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

We performed two subsequent analyses to explore whether the LPTCs explain the dissemination of AIV in China. First, we examined the estimated among-province lineage transition rates (i.e., those reported in Fig. 1 for all three AIV subtypes). We found that transition rates between provinces in the same LPTC (H5N1 mean = 1.08; H5N6 mean = 1.06; H7N9 mean = 1.07) were on average higher than those for provinces in different LPTCs (H5N1 mean = 0.98; H5N6 mean = 0.98; H7N9 mean = 0.97). Second, we conducted a randomization test in which locations (i.e., provinces) were randomly assigned to five communities (with the same number of members as our empirical LPTCs). For each randomly generated community (RGC), we calculated the mean within-and among-community lineage transition rates between locations (as above). This randomization procedure was repeated 1,000 times. As expected, in the randomly generated communities there was no difference between the mean transition rate for location pairs in the same community versus the mean transition rate for location pairs in different communities (Fig. 5) . The results in Fig. 5 demonstrate that the LPTC in Fig. 3 does indeed contribute to the pattern of AIV lineage movement in China.