Multiple LF.7+S:A475V branches (10 Branches as of Jan 9)

[xz-keg]

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1. Branch 1, LF.7+T20799C+S:A475V, Designated LF.7.2.1, GISAID query: T20799C,C22986T, 19 seqs, Singapore, USA, Turkey,Belgium, UK, Canada, Australia,Nigeria
2. Branch 2, LF.7.1+S:A475V, Designated LF.7.1.2, LF.7.1+S:A475V(35 seqs, 4 places, 45% Qatar) cov-lineages/pango-designation#2805
3. Branch 3, LF.7+S:A475V, GISAID query:T3565C,C8818T, T16600C,C22986T,-16017,-A4838G,-C2003T,-25624,-A1124G,-G8017T,-C17436T,-T20799C,-C6310T,-T847C,-C24444T,-C7688T,-C7051T,-G4504A 18 seqs, USA, Poland, Nigeria,Ireland, Denmark, Ghana (GBW), England, South Korea,Russia,Sweden,France,Qatar,Oman,Canada,
4. Branch 4 Designated LF.7.3.1 Now proposed in LF.7.3 + Orf1a:P2046L + S:A475V (23 samples, > 10 Places) cov-lineages/pango-designation#2836 LF.7.3 (C17436T) > Orf1a:P2046L (C6402T) > S:A475V (C22986T) Query: C17436T,C6402T,C22986T, 23 seqs, Sweden, Hong Kong, Texas, NY, England, Qatar, France UK, Israel, Germany,Spain,Denmark
5. Branch 5 Dead LF.7 > C29119T > Orf1a:T224I (C936T), G8017T>ORF1a:T1542I (C4890T), ORF1a:P3767L (C11565T), S:H146H(C22000T), S:A475V (C22986T),G25012A,Query: C4890T, C11565T, G25012A, Seq : 1, Qatar
6. Branch 6 Dead LF.7.1.3 + 475V Seq.1 Netherlands LF.7.3.1 > ORF1a :L2062F, ORF3a:L41H(T25514A)> ORF1a:L590F (G2035T), T17688C, S:A475V (C22986T),ORF3a:G44R (G25522C) Query:G2035T, T17688C, G25522C , 2 Seq, Netherlands, Germany
7. Branch 7 LF.7.1>> ORF1a:A2249V (C7011T) > G2659A, T3649C,G5539A,S:A475V (C22986T) Query: G2659A, T3649C,G5539A,t3565C Samples: 2 Qatar,Singapore
8. Branch 8 LF.7.1.3 >> S:A475V (C22986T) Query:C4068T,C22986T,T3565C,-G25699A,-C3828T,-C6449T Samples:6 Russia found by @Over-There-Is
9. Branch 9 LF.7.1.3 >> Orf1a:S1188L (C3828T)>T14619C,S:A475V (C22986T), C24130T, C25276T Query:C4068T,C3828T,T14619C Samples: 3 Japan found by @Over-There-Is
10. Branch 10 LF.7.1.3 >> Orf3a:A103T (G25699A)>> Orf1a:E37D (G376T),S:A475V (C22986T) Query: G25699A,G376T,T3565C Samples:2 Russia found by @Over-There-Is

Original proposal:

LF.7+T20799C+C22986T(S:A475V)

GISAID query: T20799C,C22986T
No. of seqs: 3(USA 2(1 from Belgium), Canada 1)

First: EPI_ISL_19348783, USA-TX, 2024-7-29
Latest: EPI_ISL_19427318, USA from Belgium, 2024-9-9

usher

[HynnSpylor]

Ah I just mentioned the branch and meant to propose it.
Actually the branch is at least 4 seqs, and one more in Sierra Leone (EPI_ISL_19421077). Another LF.7+S:A475V seq in MD, US is EPI_19420046 without T20799C.

[xz-keg]

Ah I just mentioned the branch and meant to propose it. Actually the branch is at least 4 seqs, and one more in Sierra Leone (EPI_ISL_19421077). Another LF.7+S:A475V seq in MD, US is EPI_19420046 without T20799C.

They shall be independent branches given many seqs get only T20799C.

[xz-keg]

+1 Australia

[FedeGueli]

3 continents for this

[FedeGueli]

+1 Scotland

there is now a second LF.7 branch w 475V coming from Nigeria this time:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice13_genome_test_7b41_d11a40.json?label=id:node_11680428
Query: C22986T,-T20799C,C8818T, A22893G,-C6310T
that catches one sample fromSpain likely recombinant of this with Kp.3.1.1

[Sinickle]

Together, these two lineages are looking quite fast so far.

