Proposal of new sub-lineage of AY.3 for Peru with principal mutation in Spike: T259I, A942T

[IrisSilvaINS]

Proposal for a new sub lineage of AY.3 with principal mutation in Spike: T259I, A942T in Peruvian genomes by Group of Genomic Surveillance INS-PERU

Description
Sub-lineage of: Potentially new sub lineage of AY.3 (S: T259I, A942T mutations in of Peruvian genomes)
Earliest sequence: hCoV-19/Peru/JUN-INS-6934/2021(2021/09/12, Peru)
Most recent sequence: hCoV-19/Peru/LAM-INS-8260/2021(2021/10/12, Peru)

Countries circulating: Peru (23)

The lineage of AY.3 was designed #121 (carried mutation: ORF1a: I3731V), the genomes of new sub lineage carried two additional mutation in Spike: T259I, A942T. This potentially AY.3.X is spread pronominally in Lima, capital of Peru.

See here for further details:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_1d473_a80600.json?tl=pango_lineage

Share of all sequences in Peru

Genomes:

New_sub_lineage.txt

[corneliusroemer]

Even 12 days later, it's still only 23 sequences, which is a bit too few to warrant a designation for now covSpectrum

[OrsonMM]

[chrisruis]

Thanks @IrisSilvaINS It looks like this clade has continued to circulate so we've added this as AY.3.2 in v1.2.111 to start on the branch with C22338T (S:T259I)