XBB.1.5 with mutation Orf6:I26V, 167 sequences, mainly in Canada (115 sequences from Quebec)

[ilevade]

XBB.1.5 lineage mainly found in Canada, with the rare mutation Orf6:I26V, detected in 3 other countries.

Cov-Spectrum: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=orf6%3AI26V&nextcladePangoLineage=XBB.1.5*&

Earliest Sequence: Canada/QC-L00570134001/2022 | EPI_ISL_16460047 | 2022-12-26

Number of Sequences: 167 (Canada, 153. USA, 10. Germany, 3. Netherlands, 1.)

Mutations Orf6:I26V is the defining mutation of this branch, but other interesting mutations, mainly in the Spike, are detected in this cluster. The sequences quality seems good.

Usher: https://genome.ucsc.edu/cgi-bin/hgPhyloPlace?db=wuhCor1&phyloPlaceTree=hgPhyloPlaceData/wuhCor1/public.plusGisaid.latest.masked.pb&subtreeSize=5000&remoteFile=https%3A%2F%2Flapis.cov-spectrum.org%2Fgisaid%2Fv1%2Fsample%2Fgisaid-epi-isl%3ForderBy%3Drandom%26limit%3D1000%26dateFrom%3D2022-09-12%26dateTo%3D2023-03-10%26aaMutations%3Dorf6%253AI26V%26nextcladePangoLineage%3DXBB.1.5*%26host%3DHuman%26accessKey%3D9Cb3CqmrFnVjO3XCxQLO6gUnKPd

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3293d_4da620.json?label=id:node_7719548

Discussion: The sequences cluster, but have a lot of additional mutations. I can confirm that the high number in sequences in Quebec is not linked to any outbreak.

Also, Orf6:I26V has a high fitness value in the JBloom's lab calculator: https://jbloomlab.github.io/SARS2-mut-fitness/ORF6.html

Genomes: https://lapis.cov-spectrum.org/gisaid/v1/sample/gisaid-epi-isl?dateFrom=2022-09-12&dateTo=2023-03-10&aaMutations=orf6%3AI26V&nextcladePangoLineage=XBB.1.5*&host=Human&accessKey=9Cb3CqmrFnVjO3XCxQLO6gUnKPd&orderBy=random

[Fyrebrand1]

What method are you using to confirm that the high number in sequences in Quebec is not linked to any outbreak?

[FedeGueli]

This mutation popped up already in Delta and Alpha, it appears slighy advantageous but a lot of uncertainty. Also BA.5 evolved in orf6 at the very start of its international spread with lineages mutated at Orf6:5 or Orf6:6 , Always interesting to track this non spike mutations. thx for proposing.

[ilevade]

What method are you using to confirm that the high number in sequences in Quebec is not linked to any outbreak?

Because I'm part of the team generating the data in Québec (Public Health Institute), so I only can talk about the sequences of this province of Canada.

[FedeGueli]

This sublineage appears circulating quite steadily in Canada : Query A27277G,C27294T,T17124C catches 434 sequences as today https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3039a_501140.json?c=userOrOld&label=id:node_6801027

Interestingly after Orf6:I26V it got C27294T silent nucleotide mutation in Orf6:31

Convergently a sublineage of FK.1 gained the same mutation and it is circulating in New Zealand. For these reasons i think a designation although not urgent could be deserved cc @InfrPopGen @corneliusroemer

PS a recent branch of this one got a mini saltation with S:T>I19V, S:S494P,N:T16M and ORF9b:R13C

[FedeGueli]

436 seqs

[DailyCovidCases]

This branch is dead, please close this issue