Closed JosetteSchoenma closed 1 month ago
where is the other issue? the one with G15372T, A19722G, C21654T now at 6
edit ah is this one!
14 in total now, 8 for the main branch
+8 (22), +6 for the branch (14)
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
First branch proposed now Designated KP.3.1.3 via https://github.com/cov-lineages/pango-designation/commit/000e4446ff22dd2a53003e11e26d99b2e3c6a2c6
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
i transfer this comment to main proposal
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
New, hopefully better query of 4(?) branches of KP.3.2 plus S:S31F. 13 samples. C22858T, C21654T, C23039G
New, hopefully better query of 4(?) branches of KP.3.2 plus S:S31F. 13 samples. C22858T, C21654T, C23039G
16 now
KP.3.2 C22858T, C21654T, C23039G 22 now
C22858T, C21654T, C23039G
Please propose it @JosetteSchoenma
New branch. 8 samples 4 countries, mostly Australia. Query: C21654T, G3839A Edit: designated KP.3.4.1
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.
Query for another KP.3.2 plus S31F branch. T772C, T12101A. 6 samples
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.
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
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
A12199G,C25609T, C23039G
Yes, that's better @FedeGueli . It bypasses the missing coverage on AA 31 common in English samples.
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.
This one is 32 samples now (Query: C22858T, C21654T, C4345T). 9 new ones from England today.
New branch. 8 samples 4 countries, mostly Australia. Query: C21654T, G3839A
This shall be KP.3.4.1 via https://github.com/cov-lineages/pango-designation/commit/4438f33f227c35fa03b639640089a447cea99264
New Japanese KP.3.3 plus S31F cluster. 8 samples. Query G6545A, C14235T
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!
Thank you very much @JosetteSchoenma
Kp.3.1.3 query: G15372T, A19722G, C21654T,-C18490T,-T19305C,-A13121T,-C4084T,-C5413T,-A20458C
This is updated finds 70
Updated with the KP.3.1.3 query
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 + 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 + 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.
KP.3.1.4 + S31F > query C18490T, A16474G, C21654T, Scotland growing from 9 to 21
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
KP.3.1.4 + S31F > query C18490T, A16474G, C21654T, Scotland growing from 9 to 21
37 now
Adjusted the main comment. Especially KP.3.2 branch 2, 29 from 8 countries now
Adjusted the main comment. Especially KP.3.2 branch 2, 29 from 8 countries now
please propose it
Adjusted the main comment. Especially KP.3.2 branch 2, 29 from 8 countries now
please propose it
It is #1650 .
none of them seems fast
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.
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.
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!
New S31F branch under KP.3.2.3, Query: C6582T,A17712G,C21654T
Everything seems resolved. Close this one.
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.