An Original Investigation of the Virome Composition and Dynamics of Migratory Birds as Vectors of Novel Influenza Viruses Across Nigeria’s Ecological Transition Zones

Migratory birds traversing Nigeria's ecological transition zones from the Sahel to the coastal wetlands constitute potential vectors for novel influenza A viruses with pandemic potential, yet systematic virological surveillance of avian influenza in Nigerian migratory bird populations represents an unaddressed gap in global pandemic preparedness. This dissertation investigates the virome composition and influenza virus dynamics in migratory bird populations at key resting and foraging sites across Nigeria's ecological zones, making original contributions to avian virology and pandemic risk surveillance science. A three-year longitudinal surveillance programme was conducted at six bird banding and sampling stations in the North West Sahel zone (Katsina), North Central plateau (Plateau State), and South South coastal mangroves (Bayelsa). Cloacal and tracheal swabs from 800 banded migratory birds across 20 species were processed by avian influenza universal RT-PCR, subtype-specific PCRs for H5, H7, and H9 haemagglutinin subtypes, and next-generation sequencing for virome characterisation. Low pathogenicity avian influenza (LPAI) viruses were detected in 8.3 percent of samples, with H9N2 and H1N1 subtypes predominant. Virome analysis identified 14 novel RNA viral sequences with partial homology to paramyxoviruses and coronaviruses in addition to influenza. Migration timing correlated significantly with seasonal LPAI prevalence peaks. The dissertation establishes the first longitudinal avian influenza surveillance dataset for Nigerian migratory bird populations and proposes a Nigeria-specific pandemic risk stratification model. Keywords: avian influenza, migratory birds, virome, pandemic surveillance, Nigeria