Evolutionary Dynamics and Cross-Species Transmission Potential of Bat-Borne Coronaviruses in Nigeria’s Guinea Savanna and Forest Transition Zones

The emergence of SARS-CoV-2 underscored the pandemic potential of bat-borne coronaviruses and exposed fundamental gaps in surveillance of these viruses at ecologically diverse wildlife-human interfaces. Nigeria's Guinea Savanna and Forest Transition Zones span the North Central and South West states and represent understudied bat diversity hotspots. This study characterises the evolutionary dynamics and cross-species transmission potential of bat-associated coronaviruses in these two ecozones. Longitudinal bat surveillance across eight sites in Kwara, Kogi, and Oyo states over three years will employ mist netting and acoustic bat detection to sample 15 bat species. Faecal, rectal, and urine samples will undergo pan-coronavirus RT-PCR and next-generation sequencing for full-genome characterisation. Receptor binding domain sequences will be structurally modelled using AlphaFold2 to predict binding affinity to ACE2 orthologues of humans and domestic animals. Bayesian phylodynamic analysis will estimate cross-species transmission rates and calculate spillover risk scores for detected novel viruses. Recombination analysis will use RDP5 to detect inter-strain recombination events. This study develops an original risk-stratified coronavirus emergence framework tailored to Nigerian ecological contexts, contributing theoretical advances in spillover risk modelling applicable to West African bat communities. Findings will provide the first comprehensive bat coronavirus evolutionary dataset from Nigeria's ecotone zones, informing national biosurveillance priorities. Keywords: bat coronaviruses, cross-species transmission, evolutionary dynamics, Nigeria, pandemic risk