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

In order to assess whether the transmission of AIV lineages belonging to all three subtypes are indeed associated with poultry trade communities in China, we undertook new discrete Bayesian phylogenetic analyses of the HA sequences belonging to AIV subtypes H5N1, H7N9, and H5N6. In these phylogeographic analyses, sequence locations were encoded using the five LPTCs. The LPTCs recapitulate important events in the phylogenetic history of all three subtypes (Fig. 4) . The H5N1 subtype initially became enzootic in southern China (LPTC-1) (19) , and major clades subsequently spread to southeastern China (LPTC-2) and midnorthern China (LPTC-4) (20) (Fig. 4A) . A similar pattern of community-structured circulation was observed for H7N9 and H5N6 (Fig. 4 B and C) . Originating from southeastern China (LPTC-2), H7N9 viruses diverged into two monophyletic groups, the Yangtze River Delta lineage and the Pearl River Delta lineage (21) , which coincide with LPTC-2 and LPTC-1 in our LPTC network. H7N9 AIV has circulated in these regions for more than three years, causing epidemic waves I through IV (22) . However, in epidemic wave V, H7N9 was found to have spread from LPTC-1 to all other LPTCs in China (22) . For H5N6, most monophyletic groups of viruses have circulated regionally within LPTC-1 and LPTC-2 (7), although AIV lineage movements among LPTCs are increasing (Fig. 4C) .