Characterisation of Foot-and-Mouth Disease Virus Strains Circulating in Cattle in North East Nigeria: Serotype Distribution and Phylogenetic Analysis

This study characterises foot-and-mouth disease virus (FMDV) strains circulating in cattle populations in North East Nigeria, encompassing Borno, Yobe, Adamawa, Gombe, Bauchi, and Taraba States, with emphasis on serotype distribution and phylogenetic relationships to inform vaccination strategy. Foot-and-mouth disease control requires serotype-matched vaccines, and the circulation of multiple FMDV serotypes in a region with porous borders and uncontrolled animal movement makes strain characterisation a prerequisite for effective immunisation. Using a cross-sectional sampling and molecular epidemiology design, epithelial tissue and oropharyngeal samples were collected from 280 clinically affected cattle across outbreaks reported in the six states between 2022 and 2024. Serotyping was performed by sandwich ELISA, followed by partial VP1 gene sequencing for phylogenetic analysis. Linkage between strain lineages and animal movement routes was investigated through network analysis of livestock trade data. The study fills a critical gap in FMDV diversity data for the North East zone. Findings revealed co-circulation of serotypes O (56%), A (27%), and SAT-2 (17%), with phylogenetic analysis indicating importation of serotype O strains via cross-border cattle movement from the Lake Chad Basin area. The study recommends regional polyvalent FMDV vaccine deployment, systematic restriction of cross-border cattle movement without vaccination certification, and establishment of a North East FMDV sentinel surveillance network. Keywords: foot-and-mouth disease, serotyping, phylogenetic analysis, North East Nigeria, transboundary disease.