📖 ABSTRACT/OVERVIEW
Characterising the spatiotemporal transmission networks of SARS-CoV-2 through Nigeria's major urban corridors, including the Lagos-Ibadan-Abuja axis, is fundamental to understanding how pandemic waves propagated and to modelling the effectiveness of non-pharmaceutical interventions (NPIs). Existing Nigerian COVID-19 modelling has relied on aggregate national data without capturing inter-city transmission dynamics. This study develops a spatiotemporal model of SARS-CoV-2 transmission networks and evaluates NPI effectiveness across Nigeria's primary urban corridors using integrated genomic, mobility, and epidemiological data. SARS-CoV-2 whole genome sequences from at least 800 Nigerian GISAID sequences will be combined with human mobility data from Meta Movement Maps and inter-city road transport records. Bayesian phylogeographic analysis using MASCOT will reconstruct transmission networks between Lagos, Ibadan, Abuja, Kano, and Port Harcourt. Time-stratified regression models will quantify the impact of school closures, movement restrictions, and mask mandates on transmission rate changes, using mobility data as a proxy for NPI compliance. Compartmental SEIR models parameterised with genomic and epidemiological inputs will simulate counterfactual epidemic trajectories under alternative NPI scenarios. This study makes an original methodological contribution by generating the first genomic mobility-integrated spatiotemporal model of COVID-19 transmission in Nigeria, providing a replicable framework for pandemic preparedness modelling applicable to future respiratory virus emergencies in West African urban systems. Keywords: SARS-CoV-2, spatiotemporal modelling, NPI effectiveness, Nigeria, phylogeography
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