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Repository for suggesting new lineages that should be added to the current scheme
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Proposal for a small sub-clade of AY.23 with S:E702V in Europe (262 sequences) #266

Closed c19850727 closed 2 years ago

c19850727 commented 3 years ago

I am thinking these small clade might be worth keeping an eye on, as it's a sub-branch of a predominantly SE Asian lineage introduced into Europe. image

Sub-lineage of: AY.23 (262 sequences) Earliest sequence: 2021/7/22 (Switzerland) Most recent sequence: 2021/10/9 (Sweden) Countries circulating: Sweden (81 sequences), Germany (77 sequences), and a few other European countries.

Cumulative prevalence and number of sequences as per Outbreak.info: image

Mutations in addition to AY.23: C15960T, then A20979G, then ORF1a:R3880G and S:E702V

Genomes: AY.23+E702V.csv

Evidence: UsHER subree of AY.23: image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_5c55_e35f00.json?c=gt-nuc_1263,11903&l=radial

Downsized sequences of AY.23 in Europe as per LeherLab: image https://nextstrain.org/groups/neherlab/ncov/sweden?c=gt-ORF1a_3880&f_pango_lineage=AY.23&p=grid&r=division

Transmission advantage of AY.23+S:E702V+ORF1a:R3880G as per CoV-Spectrum: image https://cov-spectrum.ethz.ch/explore/World/AllSamples/AllTimes/variants/json=%7B%22variant%22%3A%7B%22mutations%22%3A[%22S%3AE702V%22%2C%22ORF1a%3A3880G%22]%7D%2C%22matchPercentage%22%3A1%7D

corneliusroemer commented 3 years ago

@c19850727 it's best if you turn on branch labels: aa for screenshots to show mutations in screenshots, or add following query parameter: branchLabel=aa See: image

Here's geography as well, looks good to me. image

https://nextstrain.org/groups/neherlab/ncov/sweden?branchLabel=aa&c=gt-ORF1a_3880&label=spike_mutations:V1264L&p=grid&r=division

Can you include S:702V in the title of the issue to make it easier to spot lineage from title alone?

corneliusroemer commented 3 years ago

It's actually died out in Switzerland (where it first popped up, before Switzerland), Germany and seemingly also Sweden: image

image

image

https://cov-spectrum-develop-git-lapis-and-refactoring-cov-spectrum.vercel.app/explore/World/AllSamples/Past3M/variants?aaMutations=S%3A702V&pangoLineage=AY.23*

chrisruis commented 2 years ago

Thanks @c19850727 We've added this as AY.23.2 in v1.2.103 to start on a branch with T3718A (synonymous), A11903G (Orf1ab:R2880G) and A23667T (S:E702V) which likely coincides with the introduction(s) into Europe