Phylogeography of Foot-and-Mouth Disease Virus and Its Implications for Livestock Trade and Public Health Policy in Nigeria

Foot-and-mouth disease remains among the most economically devastating livestock diseases in Nigeria, and its phylogeographic characterization is essential for designing rational vaccination and trade policies. This study investigated the phylogeographic distribution of foot-and-mouth disease virus serotypes and lineages across Nigeria's six geopolitical zones and analyzed implications for livestock trade policy and animal health governance. Oropharyngeal fluid and vesicular fluid samples were collected from 180 outbreak episodes across 24 states over a three-year period through active collaboration with state veterinary services. Full genome sequencing was performed on 96 confirmed foot-and-mouth disease virus isolates using next-generation sequencing. Bayesian phylogeographic inference was applied using BEAST software to reconstruct evolutionary relationships and spatial spread. Serotypes O, A, and SAT2 co-circulated, with serotype O lineage MEA-SA-1 being dominant across northern zones. Bayesian analysis identified multiple independent introductions from neighboring countries coinciding with livestock market periods, and phylogeographic diffusion corridors aligned with major cattle transit routes from Niger and Cameroon. Trade-linked introduction events accounted for an estimated 63% of phylogenetically distinct outbreaks. The study provides the most comprehensive phylogeographic analysis of foot-and-mouth disease virus in Nigeria to date. Findings directly inform recommendations for evidence-based serotype-matched vaccination programs, border control protocols, and livestock trade risk management policies within the ECOWAS region. Keywords: foot-and-mouth disease, phylogeography, livestock trade, Nigeria, serotype evolution