Role of Bats as Reservoirs of Coronaviruses in Rainforest Ecosystems of Cross River State

Bats are the natural reservoir hosts of diverse coronaviruses, some of which have pandemic potential as demonstrated by the SARS-CoV, MERS-CoV, and SARS-CoV-2 spillover events. Cross River State in South South Nigeria harbours one of Nigeria's most biodiverse bat communities within its contiguous rainforest ecosystems, yet systematic coronavirus surveillance in these populations is non-existent. This study characterises the diversity and prevalence of coronaviruses in bat populations across three forest sites in Cross River State: Afi Mountain Wildlife Sanctuary, Mbe Mountains Community Forest, and Boshi Extended Forest. Bats will be captured using mist nets over four seasonal trapping sessions. Faecal swabs and intestinal tissue samples will be collected from morphologically identified bats and subjected to pan-coronavirus RT-PCR using degenerate primers targeting the RdRp gene. Positive samples will undergo full-length genome sequencing using nanopore sequencing. Phylogenetic analysis will classify detected coronaviruses into genera and assess genetic similarity to known human-infective strains. Bat species-specific carriage rates will be reported. The absence of bat coronavirus surveillance in Nigeria's highly biodiverse Cross River forests represents a significant gap in West African emerging virus preparedness. Findings will generate foundational bat coronavirus ecological data for Cross River State and provide sequence information essential for risk assessment of potential human spillover events. Keywords: bat coronaviruses, reservoir surveillance, Cross River State, rainforest, zoonotic spillover