search

sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
43 stars 2 forks source link

KP.3.1.1+S:P85S(40 seqs, >10 places) 6% in NZL #1934

Open xz-keg opened 2 months ago

xz-keg commented 2 months ago

KP.3.1.1+C21815T(S:P85S)

GISAID query: C21815T,C12616T,A13121T,-17430,-10681,C23039G,-25595,-29716,-15750,-T4579A,-9559,-19220 No. of seqs: 6(UK 3 USA 1 Portugal 1 Italy 1)

First: EPI_ISL_19321477, USA, 2024-7-11 Latest: EPI_ISL_19357802, UK, 2024-8-8

Usher seems to be putting it on a flip-flop reversion branch together with some unrelated seqs with S:85 missing coverage. This needs a fix @AngieHinrichs usher

image

AngieHinrichs commented 2 months ago

Usher seems to be putting it on a flip-flop reversion branch together with some unrelated seqs with S:85 missing coverage.

I see the flip-flop on 22858, but there are a lot of sequences that have A13121T and C12616T in common with this and that will probably keep pulling this in. Are they really unrelated? The path to this branch is

KP.3.1 > C22858T > A13121T > C12616T > C21815T > T22858C (rev)

Only one sequence (Italy/FVG-TS-65330394/2024|EPI_ISL_19323845) is supporting the node with C21815T, and only one sequence supports the node with A13121T (Spain/MD-H12O_282/2024|EPI_ISL_19243495), but there are a lot more seqs supporting the other nodes.

If you have a list of sequences missing coverage at S:85 then I could try prune & replace.

xz-keg commented 2 months ago

If you have a list of sequences missing coverage at S:85 then I could try prune & replace.

Get all seqs here(I don't know what's attracted to this branch in the new tree), and exclude GISAID seqs with C21815T,C12616T,A13121T, the remaining shall be missing coverage at S:85.

List of real S:P85S(C21815T,C12616T,A13121T) seqs

EPI_ISL_19321477, EPI_ISL_19323845, EPI_ISL_19327564, EPI_ISL_19332977, EPI_ISL_19332985, EPI_ISL_19357802, EPI_ISL_19362100

You Shall Exclude them and take everything else.

xz-keg commented 1 month ago

11, France, Spain, New Zealand

xz-keg commented 1 month ago

+1 Switzerland

FedeGueli commented 1 month ago

15 , Denmark

FedeGueli commented 1 month ago

21

Over-There-Is commented 1 month ago

T572I?

FedeGueli commented 1 month ago

C21815T,C12616T,A13121T

old ones not?

xz-keg commented 1 month ago

+1 Netherlands

FedeGueli commented 1 month ago

25 , Canada

FedeGueli commented 4 weeks ago

39 with a big batch in NZL where it is around 6% 16/39 sampled in September

xz-keg commented 2 weeks ago

47, also in Czech Republic

FedeGueli commented 1 week ago

Please propose it

DailyCovidCases commented 1 week ago

@xz-keg Please propose it

xz-keg commented 1 week ago

usher seems fixed the misplacement bug, and I add a lot of -s, real toll shall be 33.

FedeGueli commented 4 days ago

36 last samples from UK