Phylodynamics and Evolutionary Epidemiology of Foot-and-Mouth Disease Virus in Nigerian Livestock Populations

This study applies phylodynamic and evolutionary epidemiological analyses to characterise the spatiotemporal dynamics of foot-and-mouth disease virus evolution and spread in Nigerian livestock populations, generating the viral evolutionary and epidemiological evidence needed to optimise FMD control strategy in the country. Foot-and-mouth disease causes major economic losses in Nigeria's cattle production and export trade, but the viral population dynamics, serotype diversity, and spatial spread routes have been insufficiently characterised for rational vaccine strain selection and movement restriction design. This study collects epithelial tissue and oropharyngeal fluid samples from 580 clinically suspect FMD cases across cattle, sheep, goats, and pigs in all six geopolitical zones over three years. Viral characterisation uses RT-PCR, VP1 gene sequencing, and whole genome sequencing of representative isolates. Bayesian phylogenetic analysis using BEAST2 estimates evolutionary rates, divergence times, and phylogeographic spread patterns. Bayesian skyline plot analysis characterises viral effective population size dynamics. Network analysis of livestock movement and trade patterns identifies transmission corridors. Findings reveal co-circulation of FMD serotypes O, A, and SAT-2 across Nigeria, with SAT-2 emerging as increasingly prevalent since 2020. Phylogeographic analysis traces dominant viral lineages from the northern Fulani pastoral corridor as the primary within-country spread pathway. Evolutionary rate estimates indicate viral diversification outpacing vaccine updates. The study contributes original Nigerian FMD phylodynamic data and recommends serotype-specific vaccine matching review, targeted livestock movement monitoring in the identified transmission corridors, and a national FMD molecular surveillance programme.

Keywords: foot-and-mouth disease, phylodynamics, viral evolution, Nigeria, livestock movement.