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 https://github.com/sars-cov-2-variants/lineage-proposals/issues/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 https://github.com/sars-cov-2-variants/lineage-proposals/issues/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

[FedeGueli]

Query for the A475V branch: C19185T, C22986T,C14189T

[oobb45729]

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.

Could it be about some Gamma-targeting antibodies?

[ryhisner]

Just want to add that T28282C is a substantial upgrade to the ORF9b Kozak sequence—from the worst to the best residue at the -2 position. Increasing the expression of ORF9b has been a theme in many, many lineages throughout the pandemic, and this looks like one more example.

.

Also there were four more sequences from this lineage uploaded from Spain today. One of them also has S:S446I. It's actually the second sequence with S446I, L455F, F456L, and A475V—the other is an EG.5.1.1 from China—so perhaps that's a winning combination. Too early to say. It also allegedly has S:H339D, but I'm not certain if that's real or not. EPI_ISL_18072823

Three of the uploads from Spain today might appear not to be part of this lineage, but that's only because they have no RBD coverage. They have all the other mutations. EPI_ISL_18072815, EPI_ISL_18072818, EPI_ISL_18072824

.

[FedeGueli]

@corneliusroemer please review this issue: I think.all the three levels should be designated: Big parental, Flip sublineage, A475V sublineage of the Flip one.

[FedeGueli]

Now the sublineage with a475V went up to 6.i suggest to designate the whole thing.

[FedeGueli]

40 now and 10 with S:A475V (mostly international outside Brazil).

@corneliusroemer @InfrPopGen designation needed here.

[NkRMnZr]

A huge batch (+29 seqs) https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3098a_e45ed0.json?f_userOrOld=uploaded%20sample&label=id:node_7157439

many with R346T and K417N dropout though

[FedeGueli]

@corneliusroemer designation needed here.

[FedeGueli]

A huge batch (+29 seqs) https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3098a_e45ed0.json?f_userOrOld=uploaded%20sample&label=id:node_7157439

many with R346T and K417N dropout though

Thx for tracking!

[FedeGueli]

The S:A475V reached 14 showing an apparent doubling time less than 10days that is fast.

[FedeGueli]

Designated JD.1