Fig 1.

A) A midpoint rooted maximum likelihood (iqtree2 using JC model) phylogeny of MPXV genomes sampled from human and non-human infections in 1970–2022 aligned against the reference genome (accession NC_063383) with one of the ITR regions (from 190788 onwards in the genome). A number of repetitive regions were also masked out. Three distinct MPXV clades are indicated, representing the deep diversity of MPXV. Clade I corresponds to the prior “Congo Basin clade”, while Clades IIa and IIb corresponds to the prior “West African clade”. Clade IIb contains a group of genomes from 2017, 2018 and 2022 sampled from human cases that likely represent sustained human-to-human transmission. We propose to label this group hMPXV1. B) Proposed nomenclature for genomes belonging to the 2017–2019 outbreaks from the UK, Israel, Nigeria, USA, and Singapore and genomes from 2022 global outbreaks as a fine-scale classification of hMPXV1 virus (MPXV clade IIb) into neutral lineages such as A, A.1, A.1.1, B.1, etc.