Monkeypox (MPX) is a zoonotic disease endemic to the rain forest in Central and Western Africa, especially in the Democratic Republic of the Congo (DRC), where the disease is considered a major public health concern. Previous studies have shown that evolutionary history of the virus matches that of other organisms associated with the African rainforest, and that genetic variability exists within the Congo Basin clade of the virus. Here, we analyzed viral genomic information of MPXV isolates from the Tshuapa Province to assess the genetic variability of the virus in the Congo basin using phylogenetic and genetic network analyses. Additionally, we examined the association between the geographic distribution of human cases of MPX and environmental attributes at reporting locations through Ecological Niche Models (ENM) using vegetation indexes. Whole genome sequences were generated for 33 MPXV isolates obtained from Tshuapa Province and included in a matrix of single nucleotide polymorphisms with additional 34 genomes available through NCBI for the region. Genetic analyses included phylogenetics, genetic networks and spatial PCA. ENMs were created using the Enhanced Vegetation Index (EVI) as environmental datasets and the locations of villages with reported human cases between 2010 and 2014 as occurrence data.
Results/Conclusions
Phylogenetic analyses showed genetic differentiation of MPXV isolates in Central Africa, corresponding to previously reported sub lineages. All isolates from Tshuapa Province were included in one single clade with high support, which could suggest influence of geography on genetic differentiation. Genetic network analyses focused on establishing a relationship between genetic data and epidemiological chains; epidemiologically linked cases showed small number of SNPs (0-2), suggesting the potential for using this measure to identify potential transmission chains when epidemiological data is not available. sPCA analyses evidence of geographic structure of the genetic variations observed in MPXV, separating isolates from north and south. ENM models showed that MPX cases seem to be associated with particular forest types/conditions within the Congo basin, supporting previous findings. These results advance our understanding of the natural history of MPXV and its evolution in an endemic area; and the utilization of genetic data to inform epidemiology. Future studies are needed to further explore the results of these analyses and potential applications on public health.