Reference sequences for A.2 and A.2.1 lineages are same

[chainorato]

Hi, I have a question about the reference sequences.

A pair of current reference sequences of A.2 and A.2.1 lineages are stated as ON674051 and MPXV_USA_2022_FL001, respectively. However, they are same sequences. Are there any specific reasons for that?

[ammaraziz]

Good catch. No reason, I think this is a typo of some sorts (probably from copying the formatting from an older proposal).

[corneliusroemer]

Hi @chainorato, that's a good question.

If you look at the release dates for the A.2* lineage sequences you see that the 2 reference sequences for A.2 were 2 out of 3 that were public at the time of designation. There weren't any basal ones, these were uploaded later.

See: https://nextstrain.org/mpox/clade-IIb?c=date_submitted&d=tree,entropy&f_date_submitted=2022-06-03&label=clade:A.2&m=div&p=full

When there are multiple reference sequences, the lineage is understood to be starting from the common ancestor of the listed sequences.

Given there are now more basal ones that have been shared, e.g.

• OP612690 (MPXV/113/19)
• OP612689 (MPXV/111/19)
• OP612691 (MPXV/191/20)

We could update the A.2 definitions, indeed.