Sean G. Young, Margaret Carrel, Andrew Kitchen, George P. Malanson, James Tamerius, Mohamad Ali, Ghazi Kayali

First introduced to Egypt in 2006, H5N1 highly pathogenic avian influenza has resulted in the death of millions of birds and caused over 350 infections and at least 117 deaths in humans. After a decade of viral circulation, outbreaks continue to occur and diffusion mechanisms between poultry farms remain unclear. Using landscape genetics techniques, we identify the distance models most strongly correlated with the genetic relatedness of the viruses, suggesting the most likely methods of viral diffusion within Egyptian poultry. Using 73 viral genetic sequences obtained from infected birds throughout northern Egypt between 2009 and 2015, we calculated the genetic dissimilarity between H5N1 viruses for all eight gene segments. Spatial correlation was evaluated using Mantel tests and correlograms and multiple regression of distance matrices within causal modeling and relative support frameworks. These tests examine spatial patterns of genetic relatedness, and compare different models of distance. Four models were evaluated: Euclidean distance, road network distance, road network distance via intervening markets, and a least-cost path model designed to approximate wild waterbird travel using niche modeling and circuit theory. Samples from backyard farms were most strongly correlated with least cost path distances. Samples from commercial farms were most strongly correlated with road network distances. Results were largely consistent across gene segments. Results suggest wild birds play an important role in viral diffusion between backyard farms, while commercial farms experience human-mediated diffusion. These results can inform avian influenza surveillance and intervention strategies in Egypt.