Molecular evolution and circulation dynamic of human non-polio enteroviruses across Africa

Human non-polio enteroviruses represent major public health concerns due to frequent outbreaks. Our study used genomic data to analyze the molecular epidemiology and circulation pattern of NPEVs in Africa, assess their inter-host transmission dynamics, and investigate the occurrence of recombination events.

Genomic data were collected from GenBank and the Intercountry Reference Laboratory for Poliomyelitis at the Institut Pasteur de Dakar. A Bayesian framework was applied to infer spatiotemporal and host-associated NPEV sequences analysis. Whole genome sequences were screened for recombination analysis.

Substitution rates ranged from 0.52 × 10⁻² to 2.29 × 10⁻² substitutions/site/year for all human non-polio enteroviruses except for the B species, which show high rate of 3.11 × 10⁻² (P-value = 0.044). The common ancestors of non-polio enteroviruses species existed 31-188 years ago. Phylogeographic analyses highlight Africa's pivotal role in global circulation, with Senegal, Cameroon, Ghana and South Africa identified as major transmission hubs. Non-human primates are key reservoirs for species A, B, and D, while humans are primary hosts for species C. Recombination was more frequent among enterovirus B species.

Our study provides new insights into the molecular epidemiology of non-polio enteroviruses in Africa and highlights the need to address critical gaps in their surveillance, host dynamics, and public health impact.