Genomic history of human monkey pox infections in the Central African Republic between 2001 and 2018

Abstract

Monkeypox is an emerging infectious disease, which has a clinical presentation similar to smallpox. In the two past decades, Central Africa has seen an increase in the frequency of cases, with many monkeypox virus (MPXV) isolates detected in the Democratic Republic of Congo (DRC) and the Central African Republic (CAR). To date, no complete MPXV viral genome has been published from the human cases identified in the CAR. The objective of this study was to sequence the full genome of 10 MPXV isolates collected during the CAR epidemics between 2001 and 2018 in order to determine their phylogenetic relationships among MPXV lineages previously described in Central Africa and West Africa. Our phylogenetic results indicate that the 10 CAR isolates belong to three lineages closely related to those found in DRC. The phylogenetic pattern shows that all of them emerged in the rainforest block of the Congo Basin. Since most human index cases in CAR occurred at the northern edge of western and eastern rainforests, transmissions from wild animals living in the rainforest is the most probable hypothesis. In addition, molecular dating estimates suggest that periods of intense political instability resulting in population movements within the country often associated also with increased poverty may have led to more frequent contact with host wild animals. The CAR socio-economic situation, armed conflicts and ecological disturbances will likely incite populations to interact more and more with wild animals and thus increase the risk of zoonotic spillover.

Figure 1

Geographic origin of the 56 monkeypox virus (MPXV) isolates analysed in this study (a). The 10 MPXV isolates collected in the CAR and specially sequenced for this study are indicated in the map of (b). The localities of reporting and years of these MPXV cases are indicated in white. As detailed in Fig. 2, the MPXV isolates belong to the West African clade (orange) or to the Central African groups I (blue), II (white), III (yellow), IV (green) and V (pink). The map was created with ggmap v3.0.0 under R 4.0.456. Maps Data: Google, 2021 NASA/TerraMetrics.

Figure 2

Phylogeny of monkeypox viruses (MPXV) based on complete genomes. The Bayesian tree was reconstructed using the GTR+G model. The two sequences used as outgroup are not shown. For each MPXV sequence, we indicated the accession number in GenBank, the geographic locality, the country, the code, and the year. The 10 MPXV genomes specially sequenced for this study are written in red. Branches with an asterisk were supported by maximal Bayesian posterior probability (PP = 1) and ML bootstrap proportions ≥ 95. The main clades were highlighted with different colours: West African clade (orange), Central African group I (blue), II (white), III (yellow), IV (green) and V (pink). For convenience, the size of longest branches shown in grey was reduced by five.

Figure 3

Bayesian chronogram of Central African monkeypox viruses (MPXVs). MPXV ge-nomes sampled between 2001 and 2018 in the Central African Republic are shown in blue. Median divergence times are indicated at the nodes and the 95% highest posterior density (HPD) is given in parentheses.