[FedeGueli]

7 England

[xz-keg]

+1 GBW from Turkey

[Sinickle]

8 seqs from Qatar today that fit into the branch with C6310T. This is a part of Qatar's first upload in the last half year, which contained 24 seqs, all collected in September.

[FedeGueli]

+1 Scotland

there is now a second LF.7 branch w 475V coming from Nigeria this time

and this went to 5 from Sweden today better proposing it

[FedeGueli]

T20799C,C22986T

not got by the query i will re look at everything

[xz-keg]

@xz-keg what about to change this issue in a multiple lineages issue for LF.7+ 475V ??

changed.

[FedeGueli]

thx

[Sinickle]

Qatar uploaded 11 more sequences today, 6 of which are the Qatar branch in this issue. So, 14/35 total from Qatar.

[FedeGueli]

Br.1 +2 Scotland

[xz-keg]

Br.1 +1 GBW from Nigeria

[FedeGueli]

ping @corneliusroemer eyes on this

[xz-keg]

BR.4 > 19 Germany

It is 23 now, also in Denmark and Spain. Propose it?

[FedeGueli]

BR.4 > 19 Germany

It is 23 now, also in Denmark and Spain. Propose it?

Now Proposed in cov-lineages/pango-designation#2836

[FedeGueli]

i think we can close this one i will track Br.3 prvtly

[FedeGueli]

Br.4 designated LF.7.3.1 via cov-lineages/pango-designation@17508bf#diff-ead4244ff49c81bc758e9f068f5ef42156bd985b9c86de8fa4d6fcd7f2829090R1297

[FedeGueli]

Singlet LF.7.1.3 + 475V from Netherlands added as branch 6

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_43629_95ae00.json?c=userOrOld&label=id:node_7222242

[FedeGueli]

Br.3 went to 15 with two GBW from Oman reopening it

[HynnSpylor]

Proposal for a new LF.7.2.1 sub-branch: LF.7.2.1>ORF1a:S539L (C1878T)>C11373T, T21973A (S:N137K)
8 seqs now (Denmark 2, Sweden 2, France 2, Netherlands 1, Tanzania 1 (detected from US International Airport)

https://nextstrain.org/fetch/genome.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_235a8f_fc1580.json

[xz-keg]

Proposal for a new LF.7.2.1 sub-branch: LF.7.2.1>ORF1a:S539L (C1878T)>C11373T, T21973A (S:N137K) 8 seqs now (Denmark 2, Sweden 2, France 2, Netherlands 1, Tanzania 1 (detected from US International Airport)

https://nextstrain.org/fetch/genome.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_235a8f_fc1580.json

make a separate proposal pls

[FedeGueli]

LF.7.2.1 is splitted in two branches by some 475V dropout sequences from Sweden cc @AngieHinrichs:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_f596_1aa100.json?label=id:node_7224291

[AngieHinrichs]

LF.7.2.1 is splitted in two branches by some 475V dropout sequences from Sweden cc @AngieHinrichs

Thanks! It should be fixed in tomorrow's build (2024-12-19).

[FedeGueli]

LF.7.2.1 is splitted in two branches by some 475V dropout sequences from Sweden cc @AngieHinrichs

Thanks! It should be fixed in tomorrow's build (2024-12-19).

Thank you Angie!

[FedeGueli]

Br.3 up to 18

[FedeGueli]

Br.3 19

[xz-keg]

Br.3 19

I'll propose it?

[FedeGueli]

Br.3 19

I'll propose it?

thx please

[xz-keg]

Br.3 19

I'll propose it?

thx please

add a lot of new -s, correct toll shall be 13.

[FedeGueli]

BR.3 now 17

[Over-There-Is]

Another LF.7.1.3+S:A475V? Russia and Japan

[FedeGueli]

Another LF.7.1.3+S:A475V? Russia and Japan

added 4 more branches thx

[FedeGueli]

Br.6 +1 old

[FedeGueli]

Br.3 new query . T3565C,C8818T, T16600C,C22986T,-16017,-A4838G,-C2003T,-25624,-A1124G,-G8017T,-C17436T,-T20799C,-C6310T,-T847C,-C24444T,-C7688T,-C7051T,-G4504A finds only 18