Molecular Epidemiology of Influenza A Virus in Pigs at Slaughterhouses in Ibadan, Oyo State

Pigs serve as mixing vessels for influenza viruses, facilitating reassortment events that can generate pandemic strains with human-infective potential. This study investigates the molecular epidemiology of influenza A virus (IAV) in pigs slaughtered at abattoirs in Ibadan, Oyo State, South West Nigeria, contributing to one-health surveillance of zoonotic influenza. Nasal swabs and lung tissue samples will be collected from 150 pigs at the Bodija Municipal Abattoir over a four-month period. Samples will undergo RNA extraction followed by RT-PCR targeting the IAV matrix gene, with positive samples subjected to haemagglutinin and neuraminidase subtyping. Phylogenetic analysis will be performed to determine the genetic relatedness of detected strains to previously characterised African and global isolates. Abattoir workers will also be recruited for paired serological testing to assess evidence of zoonotic transmission. Prior studies from Nigeria's South West and North Central zones have detected H1N1 and H3N2 strains in pigs, with some sequences showing avian-origin gene segments. Findings will contribute to the national influenza surveillance network operated through the Nigeria Centre for Disease Control and provide critical data on swine-origin influenza activity in a major abattoir servicing West Africa's most populous city. This study strengthens the one-health framework for emerging viral disease prevention in Nigeria. Keywords: influenza A virus, swine influenza, molecular epidemiology, slaughterhouse, Ibadan