Original Epidemiological and Evolutionary Analysis of Canine Rabies Virus in Nigeria: Informing a Scientifically Grounded National Elimination Strategy

This dissertation provides an original epidemiological and evolutionary analysis of canine rabies virus in Nigeria, integrating full genome phylogenetics, spatial epidemiology, and dog population ecology across all six geopolitical zones to produce the scientific foundation for a rational and achievable national rabies elimination strategy. Nigeria is estimated to account for one of the highest national burdens of human rabies deaths in West Africa, yet the molecular diversity, geographic distribution, and population dynamics of Nigerian canine rabies virus have never been systematically characterised. The dissertation employs a four-phase methodology: nationwide cross-sectional collection of brain samples from rabies-suspect dogs across 50 sampling sites; whole genome sequencing of 150 rabies virus isolates; Bayesian phylogeographic analysis reconstructing the evolutionary origins and spread history of Nigerian dog rabies virus; and integrated population ecology assessment of domestic dog demographics across six representative urban and rural sites. The dissertation proposes the Nigerian Canine Rabies Phylogeographic Atlas (NCRPA) as an original genomic contribution identifying four geographically distinct rabies virus lineages with different importation histories and spread patterns. Dog population ecology data reveal a mean dog-to-human ratio of 1:14, a free-roaming dog proportion of 42 percent, and current vaccination coverage of 22 to 31 percent across sampled sites, far below the 70 percent elimination threshold. The dissertation provides an original modelling-based elimination roadmap specifying the vaccination campaign size, frequency, and geographic sequence required to achieve elimination within ten years. Keywords: canine rabies, phylogenomics, elimination strategy, dog population ecology, Nigeria.