Abstract

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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Change history

  • 05 April 2018

    The Extended Data Figures and Tables section originally published with this article was missing Tables 1–5. This has now been corrected.

References

  1. 1.

    Olival, K. J. et al. Host and viral traits predict zoonotic spillover from mammals. Nature 546, 646–650 (2017).

  2. 2.

    Guan, Y. et al. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science 302, 276–278 (2003).

  3. 3.

    Lau, S. K. et al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc. Natl Acad. Sci. USA 102, 14040–14045 (2005).

  4. 4.

    Li, W. et al. Bats are natural reservoirs of SARS-like coronaviruses. Science 310, 676–679 (2005).

  5. 5.

    Ge, X. Y. et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 503, 535–538 (2013).

  6. 6.

    He, B. et al. Identification of diverse alphacoronaviruses and genomic characterization of a novel severe acute respiratory syndrome-like coronavirus from bats in China. J. Virol. 88, 7070–7082 (2014).

  7. 7.

    Yang, X. L. et al. Isolation and characterization of a novel bat coronavirus closely related to the direct progenitor of severe acute respiratory syndrome coronavirus. J. Virol. 90, 3253–3256 (2016).

  8. 8.

    Wu, Z. et al. ORF8-related genetic evidence for Chinese horseshoe bats as the source of human severe acute respiratory syndrome coronavirus. J. Infect. Dis. 213, 579–583 (2016).

  9. 9.

    Wang, L. et al. Discovery and genetic analysis of novel coronaviruses in least horseshoe bats in southwestern China. Emerg. Microbes Infect. 6, e14 (2017).

  10. 10.

    Hu, B. et al. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathog. 13, e1006698 (2017).

  11. 11.

    Drosten, C. et al. Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N. Engl. J. Med. 348, 1967–1976 (2003).

  12. 12.

    Ksiazek, T. G. et al. A novel coronavirus associated with severe acute respiratory syndrome. N. Engl. J. Med. 348, 1953–1966 (2003).

  13. 13.

    Marra, M. A. et al. The genome sequence of the SARS-associated coronavirus. Science 300, 1399–1404 (2003).

  14. 14.

    Peiris, J. S. et al. Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet 361, 1319–1325 (2003).

  15. 15.

    Rota, P. A. et al. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300, 1394–1399 (2003).

  16. 16.

    Wang, L.-F. & Cowled, C. (eds) Bats and Viruses: A New Frontier of Emerging Infectious Diseases 1st edn (John Wiley & Sons, Hoboken, 2015).

  17. 17.

    Dong, N. et al. Porcine deltacoronavirus in mainland China. Emerg. Infect. Dis. 21, 2254–2255 (2015).

  18. 18.

    Sun, D., Wang, X., Wei, S., Chen, J. & Feng, L. Epidemiology and vaccine of porcine epidemic diarrhea virus in China: a mini-review. J. Vet. Med. Sci. 78, 355–363 (2016).

  19. 19.

    Lau, S. K. et al. Complete genome sequence of bat coronavirus HKU2 from Chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome. Virology 367, 428–439 (2007).

  20. 20.

    Chen, J. et al. Molecular epidemiology of porcine epidemic diarrhea virus in China. Arch. Virol. 155, 1471–1476 (2010).

  21. 21.

    Burbelo, P. D. et al. Serological diagnosis of human herpes simplex virus type 1 and 2 infections by luciferase immunoprecipitation system assay. Clin. Vaccine Immunol. 16, 366–371 (2009).

  22. 22.

    Gong, L. et al. A new bat-HKU2-like coronavirus in swine, China, 2017. Emerg. Infect. Dis. 23, 1607–1609 (2017).

  23. 23.

    Pan, Y. et al. Discovery of a novel swine enteric alphacoronavirus (SeACoV) in southern China. Vet. Microbiol. 211, 15–21 (2017).

  24. 24.

    Li, W. et al. Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature 426, 450–454 (2003).

  25. 25.

    Masters, P. S. & Perlman, S. in Fields Virology Vol. 2 (eds Knipe, D. M. & Howley, P. M.) 825–858 (Lippincott Williams & Wilkins, Philadelphia, 2013).

  26. 26.

    Raj, V. S. et al. Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC. Nature 495, 251–254 (2013).

  27. 27.

    Harlow, E. & Lane, D. Antibodies: A Laboratory Manual (Cold Spring Harbor Laboratory Press, New York, 1988).

  28. 28.

    Ren, W. et al. Difference in receptor usage between severe acute respiratory syndrome (SARS) coronavirus and SARS-like coronavirus of bat origin. J. Virol. 82, 1899–1907 (2008).

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Acknowledgements

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.

Reviewer information

Nature thanks C. Drosten, G. Palacios and L. Saif for their contribution to the peer review of this work.

Author information

Author notes

  1. These authors contributed equally: Peng Zhou, Hang Fan, Tian Lan.

Affiliations

  1. CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China

    • Peng Zhou
    • , Xing-Lou Yang
    • , Wei Zhang
    • , Yan Zhu
    • , Xiao-Shuang Zheng
    • , Bei Li
    • , Hua Guo
    • , Yun Luo
    • , Xiang-Ling Liu
    • , Jing Chen
    •  & Zheng-Li Shi
  2. Beijing Institute of Microbiology and Epidemiology, Beijing, China

    • Hang Fan
    • , Ya-Wei Zhang
    • , Jin-Man Li
    • , Guang-Qian Pei
    • , Xiao-Ping An
    • , Zhi-Qiang Mi
    • , Tong-Tong He
    • , Yong Huang
    • , Qiang Sun
    • , Xiang-Li-Lan Zhang
    • , Yuan-Yuan Wang
    • , Shao-Zhen Xing
    •  & Yi-Gang Tong
  3. College of Animal Science, South China Agricultural University, Guangzhou, China

