XBB.1.5 sublineage with C14085T, C19488T, and C6896T (>1000 seq, >80% in Amazonas, Brazil) and a further sublineage with S:L455F, S:F456L (>70 seq. Brazil, USA, Netherlands, Canada, Spain, France, Ireland)

[oobb45729]

Transferred from sars-cov-2-variants/lineage-proposals#136
Substitutions on top of XBB.1.5: C14085T then C19488T+C6896T
XBB.1.5+C14085T+C19488T+C6896T is a relatively large undesignated subbranch of XBB.1.5 that seems to be dominant in Amazonas for months.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3d97f_b51360.json?c=gt-S_455&label=id:node_6752165

https://cov-spectrum.org/explore/Brazil/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AXBB.1.5*%26C14085T%26C19488T%26C6896T&
There have been interesting sublineages of XBB.1.5+C14085T+C19488T+C6896T, including sars-cov-2-variants/lineage-proposals#243.
The sublineage proposed here is the subbranch that further acquired A14634G, S:L455F(G22927T), S:F456L(T22928C), and T28282C.

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AXBB.1.5*%26S%3AL455F%26S%3AF456L%26T28282C&

[FedeGueli]

8th sample came from Netherlands . being another 455-456 already seeding outside Brazil i suggest a rapid review of this one. @corneliusroemer @InfrPopGen @AngieHinrichs @thomaspeacock

Rapid Gisaid Query: A19182G, G22927T better query: A14634G,G22927T, T22928C, T28282C

[FedeGueli]

ninth sequence from Honolulu , Hawaii , US

[FedeGueli]

11 as today last 2 are samples collected in Brazil , may 2023.

[FedeGueli]

15 as today 3 of them doesnt have S:P1162S:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice7_genome_41326_fbae00.json?label=id:node_6919673

My new query: A14634G, G22927T ,T22928C, T28282C finds 13

[FedeGueli]

A14634G, G22927T ,T22928C, T28282C finds now 22
and USHER is now very different looking from the original proposal in the other page:

two branches:
one growing recently with Orf1b:A241V with a notably recent international cluster with S:A475V, negative for binding but increasing RBD expression :

the other is the one originally proposed with S:P1162S:

[FedeGueli]

@corneliusroemer > 20 seqs, international spread , 2 different branches, sublineages of interest, emerging from a relevant region for SC2 (amazonas) , carrying two mutations which have led two lineages to dominance in two areas of the world (Asturias, Federal Dsitrict Brazil). I think the deisgnation of this one should be prioritized

[FedeGueli]

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice6_genome_test_2a90b_96a580.json?c=userOrOld&label=id:node_6977010

[Sinickle]

I independently noticed the branch with A475V because it looks very quick so far, but with a sample size that there's no way to be confident.

I don't think A475V should be good here if there's not epistatic effects.

The Jbloom calculator shows that it mostly is targeted by the same ABs that F456L and L455F are targeted by. So, A475V appears redundant on top of them.

However, it is within 10 angstroms of S:456, so I wonder if there is some sort of epistatic effect.

[FedeGueli]

This is now up.to 25 with 5 sequences with S:A475V the last one with it from France.
Interestingly GK.3.1 has S:A475V too

@Sinickle so this convergence could point to some advantages

Cc @corneliusroemer