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Updated: Sep 4, 2025

Vaccinia Virus Infection & Temporal Analysis of Virus Gene Expression: Part 2
Published on: April 10, 2009
Geographic Structuring and Divergence Time Frame of Monkeypox Virus in the Endemic Region
Diego Forni1, Cristian Molteni1, Rachele Cagliani1
1Bioinformatics, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy.
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.
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