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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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Multiple KP.3 and sub lineageas with S:S31F: #1576

Closed JosetteSchoenma closed 1 month ago

JosetteSchoenma commented 5 months ago

Edited 14/7/24 because of designations and extra branches KP.3 (S:Q493E=C23039G) plus S:S31F (=C21654T)

KP.3.1 (G15372T, A19722G) KP.3.1.1 + S31F > query C12616T, A13121T, C21654T > 118 samples Denmark (considering this an artifact as long as it does not show up in another country) KP.3.1.3 > G15372T, A19722G, C21654T,-C18490T,-T19305C,-A13121T,-C4084T,-C5413T,-A20458C > designated KP.3.1.4 + S31F > query C18490T, A16474G, C21654T > 40 samples, Scotland, France (GBW) ( parental branch proposed here ) MK.1 (KP.3.1.6.1) > query T19305C, C21654T, C23039G > designated

KP.3.2 (A2611C, C22858T) branch 1 > query C22858T, C21654T, C4345T > 36 samples, England Pseudo branch 2 > T772C, T12101A > 29 samples, 8 countries Actually a recombinant: https://github.com/sars-cov-2-variants/lineage-proposals/issues/1650 Or https://github.com/cov-lineages/pango-designation/issues/2731 branch 3 > C21654T, A8302G > 32 samples, USA (1 traveler Qatar) and Mexico KP.3.2.4 + S31F > A2611C, C25609T, C21654T > 2 samples, Spain , Portugal

KP.3.3 (C28884C) Query G6545A, C14235T > 8 samples Japan

KP.3.4.1 > query C21654T, G3839A > designated

Original KP.3 seems to have gained S:S31F on 4 different branches, with samples from Canada, England, USA, Scotland and Spain. EDITED 19/6: Better KP.3.2 S31F query: C22858T, C21654T, C23039G

Edited 19/6 Another. KP.3 Query: C21654T, G3839A

Original Proposal With the biggest branch of 5 samples having G15372T and A19722G. Query: Spike_Q493E, C21654T. Branch query: G15372T, A19722G, C21654T

Note: this is a downsampled tree! And the Scottish sample is being misplaced because of missing coverage. image

FedeGueli commented 4 months ago

where is the other issue? the one with G15372T, A19722G, C21654T now at 6

edit ah is this one!

JosetteSchoenma commented 4 months ago

14 in total now, 8 for the main branch

JosetteSchoenma commented 4 months ago

+8 (22), +6 for the branch (14)

JosetteSchoenma commented 4 months ago

KP.3.1.3 has been assigned for the main branch

Since there is a branch (KP.3.2) that has grown to 7 now, I made a query for that one as well. C7113T, C22858T, C21654T image

FedeGueli commented 4 months ago

First branch proposed now Designated KP.3.1.3 via https://github.com/cov-lineages/pango-designation/commit/000e4446ff22dd2a53003e11e26d99b2e3c6a2c6

FedeGueli commented 4 months ago

KP.3.1.3 has been assigned for the main branch

Since there is a branch (KP.3.2) that has grown to 7 now, I made a query for that one as well. C7113T, C22858T, C21654T image

i transfer this comment to main proposal

JosetteSchoenma commented 4 months ago

Here it is proposed by @aviczhl2 that the first branch is actually 2 branches. So, not all KP.3.1.3. Query: T19305C,C21654T,C23039G https://github.com/sars-cov-2-variants/lineage-proposals/issues/1605

JosetteSchoenma commented 4 months ago

New, hopefully better query of 4(?) branches of KP.3.2 plus S:S31F. 13 samples. C22858T, C21654T, C23039G image

JosetteSchoenma commented 4 months ago

New, hopefully better query of 4(?) branches of KP.3.2 plus S:S31F. 13 samples. C22858T, C21654T, C23039G image

16 now

JosetteSchoenma commented 4 months ago

KP.3.2 C22858T, C21654T, C23039G 22 now

FedeGueli commented 4 months ago

C22858T, C21654T, C23039G

Please propose it @JosetteSchoenma

JosetteSchoenma commented 4 months ago

New branch. 8 samples 4 countries, mostly Australia. Query: C21654T, G3839A Edit: designated KP.3.4.1 image

JosetteSchoenma commented 4 months ago

Query: C22858T, C21654T, C4345T Because I doubt that the KP.3.2 has only one S31F branch, I made this new query to select for the biggest English branch. 15 samples. image

JosetteSchoenma commented 4 months ago

Query for another KP.3.2 plus S31F branch. T772C, T12101A. 6 samples

FedeGueli commented 4 months ago

Query for another KP.3.2 plus S31F branch. T772C, T12101A. 6 samples

now proposed in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1650 by @aviczhl2 as a recombinant.

JosetteSchoenma commented 3 months ago

KP.3 branch almost at the bottom, 10 samples, 5 countries (1 English one not yet on GISAID) Query: G3839A, C21654T, Spike_Q493E Edit: KP.3.4.1 designated image image

FedeGueli commented 3 months ago

KP.3 branch almost at the bottom, 10 samples, 5 countries (1 English one not yet on GISAID) Query: C3839A, C21654T, Spike_Q493E

thx @JosetteSchoenma, i ve found a better query: A12199G,C25609T, C23039G (pls check if it is the same lineage, it gives 10 samples on Gisaid Edit: KP.3.4.1 designated

JosetteSchoenma commented 3 months ago

A12199G,C25609T, C23039G

Yes, that's better @FedeGueli . It bypasses the missing coverage on AA 31 common in English samples.

