Spatiotemporal Dynamics of Malaria Parasite Population Structure and Transmission Networks Across Nigeria Using High-Resolution Genomics

High-resolution genomic approaches applied to large-scale malaria parasite collections offer unprecedented power to reconstruct transmission networks, identify importation events, and characterise parasite population dynamics at national scale. This doctoral study reconstructed the spatiotemporal transmission network dynamics of P. falciparum across Nigeria using genome-wide single nucleotide polymorphism data. Dried blood spot samples from 960 malaria-positive patients were collected from 32 sites spanning all six geopolitical zones over three years. Genome-wide genotyping was performed using a validated 2,000 SNP molecular inversion probe panel. Identity-by-descent analysis, relatedness networks, and migration modelling using EEMS software characterised parasite gene flow. Temporal trends in genetic diversity were assessed across sampling years. High overall parasite diversity (mean He = 0.87) reflected intense ongoing transmission. Identity-by-descent analysis identified 114 closely related parasite pairs, predominantly within geopolitical zones, consistent with local transmission dominance. Inter-zonal parasite movement was concentrated along major road corridors, particularly the Lagos-Kano and Port Harcourt-Enugu axes. A significant decline in diversity at northern sites between 2021 and 2024 was consistent with population contraction under intensified intervention pressure. Importation from Cameroon was genomically inferred for three Northeast zone isolates. This study delivers the most comprehensive P. falciparum genomic transmission map of Nigeria to date, providing an actionable evidence base for spatially targeted intervention intensification. Keywords: Plasmodium falciparum, population genomics, transmission networks, gene flow, Nigeria.