Genomic Surveillance of Influenza A H3N2 Variants and Antiviral Resistance in South West Nigeria

Influenza A H3N2 is a major cause of seasonal influenza morbidity, and oseltamivir resistance surveillance is a global priority given the clinical reliance on neuraminidase inhibitors for treatment. In South West Nigeria, H3N2 strain diversity and oseltamivir resistance patterns are largely uncharacterised due to limited influenza genomic surveillance infrastructure. This study performs genomic surveillance of influenza A H3N2 circulating in South West Nigeria and screens for antiviral resistance markers. Nasopharyngeal swabs from 500 influenza-positive patients at sentinel sites in Lagos, Ogun, Oyo, and Osun states collected over two influenza seasons will be subjected to influenza A H3N2 confirmation by RT-PCR and hemagglutinin inhibition assay. H3N2-confirmed samples will undergo full-genome next-generation sequencing, and phylogenetic analysis using BEAST and IQ-TREE will reconstruct evolutionary relationships and estimate evolutionary rates. Neuraminidase sequences will be screened for oseltamivir resistance mutations (H275Y equivalent). Antigenic cartography will compare circulating strains against current northern and southern hemisphere vaccine strains. South West Nigeria contributes a large febrile patient population to potential influenza transmission networks, yet its contribution to WHO FLUNET is minimal. Findings will characterise H3N2 evolutionary dynamics in South West Nigeria and provide actionable antiviral resistance data to clinical microbiologists and public health agencies in the zone. Keywords: influenza H3N2, genomic surveillance, oseltamivir resistance, South West Nigeria, phylogenetics