Proposal for a BA.2.12 sublineage with S:R357K and ORF7a:Q62R (533 sequences as of 2022-05-30, Australia)

[c19850727]

Description

Potential sublineage of: BA.2.12
Earliest sequence: 2022/02/05 (Australia-VIC)
Most recent sequence: 2022/5/23 (Australia-TAS)
Mutations on top of BA.2.12: C11674T, C17586T, G22632A (S:R357K), A27578G (ORF7a:Q62R)
Countries circulating: Australia (~3.3% prevalence in Victoria, ~1.2% prevalence in Tasmania in recent 3 months as per Covspectrum)
Border-entry cases:

• Japan ex-Australia (1 sequence),
• Singapore ex-Australia (3 sequences),
• Hong Kong ex-Australia (1 sequence),
• New Zealand MIQ (5 sequences) (MIQ=managed isolation & quarantine).

Evidence

Nextstrain Oceania-focused subsampling dataset:

Usher tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1915f_582a20.json?branchLabel=aa%20mutations&c=country&label=nuc%20mutations:C17586T,A27578G&tl=country

Genomes:

BA.2.12 R357K.csv

[InfrPopGen]

Thanks for submitting. We've added lineage BA.2.12.2 with 220 newly designated sequences, and 216 updated designations from BA.2.12. Defining mutation(s) G22632A (S:R357K).