Cross-species transmission of viruses from wildlife animal reservoirs poses a marked threat to human and animal health1. Bats have been recognized as one of the most important reservoirs for emerging viruses and the transmission of a coronavirus that originated in bats to humans via intermediate hosts was responsible for the high-impact emerging zoonosis, severe acute respiratory syndrome (SARS)2,3,4,5,6,7,8,9,10. Here we provide virological, epidemiological, evolutionary and experimental evidence that a novel HKU2-related bat coronavirus, swine acute diarrhoea syndrome coronavirus (SADS-CoV), is the aetiological agent that was responsible for a large-scale outbreak of fatal disease in pigs in China that has caused the death of 24,693 piglets across four farms. Notably, the outbreak began in Guangdong province in the vicinity of the origin of the SARS pandemic. Furthermore, we identified SADS-related CoVs with 96–98% sequence identity in 9.8% (58 out of 591) of anal swabs collected from bats in Guangdong province during 2013–2016, predominantly in horseshoe bats (Rhinolophus spp.) that are known reservoirs of SARS-related CoVs. We found that there were striking similarities between the SADS and SARS outbreaks in geographical, temporal, ecological and aetiological settings. This study highlights the importance of identifying coronavirus diversity and distribution in bats to mitigate future outbreaks that could threaten livestock, public health and economic growth.
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We thank S.-B. Xiao for providing pig cell lines, P. Burbelo for providing the luciferase immunoprecipitation system vector and L. Zhu for enabling the rapid synthesis of the S gene; the WIV animal facilities; J. Min for help with the preparation of the immunohistochemistry samples; and G.-J. Zhu and A. A. Chmura for assistance with bat sampling. This work was jointly supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDPB0301) to Z.-L.S., China Natural Science Foundation (81290341 and 31621061 to Z.-L.S., 81661148058 to P.Z., 31672564 and 31472217 to J.-Y.M., 81572045, 81672001 and 81621005 to Y.-G.T.), National Key Research and Development Program of China (2015AA020108, 2016YFC1202705, AWS16J020 and AWS15J006) to Y.-G.T.; National Science and Technology Spark Program (2012GA780026) and Guangdong Province Agricultural Industry Technology System Project (2016LM1112) to J.-Y.M., State Key Laboratory of Pathogen and Biosecurity (SKLPBS1518) to Y.-G.T., Taishan Scholars program of Shandong province (ts201511056 to W.-F.S.), NRF grants NRF2012NRF-CRP001–056, NRF2016NRF-NSFC002-013 and NMRC grant CDPHRG/0006/2014 to L.-F.W., Funds for Environment Construction & Capacity Building of GDAS’ Research Platform (2016GDASPT-0215) to LBZ, United States Agency for International Development Emerging Pandemic Threats PREDICT project (AID-OAA-A-14-00102), National Institute of Allergy and Infectious Diseases of the National Institutes of Health (Award Number R01AI110964) to P.D. and Z.-L.S.
Nature thanks C. Drosten, G. Palacios and L. Saif for their contribution to the peer review of this work.