign of rapid growth), and then manually look at them.

This reduces the amount of seqs we have to look at to ~10%, or makes us looking at branches ~10 times more efficiently.

[FedeGueli]

New sample from Taiwan but not super recent

[FedeGueli]

21 reopening it

[xz-keg]

21 reopening it

It is already designated MG.3

[FedeGueli]

21 reopening it

It is already designated MG.3

aah thx! i was checking random queries that i have archived. thank you