Characterisation of Influenza Virus Strains Isolated from Febrile Patients in North East Nigeria During Three Consecutive Flu Seasons

Seasonal influenza causes substantial morbidity and mortality globally, yet influenza surveillance in northern Nigeria is limited to a small number of sentinel sites that do not adequately represent North East populations. Characterisation of locally circulating strains is essential for influenza vaccine composition recommendations applicable to Nigerian epidemiology. This study isolates and characterises influenza virus strains from febrile patients at sentinel facilities in Borno, Adamawa, and Gombe states over three consecutive influenza seasons (2022 to 2025). Nasopharyngeal swabs from 900 influenza-like illness patients meeting WHO case definitions will be collected and subjected to RT-PCR for influenza A and B typing, followed by virus isolation in MDCK cells for positive samples. Haemagglutinin and neuraminidase gene sequencing will be performed, and phylogenetic analysis will compare North East strains against northern hemisphere and WHO seasonal vaccine reference strains. Co-infection with SARS-CoV-2 and RSV will be assessed concurrently. The near-absence of North East Nigeria influenza strain data from WHO FluNet limits global knowledge of influenza strain circulation in this high-density population corridor. Findings will contribute to the WHO Global Influenza Surveillance and Response System and provide evidence for the NCDC to expand sentinel influenza surveillance to North East zone facilities. Keywords: influenza virus, strain characterisation, North East Nigeria, febrile illness, sentinel surveillance