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

Abstract

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.

Keywords: Orthopoxvirus; molecular dating; monkeypox virus; population structure.

Figure 1.

Divergence of monkeypox virus (MPXV) genomes. Neighbor-net split network of 90 MPXV genome sequences. Each sample is shown as a dot and colors represent country of origin (as indicated in the legend). Nucleotide diversity is reported for clades 1 and 2/3, along with an enlargement of clade 1 genetic relationships.

Figure 2.

Population structure of monkeypox virus (MPXV). (A) Bar plot representing the proportion of ancestral population components for K = 2. Each vertical line represents an MPXV genome, and it is colored by the proportion of sites that have been assigned to the 2 populations by STRUCTURE. Viral genomes are ordered by country (B) Distributions of F values for the 2 populations. Colors are as in (A). CAR, Central African Republic; DRC, Democratic Republic of the Congo.

Figure 3.

Population structure of monkeypox virus (MPXV) clades. Bar plots representing the proportion of ancestral population components for clades 2/3 (K = 2) (A) and clade 1 (K = 4) (B). Each vertical line represents an MPXV genome and is colored by the proportion of sites that have been assigned to the different subpopulations by STRUCTURE. Viral genomes are ordered by country. Distributions of F values are also reported next to the bar plots. Asterisks indicate rodent-derived viral samples cited in the text. CAR, Central African Republic; DRC, Democratic Republic of the Congo.

Figure 4.

Geographical distribution of monkeypox virus genomes. Each viral sequence is shown as a pie chart, with colors representing the proportion of ancestral population components estimated by STRUCTURE (see Figure 3 and the legend for color scheming). Viral strains are placed on the map using country or, when possible, subregion sampling information (Supplementary Table 1). Identical locations were jittered to allow the visualization of ancestral population components. When “country” was the only available information, strains were placed in the center of that country. Three Nigerian strains were not plotted on the map due to the lack of clear sampling information. Dotted circles indicate rodent-derived viral samples cited in the text. Terrestrial biomes of the sampling locations of viral strains are also shown on the map (see the legend for details). Information was retrieved from the Digital Observatory for Protected Areas (https://dopa.jrc.ec.europa.eu/dopa/). An insert with the geographic distribution of Funisciurus anerythrus is also reported (figure adapted from https://www.iucnredlist.org/). The map was created using maps (v.3.4.0) and ggplot2 (v.3.3.5) R (v.4.0.5) packages. DRC, Democratic Republic of the Congo.

Figure 5.

Time-scaled monkeypox virus (MPXV) phylogenetic tree. Dated maximum credibility tree estimated using the nonrecombinant region of MPXV genomes. Branch lengths represent the evolutionary time in years, and a timescale grid is shown at the tree base. Node bars indicate 95% highest posterior density intervals of node ages, and black dots indicate nodes with bootstrap support higher than 0.8. The MPXV strains are colored according to the major ancestry component identified by STRUCTURE, with black indicating admixed samples. The generally accepted time frames for the Warm Medieval Period, the Little Ice Age, and the Colonial Period are also reported [39, 40].