Phylodynamics of African Swine Fever Virus in Nigeria: Reconstructing Transmission History, Evolutionary Drivers, and Vaccination Target Sites

This dissertation provides an original phylodynamic reconstruction of African swine fever virus (ASFV) evolution and transmission history in Nigeria, integrating whole genome sequencing, Bayesian evolutionary analysis, and livestock trade network data to characterise the drivers of ASFV spread and identify rational targets for vaccine and control strategies. ASFV causes 100 percent fatality in naive pig populations and has devastated pig production across Nigeria for decades, yet no Nigerian phylodynamic study has been conducted, creating a profound gap in understanding the molecular and spatial epidemiology of the Nigerian ASFV lineage. The dissertation employs a longitudinal molecular epidemiology design spanning 2020 to 2024, collecting ASFV-positive samples from pig outbreaks across all six geopolitical zones. Whole genome sequencing using Illumina and Oxford Nanopore platforms is performed on 120 isolates. Bayesian phylodynamic analysis using BEAST2 reconstructs the time-calibrated evolutionary history and migration patterns of Nigerian ASFV strains. Recombination analysis, positive selection analysis, and structural homology modelling of candidate vaccine antigen proteins are conducted. Network analysis of pig trade routes identifies transmission super-spreader nodes. The dissertation proposes an original evolutionary framework termed the Nigerian ASFV Phylodynamic Atlas, identifying three primary genomic clusters with distinct evolutionary trajectories and geographic spread patterns. Original contributions include the ASFV whole genome reference panel, the phylodynamic atlas, and a rational vaccine antigen target shortlist based on positive selection analysis. Keywords: African swine fever virus, phylodynamics, whole genome sequencing, vaccine targets, Nigeria.