Proposal of new sub-lineage of BA.2.12.1 with additional mutation nuc:T18753C only in peruvian genomes

[LuisBarcenaF]

Proposal of new sub-lineage of BA.2.12.1 with additional mutation nuc:T18753C only in peruvian genomes by Group of Genomic Surveillance INS-PERU

Description
Sub-lineage of: Potential new sub-lineage of BA.2.12.1 (nuc: T18753C mutation mainly in Peruvian genomes)
Earliest sequence: hCoV-19/Peru/LIM-INS-16842/2022 (26/04/2022, Peru)
Most recent sequence: hCoV-19/USA/CA-CDC-STM-E9YV3JUR5/2022 (11/05/2022, USA)

Countries circulating
Peru (10), USA (3)

Some of the genomes of new sub lineage carried a reversion in Spike:S408R. This potential BA.2.12.1 is principally distributed in Lima, Peru

Genomes
genomes.txt

Evidence
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_1d6ab_3be9c0.json?branchLabel=aa%20mutations&c=gt-nuc_18753&label=nuc%20mutations:T15009C,C21721T

Proposed lineage name
BA.2.12.X

[Vjimenez-vasquez]

Nice observation @LuisBarcenaF, this clade could be (maybe) the explanation for the last COVID-19 rise in Peru.

[LuisBarcenaF]

Nine genomes more from Peru

EPI_ISL_13022089
EPI_ISL_13022097
EPI_ISL_13022213
EPI_ISL_13022123
EPI_ISL_13022182
EPI_ISL_13022171
EPI_ISL_13022214
EPI_ISL_13022215
EPI_ISL_13022203

[Vjimenez-vasquez]

And still growing !

[OrsonMM]

Now are 75 genomes BA.2.12.1 and 20 of these carring the mutation proposed here (represent 26% of this lineage).

[OrsonMM]

36 genomes now

[chrisruis]

Thanks @LuisBarcenaF We now need new Pango lineages to be defined by at least one nonsynonymous mutation. We've therefore moved the start of this lineage one branch back in the tree so it includes several USA and UK sequences. We've therefore added this as BG.1 (with BG being an alias for BA.2.12.1) to start on the branch with A6458G (Orf1a:N2065D)