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

Sequence Data. We accessed HA gene segment sequences of H5N1 AIVs sampled from 1996 to 2014 from the GenBank database, and obtained HA gene segment sequences for H7N9 and H5N6 AIVs sampled from 2013 to 2017 from the Global Initiative on Sharing All Influenza Data (GISAID) database. In order to focus on virus dissemination among poultry, it was first necessary to exclude from the viral phylogenies those chains of AIV transmission that derive from interspecies transmission events and occur in wild bird populations. This was achieved by reconstructing the movement of AIV lineages between wild birds and domestic poultry using a range of sampling and analysis strategies. AIV sequences belonging to phylogenetic clusters that were determined to represent transmission wholly or predominately in or from wild birds were removed from the datasets (SI Appendix, Fig. S7 ), which means that poultry AIV sequences found within clades dominated by wild bird AIV sequences were also excluded. Consequently, only those lineages determined to be circulating in domestic poultry populations were retained for further analysis. In order to ameliorate potential sampling biases, we subsequently randomly subsampled these datasets in a stratified manner to create a more equitable spatiotemporal distribution of AIV sequences (SI Appendix, Fig. S11) . A strong phylogenetic temporal structure was detected in all datasets (SI Appendix, Fig. S12 ).