The Role of Landscape and Ecological factors on the Spatiotemporal Evolution of Pandemic Swine Influenza in the United States

Keywords: infectious disease, landscape genetics, disease ecology, zoonotic diseases, spatial epidemiology, one health, influenza, human-animal interface, phylogeography
Abstract Type: Paper Abstract

Abstract

Influenza-A viruses (IAVs) present a considerable public health challenge, and contribute to substantial human and animal morbidity and mortality. In particular, pigs can serve as important intermediate host “mixing vessels” that generate pandemic IAV strains through genetic reassortment among avian, swine, and/or human IAVs. In the US, swine influenza viruses (SIVs) are endemic in pigs housed in concentrated animal feeding operations (CAFOs), and move across space and time based on the flow of pigs as part of coordinated production systems that often span multiple states. We geocoded over 1500 SIV sequences obtained from passive disease surveillance systems across 500 swine farms in mid-western US. We conducted a bayesian phylogeographic analysis to categorize distinct SIV strains and map their spatio-temporal movement across farms from 2015-2022. Subsequently, we ran a spatio-temporal bayesian model to examine the impact of factors such as farm level and neighborhood hog density, seasonality, humidity, population density, and proximity to poultry and feral hogs. Preliminary results suggest that while most SIV strains are clustered and move within closed hog production systems, there is some evidence of ‘isolation by distance’, suggesting that IAV may spillover into other nearby systems potentially due to swine worker movement and gaps in farm biosecurity measures. Additionally, population density, and proximity to poultry farms and feral hogs are associated with increased SIV evolution. These results enhance our understanding of the geographic context influencing SIV evolution and can boost IAV surveillance by targeting high-risk areas of enhanced SIV evolution at the human-animal interface.