Assessing the role of live poultry trade in community-structured transmission of avian influenza in China

Yang, Qiqi; Zhao, Xiang; Lemey, Philippe; Suchard, Marc A.; Bi, Yuhai; Shi, Weifeng; Liu, Di; Qi, Wenbao; Zhang, Guogang; Stenseth, Nils Chr.; Pybus, Oliver G.; Tian, Huaiyu

Here we combine poultry trade movements (inferred using a gravity model) in China with large-scale analysis of AIV genome sequences in order to reconstruct hidden virus transmission routes and test the hypothesis that the live poultry trade in China affects the spread of HP AIV in the country. We reconstruct the estimated transmission dynamics in China of HPAI H5N1 from 1996, and compare them with the dynamics of other, more recently emerged, HP AIV lineages. We find that AIV transmission patterns can be explained by a national-level community structure of the poultry trade network in China. Our results provide insights into the large-scale structure and repeatability of AIV lineage emergence in Asia and may be useful in predicting the emergence of other AIV strains in other regions.