Proposed sublineage of B.1.617.2 with Orf1a:S2048F originated in East Africa and then spread into Europe

[FedeGueli]

Proposal of AY.** , sublineage of B.1.617.2 with NUC: C6408T, NUC A25003G and Orf1a:S2048F

Early sequences in Ethiopia (17/7/21) Last sequence Italy (14/10/21)

Tree: Africa (neher lab) https://nextstrain.org/groups/neherlab/ncov/africa?c=gt-nuc_6408,25003

UK Neher Lab:

https://nextstrain.org/groups/neherlab/ncov/united-kingdom?c=gt-nuc_6408,25003

It appears to account for 2-3% of UK sequences

And for the vast mayority of sequences from Ethiopia

Globally during week 40 accounted for 1,70% of sequences https://cov-spectrum-develop-git-lapis-and-refactoring-cov-spectrum.vercel.app/explore/World/AllSamples/AllTimes/variants?nucMutations=C6408T%2CA25003G&pangoLineage=B.1.617.2*

Notably some subclade of this sublineage carry additional spike mutations S:T51I or S:H66Y:

[FedeGueli]

Hi @corneliusroemer i was checking back open proposals, this one seemed interesting cause this lineage seems to resist quite well in Uk And circulating as well in Italy

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_1aabe_78ea50.json?branchLabel=Spike%20mutations&label=nuc%20mutations:G174T,C7105T,C13138T,C21758T,T27017A&tl=pango_lineage_usher

https://nextstrain.org/groups/neherlab/ncov/united-kingdom?c=gt-nuc_6408,25003

covspectrum for italy: https://cov-spectrum.ethz.ch/explore/United%20Kingdom/AllSamples/Past3M/variants?aaMutations=Orf1a%3A2048F&nucMutations=6408T%2CA25003G&pangoLineage=B.1.617.2*

[FedeGueli]

@chrisruis @corneliusroemer it has been designated AY.120 commit: https://github.com/cov-lineages/pango-designation/commit/e3425b2837b72b910bf2a3d9cb39af509fab2b73

And his sublimeage with S:H66Y highlighted in this issue has beem designated AY.120.2 commit: https://github.com/cov-lineages/pango-designation/commit/900095e52a0caf0d57c37b34795d03bc98c57742