Characterising the epidemiology of influenza A viruses at the swine-human interface: Study Protocol of the PigFluCam+ project in Cambodia (Preprint)

<sec> <title>UNSTRUCTURED</title> Influenza A viruses are a significant cause of global morbidity, mortality and economic losses. Swine are considered an important host for pandemic emergence; however, knowledge on the ecology and evolution of swine influenza viruses in relation to pig production and exchange systems is limited. The PigFluCam+ project was first initiated in 2019 as a One Health-focussed research collaboration between public and animal health stakeholders. The primary goal of the project was to characterise the risk of zoonotic influenza arising from the rapidly changing pig sectors in Cambodia. This paper outlines the detailed methods and approaches used by the project, serving as a resource for future research initiatives with similar aims. These approaches consist of systematic sample collections and survey studies. Serological and virological investigations were conducted over a two-year period through nasal swab and blood sampling in pigs at multiple slaughterhouses across various provinces. Cross-sectional surveys were conducted to characterise pig production practices and trading networks. In parallel, a cohort study was carried out involving households with and without occupational exposure to live pigs to compare the seroprevalence of influenza A viruses among different swine-associated occupational groups. Despite disruptions caused by the COVID-19 pandemic and the introduction of African Swine Fever into the region, the project has successfully generated a wealth of data on the epidemiology of influenza at the human-swine interface and provided phylogenetic inferences into the evolutionary and transmission dynamics of swine influenza viruses in pigs. This project has developed surveillance protocols and modern technologies for establishing active zoonotic disease surveillance. These efforts support the region’s capability to effectively identify zoonotic pathogens and enhance the prediction and response to zoonotic outbreaks and pandemic risk associated with pig production systems in the Lower Mekong region. </sec>