Avian Influenza

I started a series of studies, some ongoing, investigating avian influenza. Several subtypes of avian influenza continue to pose credible pandemic threats, and my work attempted to assist pandemic preparedness efforts, with particular emphasis on the country of Egypt. Egypt has emerged as a hotspot of avian influenza activity in both humans and poultry.


I lead a research team that developed new geospatial disease modeling techniques to predict areas with increased risk of co-infection, a precursor to pandemic emergence. In this project I examined the ecological niche of competing virus subtypes (H5N1 and H9N2) in northern Egypt, and predicted locations with high co-infection potential.

Young, S.G., Carrel, M., Malanson, G.P., Ali, M.A., & Kayali, G. (2016). Predicting avian influenza co-infection with H5N1 and H9N2 in northern Egypt. International Journal of Environmental Research and Public Health, 13(9), 886. doi: 10.3390/ijerph13090886

Many important questions about the ecology and epidemiology of the avian influenza virus were contested, including the role of wild waterfowl in spreading the disease between poultry flocks and the relative importance of commercial vs backyard farms. We used landscape genetics techniques to investigate diffusion mechanisms, providing compelling genetic evidence that traditional backyard poultry farms are being infected by wild birds, while commercial farms are spreading the virus via human travel.

Young, S.G., Carrel, M., Kitchen, A., Tamerius, J., Malanson, G.P., Ali, M.A., & Kayali, G. (2017). How’s the flu getting through? Landscape genetics suggests both humans and birds spread H5N1 in Egypt. Infection, Genetics and Evolution, 49, 293-299. doi: 10.1016/j.meedgid.2017.02.005

A third study identified areas in Egypt where key viral mutations that increase pandemic risk are emerging most frequently. I was the lead investigator for all of the above, which were part of my doctoral dissertation. My work in this area is ongoing.

Young S.G., Kitchen A., Kayali G., & Carrel M. (2018). Unlocking pandemic potential: prevalence and spatial patterns of key substitutions in avian influenza H5N1 in Egyptian isolates. BMC Infectious Diseases, 18(1), 314. doi: 10.1186/s12879-018-3222-6

As a co-investigator I also participated in a multi-disciplinary investigation of feral swine exposure to influenza in the US, finding both avian and swine viruses are infecting feral swine.

Martin, B.E., Carrel, M., Baroch, J.A., Young, S.G., Schmit, B., Nolting, J., Yoon, K.-J., Lutman, M.W., Pedersen, K., Bowman, A., Slemons, R., Smith, D.R., DeLiberto, T., & Wan, X.-F. (2017). US feral swine were exposed to both avian and swine influenza A viruses. Applied and Environmental Microbiology, 01346-17. doi: 10.1128/AEM.01346-17