Geographic Structuring and Divergence Time Frame of Monkeypox Virus in the Endemic Region

BACKGROUND: Monkeypox is an emerging zoonosis endemic to Central and West Africa. Monkeypox virus (MPXV) is genetically structured in 2 major clades (clades 1 and 2/3), but its evolution is poorly explored. METHODS: We retrieved MPXV genomes from public repositories and we analyzed geographic patterns using STRUCTURE. Molecular dating was performed using a using a Bayesian approach. RESULTS: We show that the population transmitted in West Africa (clades 2/3) experienced limited drift. Conversely, clade 1 (transmitted in the Congo Basin) possibly underwent a bottleneck or founder effect. Depending on the model used, we estimated that the 2 clades separated ∼560–860 (highest posterior density: 450–960) years ago, a period characterized by expansions and contractions of rainforest areas, possibly creating the ecological conditions for the MPXV reservoir(s) to migrate. In the Congo Basin, MPXV diversity is characterized by 4 subpopulations that show no geographic structuring. Conversely, clades 2/3 are spatially structured with 2 populations located West and East of the Dahomey Gap. CONCLUSIONS: The distinct histories of the 2 clades may derive from differences in MPXV ecology in West and Central Africa.