21L(Omicron, BA.2) showing up as B.1.1.529

One sample I ran through IDSeq+Nextclade barcode12/ARTIC/medaka MN908947.3 is reporting as 21L Omicron B.1.1.529, shouldn’t this be BA.2?


Hi Lucy, that’s a great question!

I’ve noticed this before.

I’m pretty sure that the sequence attached to this internal node here that has BA.2 as the parent and BA.4 and BA.5 as children, the turquoise T on the left of the 22B label

Due to the way internal nodes are labelled, this one gets the B.1.1.529 label: the node is neither clearly BA.4 (B.1.1.529.4) nor BA.5 (B.1.1.529.5) so the next level up is B.1.1.529.

With what we know now, BA.4/5 should probably be called BA.2.? (instead of BA.4) and X? (instead of BA.5 - as BA.5 pretty clearly is a recombinant involving BA.4 up to a segment from an ancestral like donor).

In practice, most sequences that attach at this internal node are low quality BA.4/5.

If we wanted to avoid this internal node, we could force BA.4 and BA.5 apart, essentially treating BA.5 like the recombinant it should have been. But that might have unintended consequences.

I hope that makes sense! Let me know if you have further questions.