search

cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
Other
1.05k stars 98 forks source link

Proposal for a Sublineage of AY.4.2.2 with Spike S13T (~3600 Sequences, the UK) #418

Closed c19850727 closed 2 years ago

c19850727 commented 2 years ago

Description Sub-lineage of: AY.4.2.2 Earliest sequence: 2021/8/31 (UK-England) Most recent sequence: 2021/1/17 (UK-Scotland) Countries circulating: UK (mainly Scotland)

Substitutions on top of AY.4.2.2:

Gene | Mutations -- | -- ORF1a | T1395A, V2857A, T4364I ORF1b | F685Y Spike | S13T nuc | T8566C

Evidence Down-sampled tree as per Neherlab (UK, filtered to AY.4.2.2, in yellow color): image https://nextstrain.org/groups/neherlab/ncov/united-kingdom?branchLabel=aa&c=gt-nuc_13356&label=Spike%20mutations:V1264L&p=full&r=division

Relative growth advantage as per cov-spectrum: image Comparison between AY.4.2.2+Spike S13T (blue line) and AY.4.2.2 (baseline): image https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?pangoLineage=AY.4.2.2*&aaMutations1=S%3AS13T&pangoLineage1=AY.4.2*&analysisMode=CompareToBaseline

Usher tree (in yellow color): image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_29960_368a30.json?c=gt-S_679,13&l=radial&label=nuc%20mutations:T8566C

Genomes: AY.4.2.2+S13T.csv

c19850727 commented 2 years ago

I'm also to propose a sublineage of above proposed #418 (AY.4.2.2+Spike S13T), with ~280 sequences, mainly circulating in Scotland.

Description Sub-lineage of: #418 Earliest sequence: 2021/10/6 (UK-Scotland) Most recent sequence: 2021/12/28 (UK-England) Countries circulating: UK (mainly Scotland)

Substitutions on top of #418:

Gene | Mutations -- | -- Spike | S98F, T323I (~50%), N679I

Evidence

Relative growth advantage as per cov-spectrum: image

Comparison between#418+Spike N679I (black line) and #418 (baseline): image https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3AS13T&pangoLineage=AY.4.2.2*&aaMutations1=S%3AS13T%2CS%3AN679I&pangoLineage1=AY.4.2.2*&analysisMode=CompareToBaseline

Usher tree (in blue color): image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_29960_368a30.json?c=gt-S_679,13&l=radial&label=nuc%20mutations:T8566C

Genomes: AY.4.2.2+S13T+N679I.csv

InfrPopGen commented 2 years ago

This lineage is no longer active (not seen within past 3 months). Closing this issue for now.