Origin, Spread, and Clinical Implications of Human Papillomavirus Genotype Diversity Among Nigerian Women: A Phylogeographic and Population-Level Investigation

Human papillomavirus (HPV) genotype diversity determines vaccine coverage effectiveness, yet the phylogeographic origin, inter-regional spread patterns, and clinical implications of HPV genotype diversity across Nigerian women have never been investigated at national scale. This dissertation conducts a phylogeographic and population-level investigation of HPV genotype diversity among Nigerian women. A nationwide cross-sectional study collected cervical samples from 600 women at gynaecology and sexual health clinics across six geopolitical zones (100 per zone). HPV DNA was detected and genotyped using the Linear Array HPV Genotyping Test. Full genome sequencing was performed on 120 selected isolates. Phylogenetic analysis reconstructed genotype evolutionary origins using BEAST2 Bayesian molecular clock methods. Cervical cytology provided disease association context. Overall HPV prevalence was 31.2 percent, with genotype distribution showing significant geographic heterogeneity. HPV 16 dominated in the South West and South South zones, while HPV 35 and HPV 45 were disproportionately prevalent in the North East and North West. Phylogeographic reconstruction traces HPV 16 lineage A to European ancestry and HPV 35 lineage B to West African origin, with indigenous lineage dominance in northern populations. Bivalent and quadrivalent vaccines would cover only 58 percent of high-risk HPV genotypes detected in the North, compared to 74 percent in the South. The dissertation provides the first national phylogeographic HPV atlas for Nigeria and demonstrates that vaccine genotype coverage is geographically heterogeneous, supporting nonavalent vaccine prioritisation. Keywords: HPV genotype diversity, phylogeography, Nigeria, cervical cancer, vaccine coverage