Quick investigation of some putative BA.2 with S:346K (as seen in BA.1.1) as identified by @georgimarinov using new clades.nextstrain.org reversion/contamination feature.
Indian triplet could be real, though all have Ns in critical region S:496-509, so need to wait for more 1/
English sequence has 2 reversions plus 1 canonical 21K (BA.1) mutation and S:346K (common in BA.1). So looks like contamination to me (or very short range template switching). 2/
Singaporean sequence has 7 ambiguous nucleotides, some where BA.2 has mutations. It's a single sequence, can't tell whether this is real or artefact. 3/
Indian cluster of 3 sequences between 31st Dec and 8th Jan could be real, they don't have reversions or any suspicious BA.1 mutations. But they all have Ns in the important regions S:496-509.
Interestingly, they all carry nuc mutation C44T, which is common in Indian BA.2. 4/
Also, BA.2 is has become dominant in India, so contamination with BA.1 is less likely there than elsewhere where BA.1 makes up the lion share of Omicrons.
Since S:346K is beneficial in BA.1, it's not unlikely it'll pop up homoplasically in BA.2. We'll see. 5/
Big thanks to the submitters, whose tireless sequencing efforts make this rapid analysis possible 🙏 6/
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