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

The Spread of H5N1, H7N9, and H5N6 in China. The hemagglutinin (HA) gene phylogenies of AIV subtypes H5N1, H7N9, and H5N6 in China exhibit frequent virus lineage movements among locations, indicating substantial geographic mixing (SI Appendix, Fig. S1 ). Taking H5N1 as an example, a discrete phylogeographic analysis of HPAI H5N1 in Chinese poultry revealed many wellsupported viral lineage movements among provinces (as previously noted in ref. 16 ). In addition to this general pattern, we further observed that lineage movements occur between pairs of provinces that are adjacent or close (Fig. 1A) . Consequently, lineage transition rates between locations are inversely related to distance, suggesting a more geographically continuous process of virus spread in poultry in China (Fig. 1B) . This pattern is consistent for all three AIV subtypes (Fig. 1) . However, some longdistance movement events were also observed, notably to or from the northern provinces of Jilin, Xinjiang (H5N1 and H7N9), and Ningxia (H7N9 only). Since virus sequences are unavailable for many of the provinces that directly neighbor Jilin, Xinjiang, and Ningxia, it is possible that AIV is present but underreported in these intermediate locations, and that virus movements occur over shorter distances.