Evolutionary Dynamics and Recombination Architecture of Lassa Virus Across the Nigeria-Cameroon-Niger Border Region: A Multi-Country Genomic Investigation

Lassa virus (LASV) evolution in West Africa is characterized by rapid mutation, geographic structuring, and sporadic intra- and inter-lineage recombination events that complicate phylogenetic inference and immunogen design. The tri-border region spanning Northwest Nigeria, Niger, and Cameroon represents an undercharacterized LASV ecological zone where Mastomys natalensis reservoir populations and human spillover dynamics are shaped by cross-border livestock trade and population movement. This dissertation presents a multi-country genomic investigation of LASV evolutionary dynamics and recombination architecture in this frontier zone, providing original characterization of forces driving LASV diversification at the Nigeria-Cameroon-Niger interface. Full LASV genome sequences were generated from 85 confirmed clinical cases and 62 Mastomys rodent reservoir specimens collected in collaboration with health authorities across Zamfara State (Nigeria), Tahoua (Niger), and Adamaoua (Cameroon) over a 36-month field collection period. Sequencing employed viral capture enrichment followed by Illumina sequencing. Phylogenetic Bayesian molecular clock analysis was conducted in BEAST2 with tip-dated models. Recombination events were analyzed using RDP5, GARD, and Bootscan methods. Selective pressure analysis applied site-specific dN/dS models in HyPhy. Bayesian phylogeographic analysis reconstructed ancestral geographic migration routes. Fourteen high-confidence recombination events were identified in the S-segment GPC gene, with nine being novel, two involving inter-lineage II to III recombination. Bayesian dating estimated these recombination events occurred within the last 25 years, correlating with increased cross-border livestock movement in the study region. Selective sweep signatures were detected at GPC residues 255-260, overlapping the GP1-GP2 cleavage site, in Nigerian lineage II isolates. These original discoveries advance understanding of LASV macro-evolutionary forces at West Africa's most complex viral hemorrhagic fever frontier zone. Keywords: Lassa virus, evolutionary dynamics, recombination, phylogeography, tri-border region.