JosetteSchoenma commented 3 months ago

Query: C22858T, C21654T, C4345T Because I doubt that the KP.3.2 has only one S31F branch, I made this new query to select for the biggest English branch. 15 samples. image

This one is 32 samples now (Query: C22858T, C21654T, C4345T). 9 new ones from England today.

xz-keg commented 3 months ago

New branch. 8 samples 4 countries, mostly Australia. Query: C21654T, G3839A image

This shall be KP.3.4.1 via https://github.com/cov-lineages/pango-designation/commit/4438f33f227c35fa03b639640089a447cea99264

JosetteSchoenma commented 3 months ago

New Japanese KP.3.3 plus S31F cluster. 8 samples. Query G6545A, C14235T

FedeGueli commented 3 months ago

New Japanese KP.3.3 plus S31F cluster. 8 samples. Query G6545A, C14235T

@JosetteSchoenma could you edit the main proposal please recapitulaing all the lineages tracked and then designated and the ones still pending? it is enough > Lineage > QUery > Designated or count if not designated, because with updates in comments i get lost!

FedeGueli commented 3 months ago

Thank you very much @JosetteSchoenma

FedeGueli commented 3 months ago

Kp.3.1.3 query: G15372T, A19722G, C21654T,-C18490T,-T19305C,-A13121T,-C4084T,-C5413T,-A20458C

This is updated finds 70

FedeGueli commented 3 months ago

Updated with the KP.3.1.3 query

JosetteSchoenma commented 3 months ago

KP.3.1.1 + S31F > query C12616T, A13121T, C21654T > 16 samples Denmark I am not completely sure I can trust those sequences though.

xz-keg commented 3 months ago

KP.3.1.1 + S31F > query C12616T, A13121T, C21654T > 16 samples Denmark I am not completely sure I can trust those sequences though.

KP.3.1.1 shall have S:31del.

JosetteSchoenma commented 3 months ago

KP.3.1.1 + S31F > query C12616T, A13121T, C21654T > 16 samples Denmark I am not completely sure I can trust those sequences though.

KP.3.1.1 shall have S:31del.

KP.3.1.1 has 2 other defining mutations, which these samples have, but a S31F instead of S31del. But it seems strange and even though the samples look oke, Danish sequencing tends to do strange things with deletions.

JosetteSchoenma commented 3 months ago

KP.3.1.4 + S31F > query C18490T, A16474G, C21654T, Scotland growing from 9 to 21

FedeGueli commented 3 months ago

KP.3.1.4 + S31F > query C18490T, A16474G, C21654T, Scotland growing from 9 to 21

this is a sub branch of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1697

JosetteSchoenma commented 3 months ago

KP.3.1.4 + S31F > query C18490T, A16474G, C21654T, Scotland growing from 9 to 21

37 now

JosetteSchoenma commented 2 months ago

Adjusted the main comment. Especially KP.3.2 branch 2, 29 from 8 countries now

FedeGueli commented 2 months ago

Adjusted the main comment. Especially KP.3.2 branch 2, 29 from 8 countries now

please propose it

xz-keg commented 2 months ago

Adjusted the main comment. Especially KP.3.2 branch 2, 29 from 8 countries now

please propose it

It is #1650 .

FedeGueli commented 2 months ago

none of them seems fast

ryhisner commented 2 months ago

17 sequences from Mexico City just uploaded with S:S31F, N:T135I, ORF3a:L101I, ORF1a:P4337S, and ORF1b:L1504F, all collected July 15 or later.

Appears to be branch 3 of the KP.3.2 lineages being discussed here (A8302G). One closely related previous travel sequence to the US from Qatar as well, collected June 25.

https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/KP.3.2_S31F_etc.json?c=gt-N_135&gmax=29533&gmin=28274&label=id:node_7049793

image
JosetteSchoenma commented 2 months ago

17 sequences from Mexico City just uploaded with S:S31F, N:T135I, ORF3a:L101I, ORF1a:P4337S, and ORF1b:L1504F, all collected July 15 or later.

Appears to be branch 3 of the KP.3.2 lineages being discussed here (A8302G). One closely related previous travel sequence to the US from Qatar as well, collected June 25.

https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/KP.3.2_S31F_etc.json?c=gt-N_135&gmax=29533&gmin=28274&label=id:node_7049793

image

Yes, that is branch 3. Thank you, @ryhisner. I see that my query C21654T, A8302G misses the 2 early Canadian samples though!

By the way, in Mexico 10/42 in week 29 and 8/20 in week 30 were this sublineage!

xz-keg commented 2 months ago

New S31F branch under KP.3.2.3, Query: C6582T,A17712G,C21654T

image

xz-keg commented 1 month ago

Everything seems resolved. Close this one.

DailyCovidCases commented 2 weeks ago

KP.3.1.3 branch now: usher https://cov-spectrum.org/explore/World/AllSamples/Y2024/variants?nextcladePangoLineage=KP.3.1.3*& Screenshot (252)