cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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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) #2071

Closed oobb45729 closed 1 year ago

oobb45729 commented 1 year ago

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. 1 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3d97f_b51360.json?c=gt-S_455&label=id:node_6752165 2 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. 3 https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AXBB.1.5*%26S%3AL455F%26S%3AF456L%26T28282C&

FedeGueli commented 1 year ago

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 commented 1 year ago

ninth sequence from Honolulu , Hawaii , US

FedeGueli commented 1 year ago

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

FedeGueli commented 1 year ago

15 as today 3 of them doesnt have S:P1162S: Schermata 2023-07-25 alle 15 33 14 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 commented 1 year ago

A14634G, G22927T ,T22928C, T28282C finds now 22 and USHER is now very different looking from the original proposal in the other page: Schermata 2023-07-28 alle 08 01 58 two branches: one growing recently with Orf1b:A241V with a notably recent international cluster with S:A475V, negative for binding but increasing RBD expression : Schermata 2023-07-28 alle 08 02 23 the other is the one originally proposed with S:P1162S: Schermata 2023-07-28 alle 08 03 25

FedeGueli commented 1 year ago

@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 commented 1 year ago

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

Schermata 2023-08-01 alle 22 31 04

Sinickle commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

Query for the A475V branch: C19185T, C22986T,C14189T

oobb45729 commented 1 year ago

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 commented 1 year ago

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.

image

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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

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FedeGueli commented 1 year ago

@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 commented 1 year ago

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

FedeGueli commented 1 year ago

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

@corneliusroemer @InfrPopGen designation needed here.

NkRMnZr commented 1 year ago

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 commented 1 year ago

@corneliusroemer designation needed here.

FedeGueli commented 1 year ago

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 commented 1 year ago

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

FedeGueli commented 1 year ago

Designated JD.1