This study was supported by the Special National Project on Research and Development of Key Biosafety Technologies (2016YFC1201900, 2016YFC1200101) and the National Natural Science Foundation of China (Grants 81672057, 81611130073). E.C.H. and M.S. are funded by an ARC Australian Laureate Fellowship to E.C.H. (FL170100022). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank students at the Zoonosis branch of the China CDC, especially W.-C. Wu, J.-W. Shao, C.-X. Li, J.-J. Guo and K.-L. Song for assistance with virus and host sequence confirmation, and we thank B. Yu for help with the collection of animal samples. We acknowledge the University of Sydney high-performance computing (HPC) service at The University of Sydney for providing resources that have contributed to the research results reported within this paper

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Nature thanks A. Rambaut and M. Worobey for their contribution to the peer review of this work.