Proposal for a Sublineage of AY.112 with Spike Y144del, E484Q, and Some with Additional P499R (~660 Sequence, ~26% Prevalence in India)

[c19850727]

First spotted by @corneliusroemer .

Description Sub-lineage of: AY.112 Earliest sequence: 2021/1/10 (probably some input error) Most recent sequence: 2021/12/16 Countries circulating: India mainly Detected at border-entry: Japan ex-India, Singapore ex-India

Substitutions on top of AY.112:

Gene | Mutations -- | -- Spike | E484Q, Y144del* nuc | G4162T, G27516A

*Not all sequences have spike Y144del

The largest clade fo this proposed sublineage also has the following additional mutations (~230 sequences):

Gene | Mutations -- | -- Spike | P499R ORF6 | W27L

Evidence Usher tree (Orange=E484Q; Green=E484Q+P499R): https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2c2d4_9ec070.json?c=gt-S_484,499&l=radial

Down-sampled tree as per Neherlab (Asia-India, filtered to B.1.617.2. Yellow=E484Q; Orange=E484Q+P499R):

Georgraphical distribution as per Neherlab (Asia-India, no filtering. Yellow=E484Q; Orange=E484Q+P499R): https://nextstrain.org/groups/neherlab/ncov/asia-india?branchLabel=none&c=gt-nuc_4162,23058&p=full&r=division

Transmission advantage as per cov-spectrum (20% with additional Spike P499R):

International comparison as per cov-spectrum (~14% prevalence in India with additional Spike P499R): https://cov-spectrum-develop-git-lapis-and-refactoring-cov-spectrum.vercel.app/explore/India/AllSamples/AllTimes/variants?aaMutations=S%3AE484Q&nucMutations=G27516A

[chaoran-chen]

Hi @c19850727. A quick note about the link to cov-spectrum: You are using a (quite old) test version of the website and it would be better to use https://cov-spectrum.org/ :-)

Here is the new page for this variant: https://cov-spectrum.org/explore/India/AllSamples/AllTimes/variants?aaMutations=S%3AE484Q&nucMutations=G27516A

[c19850727]

Thanks @chaoran-chen! and my apologies I was being lazy and relying too much on my browser to auto-complete URLs...

[FedeGueli]

This clade+S:499R had a substantial growth rate advantage versus B.1.617.2 all sublineages baseline:

[corneliusroemer]

@chrisruis I think this would be a good Delta designation because it shows:

• Interesting mutations (S:484, S:144-, S:499) that we know things about
• Significant growth advantage and made up 15+ % in a huge country (India)
• Geographic association

[InfrPopGen]

Thanks for submitting. We've added lineage AY.112.2 with 1043 newly designated sequences, in v1.2.138