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Repository for suggesting new lineages that should be added to the current scheme
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Proposal for a sublineage of AY.4 with E:V58F (~3k sequences, ~18% prevalence in Aruba) #291

Closed c19850727 closed 2 years ago

c19850727 commented 3 years ago

Description Sub-lineage of: AY.4, Clade 21J (3004 sequences) Earliest sequence: 2021/2/9 (Slovakia) Most recent sequence: 2021/10/14 (Germany) Countries circulating: the Netherlands (619 sequences), Aruba (435 sequences), Germany (434 sequences), Denmark (314 sequences), among a few other countries.

Cumulative prevalence and number of samples sequenced as per Outbreak.info (truncated): image

Mutations in addition to AY.4: ORF1a:A2529V, then ORF1b:E1242D, ORF9b:P3L, then ORF1b:M454I, then E:V58F

Genomes: AY.4 V58F.csv

Evidence Down-sampled tree as per NeherLab (sa-Aruba, filtered to AY.4, shown in orange color): image https://nextstrain.org/groups/neherlab/ncov/sa-aruba?c=gt-nuc_7851,26416&f_pango_lineage=AY.4&p=full&r=division

Geography prevalence as per NeherLab (sa-Aruba): image

UShER subtree: image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_20b79_505740.json?c=gt-E_58&l=radial

Transmission advantage as per CoV-Spectrum: image image https://cov-spectrum-develop-git-lapis-and-refactoring-cov-spectrum.vercel.app/explore/World/AllSamples/AllTimes/variants?aaMutations=E%3AV58F%2CORF1b%3AM454I

FedeGueli commented 2 years ago

Hi @c19850727 @chrisruis this showed very limited spread in Europe, it was stable in Aruba around 15/20% of sequences.

https://cov-spectrum.org/explore/Europe/AllSamples/Past3M/variants?aaMutations=E%3AV58F&pangoLineage=ay.4*

I dont know if it really deserves a designation, it could be monitored in Aruba well with the covspectrum tool due to its limited geographical spread.

Sorry for bothering, trying to help with frozen issues ;)

chrisruis commented 2 years ago

I think this clade warrants a designation. We've added this as AY.4.7 in v1.2.110 to start on the branch with G26416T (E:V58F)