Molecular Characterization and Phylogenetic Analysis of Foot-and-Mouth Disease Virus in Nigeria

Abstract Foot-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, and 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 to be having FMD based on clinical manifestation from December 2023 to November 2024 in representative states of four geopolitical zones in Nigeria. RNA Extraction, molecular detection for all known serotypes (O, A, C, SAT 1, SAT 2, SAT 3 and Asia 1), molecular serotyping, nucleotide sequencing, phylogenetic and other deep bioinformatic analyses were carried out. Ethical approval for the study was obtained from the ethical review board at National Veterinary Research Institute (NVRI), Vom, Nigeria. Out of the 298 epithelial tissue samples extracted and amplified, a total of 73 samples were positive with 44 (60% of the positive samples) used for further analysis. Serotypes A, C and Asia 1 were detected from six samples which underwent sequencing and received accession numbers PX872161 to PX872166. This study reports a recombinant isolate (PX872163) that shared 97.3% and 93.1% nucleotide identity with PX872165, a major parent and PX872166, a minor parent respectively. This work provides evidence for the circulation of a recombinant FMDV serotype A in Nigeria and proposes that immune pressure arising from persistent viral infections, together with genetic recombination events, may be important drivers of FMDV evolution in the country.