Molecular characterization and phylogenetic analysis of foot-and-mouth disease virus in Nigeria

Foot-and-Mouth Disease (FMD) is a viral disease that affects various cloven-hoofed animals, causing huge economic losses in the livestock sector worldwide. Foot-and-Mouth Disease virus (FMDV), the causative agent of FMD, is recognized to have seven antigenically and immunogenically distinct serotypes, namely, A, O, C, Asia 1, SAT 1, SAT 2, and SAT 3. There are considerable antigenic and genetic diversities within each serotype, resulting in numerous subtypes. This study was aimed at providing updated information on the circulating FMDV strains in Nigeria. We collected 298 epithelial tissue samples aseptically from the oral cavity of cattle suspected of having FMD based on clinical manifestations from December 2023 to November 2024 in representative states of four geopolitical zones in Nigeria. RNA extraction, molecular detection, molecular serotyping, nucleotide sequencing, phylogenetic, and other deep bioinformatic analyses were carried out. Out of the 298 epithelial tissue samples extracted and amplified, a total of 73 (24.5%) samples were positive for FMDV, and 44 (60.3%) were further analyzed. Six out of the 44 samples were sequenced, which, after BLAST analysis, all yielded serotype A, based on VP1 sequences. Phylogenetic analysis placed the study sequences in a distinct cluster separate from the previously reported Nigerian strains, but showed that they evolved from the A/Africa genotype IV topotype. Our analysis also identified a recombinant isolate (PX872163) that shared 97.3% and 93.1% nucleotide identity with PX872165, a major parent, and PX872166, a minor parent, respectively. Five putative B-cell epitopes were identified within the VP1 capsid protein, two of which were localized within the loop regions. In addition, a novel epitope, ₁₆₂(RAESIQE)₁₆₈, was identified adjacent to the G-H loop. This study provides the first evidence for the circulation of a recombinant FMDV serotype A in Nigeria and suggests that both genetic recombination events and antibody-mediated immune pressure may be important drivers shaping FMDV evolution in the country.