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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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Proposal for a delta (21A) lineage with Spike S255F (~900 sequences, ~53% prevalence in Jordan) #287

Closed c19850727 closed 2 years ago

c19850727 commented 3 years ago

Description Sub-lineage of: B.1.617.2, Clade 21A (889 sequences) Earliest sequence: 2021/4/17 Most recent sequence: 2021/10/15 (Jordan) Countries circulating: Germany (204 sequences), Jordan (84 sequences), and other countries

Mutations in addition to B.1.617.2: nuc C9811T, then S:S255F

Evidence

Down-sampled tree as per Neherlab (Asia-Jordan, filtered to Clade 21A only): image https://nextstrain.org/groups/neherlab/ncov/asia-jordan?branchLabel=aa&c=gt-S_255&f_clade_membership=21A%20%28Delta%29&label=spike_mutations:I95T&p=full&r=division&tl=country

Down-sampled tree as per Neherlab showing country of submission: image

Geographical distribution as per NeherLab: image

UShER subtree: image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_103d8_2f2920.json?c=gt-S_255&l=radial

Transmission advantage and geographical distribution as per CoV-Spectrum: image image https://cov-spectrum-develop-git-lapis-and-refactoring-cov-spectrum.vercel.app/explore/World/AllSamples/AllTimes/variants?aaMutations=S%3AS255F&nucMutations=C9811T

FedeGueli commented 3 years ago

This has been designated as AY.106 with S:S255F

commit: https://github.com/cov-lineages/pango-designation/commit/61248ea86a3e5912440d76081da88805c074b3cc

cc @corneliusroemer @chrisruis

FedeGueli commented 3 years ago

Screenshot_2021-11-05-11-54-18-095_com android chrome

AY.106 seems steadily growing in Germany

corneliusroemer commented 3 years ago

These are all the German sequences with S:255F, there are homplasies. AY.106 doesn't cover all of them, but the biggest chunk. https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_1c4a5_520b10.json

https://genome.ucsc.edu/cgi-bin/hgPhyloPlace?db=wuhCor1&phyloPlaceTree=hgPhyloPlaceData/wuhCor1/public.plusGisaid.latest.masked.pb&subtreeSize=1000&remoteFile=https%3A%2F%2Fcov-spectrum.ethz.ch%2Fgisaid%2Fapi%2Fv1%2Fsample%2Fstrain-names%3Fhost%3DHuman%26country%3DGermany%26dateFrom%3D2020-01-06%26aaMutations%3DS%253A255F%26pangoLineage%3DB.1.617.2*

image