Discrepancy between Usher and Nextclade lineage calls for mpox

Question originally submitted by a user via email

I have noticed that occasionally there are discrepancies between the Mpox lineage assigned by Usher and Nextclade. For example, Nextclade recently gave me a B.1.4 while on UShER it was a B.1

Please let me know how these can be reconciled.

Given that Usher and Nextclade use different algorithms, it’s expected that they occasionally disagree. Sometimes it’s not unambiguous which lineage a sequence should be classified as, sometimes there are artefacts in the sequences that make Usher and Nextclade produce different results.

Generally speaking, if the sequence has 34308A, it should be B.1.4. But due to homoplasy this isn’t necessarily always the case. The same is true if that site isn’t mutated. In that case the lack of mutation could be an artefact.

See: lineage-designation/lineages.md at master · mpxv-lineages/lineage-designation · GitHub for a description of what defines B.1.4 (and all the other mpox lineages for that matter)