Genomic Surveillance of Avian Influenza Viruses at the Poultry-Wild Bird Interface in Nigeria: Temporal and Spatial Evolution

Avian influenza viruses at the poultry-wild bird interface undergo rapid evolutionary change, and genomic surveillance is essential for understanding strain diversity, reassortment dynamics, and pandemic preparedness. This study conducted comprehensive genomic surveillance of avian influenza viruses at poultry-wild bird interfaces across Nigeria's major flyways and commercial poultry zones over a three-year period from 2021 to 2024. Cloacal and oropharyngeal swabs were collected from 800 migratory and resident wild birds at wetland sites and from 600 domestic poultry from neighboring commercial and backyard farms across nine states. Samples were tested by real-time reverse transcriptase PCR for influenza A, and positives were subjected to whole-genome sequencing on the Illumina MiSeq platform. Phylogeographic analysis used Bayesian approaches to characterize spatial spread and reassortment events. A total of 68 avian influenza virus genomes were obtained, comprising subtypes H5N1, H5N8, H9N2, and novel H5N6 detections. Genomic analysis revealed multiple reassortment events between wild bird-derived and poultry-adapted strains, particularly in H5N1 hemagglutinin gene segments. Spatiotemporal analysis identified Niger Delta wetlands and Lake Chad basin fringe areas as primary introduction corridors. H9N2 strains circulating in commercial flocks showed mammalian adaptation markers in the polymerase genes. The study provides the most genomically comprehensive avian influenza surveillance dataset from Nigeria, with direct implications for human pandemic preparedness and national poultry health policy. Keywords: avian influenza, genomic surveillance, wild birds, Nigeria, reassortment