A.E.G., F.R.S., and J.N. are supported by funding from Google (OICB150153). A.S. is supported by funding from the Bill & Melinda Gates Foundation (OPP1106427, 1032350). C.L. is supported by funding from the Belgian Science Policy (SR/00/304). A.J.T. is supported by funding from NIH/NIAID (U19AI089674), the Bill & Melinda Gates Foundation (OPP1106427, 1032350), and the RAPIDD program of the Science and Technology Directorate, Department of Homeland Security, and the Fogarty International Center, National Institutes of Health. S.I.H. is funded by a Senior Research Fellowship from the Wellcome Trust (#095066), and grants from the Bill & Melinda Gates Foundation (OPP1119467, OPP1106023 and OPP1093011). S.I.H. would also like to acknowledge funding support from the RAPIDD program of the Science & Technology Directorate, Department of Homeland Security, and the Fogarty International Center, National Institutes of Health. H.Y. is supported by the National Science Fund for Distinguished Young Scholars (No. 81525023), Ministry of Science and Technology of China (2012 ZX10004-201, 2014BAI13B05), NIH (U19 AI51915) and the Harvard Center for Communicable Disease Dynamics (U54 GM088558). X.Y. is supported by the Natural Science Foundation of China (41430637; 41329001), and Chinese Ministry of Education (13JJD790008). This work forms part of the WorldPop Project (www.worldpop.org). We thank Dr Yilan Liao from the Institute of Geographic Sciences and Natural Resources Research of Chinese Academy of Sciences and Dr Xiaojuan Jiang from the Gansu Center for Disease Control and Prevention in data collections. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.