LB.1 branch collecting various unrelated LB.1+FullQuad branches and a LB.1.3.1/Jn.1.7 recombinant (1,Mexico)

[FedeGueli]

see now : #1792 where the main branch originally proposed here and now identified as LB.1.2 by @aviczhl2 will be tracked. Hence i will rearrange this archiving the proposal to track the tracks gathered together and the recombinant described here

Original Proposal

After LB.1.3.2/MH.1 have been designated there is another LB.1 FULL QUAD to track LB.1 with S:S31del> S:T572I (C23277T) Query:Del21653,C23277T,G22111T, -C7869T,-C18131T,-C5770T,-C13721T,-C4784T Samples: 5 Countries: 5 ( Israel, Malaysia, Peru, US (NY,FLorida), Canada, Ireland , Wales) Usher: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_6289e_f99640.json?c=userOrOld&label=id:node_7193830

1) LB.1.2.2 from #1792

2) Recombinant branch: On July 2 one sample placed by Usher in this lineage has been collected in Mexico but it is likely a recombinant between LB.1.3.1 and JN.1.7 featuring a FULLQUAD spike plus S:Q183H S:V445P and S:E1150D. Query for it: T1165C, A2707G, C2841A,T3565C

2) Branches not tracked in #1792 : LB.1 with S:S31del> S:T572I (C23277T) New Query: Del21653,C23277T,G22111T, -C7869T,-C24844T,-C18131T,-C5770T,-C13721T,-C4784T,-G19669A,-T1165C,-G25534A,-G21123T, Samples: 5 Countries: 3 Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_455e0_742490.json?f_userOrOld=uploaded%20sample&label=id:node_7224080

[FedeGueli]

New sample came from Mexico this seems to be very widespread suggesting it could have a good growth advantage

[FedeGueli]

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The mexican sample belongs to this lineage but i have now adjusted the query to exclude unrelated LB-fullquad samples: Del21653,C23277T,G22111T, -C7869T,-C18131T,-C5770T,-C13721T,-C4784T . still remarkable geographical expansion but too early to say.

[FedeGueli]

Wait wait the recent mexican samples is the same i mentioned in the recombinants issue @aviczhl2 : it is palced in this lineage but likely it doesn't belong to it being likely a recombinant with LB.1.3.1 (445P) and JN.1.7 (572I-1150D)

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4200c_4ecf60.json

[aviczhl2]

So it is 31del+183H+346T+456L+445P+572I+1150D?

[FedeGueli]

So it is 31del+183H+346T+456L+445P+572I+1150D?

Exactly

[FedeGueli]

+1 Spain

[FedeGueli]

this jumped to 21 with multiple GBW samples from 3 continents including Netherlands Japan and Guatemala and more samples from Peru' and Guatemala

[aviczhl2]

This seems to be a gather of multiple LB.1+S:T572I s. At least the top big branch must be sub-branch of LB.1.2.

[FedeGueli]

This seems to be a gather of multiple LB.1+S:T572I s. At least the top big branch must be sub-branch of LB.1.2.

yeah agree . lets see how it evolves.