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 similar to 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. Within the endemic region, MPXV clades show distinctive geographic structuring of genetic diversity. Separation of major lineages occurred in a period ranging from the Medieval Warm Period to the Little Ice Age, which was characterized by changes in rainforest coverage.

Automated summary

This study explores the evolution and geographic patterns of the monkeypox virus (MPXV) in Central and West Africa. The results show that the two major clades of MPXV have distinct histories, possibly due to differences in ecology. The study also reveals geographic structuring of MPXV diversity and suggests that the separation of major lineages occurred during a period of rainforest coverage changes.