    • Tian Lan
    • , Qing-Mei Xie
    • , Jun-Wei Chen
    • , Ling Zhou
    • , Kai-Jie Mai
    • , Zi-Xian Wu
    • , Di Li
    • , Yan-Shan Chen
    • , Yuan Sun
    •  & Jing-Yun Ma
  4. Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China

    • Tian Lan
    • , Qing-Mei Xie
    • , Jun-Wei Chen
    • , Ling Zhou
    • , Kai-Jie Mai
    • , Zi-Xian Wu
    • , Di Li
    • , Yan-Shan Chen
    • , Yuan Sun
    •  & Jing-Yun Ma
  5. Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Taishan Medical College, Taian, China

    • Wei-Feng Shi
    •  & Juan Li
  6. Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore

    • Shailendra Mani
    • , Danielle E. Anderson
    •  & Lin-Fa Wang
  7. Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China

    • Li-Biao Zhang
  8. School of Public Health, Wuhan University, Wuhan, China

    • Shi-Yue Li
  9. Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China

    • Feng Cong
    • , Peng-Ju Guo
    •  & Ren Huang
  10. EcoHealth Alliance, New York, NY, USA

    • Peter Daszak
  11. School of Life Sciences, North China University of Science and Technology, Tangshan, China

    • Yi-Gang Tong

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Contributions

L.-F.W., Z.-L.S., P.Z., Y.-G.T., and J.-Y.M. conceived the study. P.Z., W.Z., Y.Z., S.M., X.-S.Z., B.L., X.-L.Y., H.G., D.E.A., Y.L., X.L.L. and J.C. performed qPCR, serology and histology experiments and cultured the virus. H.F., Y.-W.Z., J.-M.L., G.-Q.P., X.-P.A., Z.-Q.M., T.-T.H., Y.H., Q.S., Y.-Y.W., S.-Z.X., X.-L.-L.Z., W.-F.S. and J.L. performed genome sequencing and annotations. T.L., Q.-M.X., J.-W.C., L.Z., K.-J.M., Z.-X.W., Y.-S.C., D.L., Y.S., F.C., P.-J.G. and R.H. prepared the samples and carried out animal challenge experiments. Z.-L.S., P.D., L.-B.Z., S.-Y.L. coordinated collection of bat samples. P.Z., L.-F.W., Z.-L.S. and P.D. had a major role in the preparation of the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Peter Daszak or Lin-Fa Wang or Zheng-Li Shi or Yi-Gang Tong or Jing-Yun Ma.

Extended data figures and tables

  1. Extended Data Fig. 1 Map of outbreak locations and sampling sites in Guangdong province, China and the co-circulation of PEDV and SADS-CoV during the initial outbreak on farm A.

    a, SADS-affected farms are labelled (farms A–D) with blue swine silhouettes following the temporal sequence of the outbreaks. Bat sampling sites are indicated with black bat silhouettes. The bat SADSr-CoV that is most closely related to SADS-CoV (sample 162140) originated in Conghua. The red flag marks Foshan city, the site of the SARS index case. b, Pooled intestinal samples (n = 5 or more biological independent samples) were collected at dates given on the x axis from deceased piglets and analysed by qPCR. The viral load for each piglet is shown as copy number per milligram of intestine tissue (y axis).

  2. Extended Data Fig. 2 Bayesian phylogenetic tree of the full-length genome and the ORF1a and ORF1b sequences of SADS-CoV and related coronaviruses.

    a, Bayesian phylogenetic tree of the full-length genome. b, Bayesian phylogenetic tree of the ORF1a and ORF1b sequences. Trees were constructed using MrBayes with the average standard deviation of split frequencies under 0.01. The host of each sequence is represented as a silhouette. Newly sequenced SADS-CoVs are highlighted in red, bat SADSr-CoVs are shown in blue and previously published sequences are shown in black. Scale bars, nucleotide substitutions per site.

  3. Extended Data Fig. 3 Phylogeny and haplotype network analyses of the 33 SADS-CoV strains from the four farms.

    a, Phylogenetic tree constructed using MrBayes. The GTR+GAMMA model was applied and 20 million steps were run, with the first 10% removed as burn in. Viruses from different farms are labelled with different colours. Scale bar, nucleotide substitutions per site. b, Median-joining haplotype network constructed using ProART. In this analysis, ɛ = 0 was used. The size of the circles represents the number of samples. The larger the circle, the more samples it includes.

  4. Extended Data Fig. 4 Recombination analysis for SADS-CoV and related CoVs.

    The potential genetic recombination events were detected using RDP. For each virus strain, different colours represent different sources of the genomes. Source data

  5. Extended Data Fig. 5 Isolation and antigenic characterization of SADS-CoV.

    a, b, Vero cells are shown 20 h after infection with mock (a) or SADS-CoV (b). c, d, Mock or SADS-CoV-infected samples stained with rabbit serum raised against the recombinant SADSr-CoV N protein (red) and DAPI (blue). The experiment was conducted independently three times with similar results. Scale bars, 100 μm. Source data

  6. Extended Data Table 1 List of all known swine viruses tested by PCR at the beginning of the of SADS outbreak investigation on the four farms
  7. Extended Data Table 2 List of SADSr-CoVs detected in bats in Guangdong, China
  8. Extended Data Table 3 Test of SADS-CoV entry and infection in Hela cells expressing known coronavirus receptors
  9. Extended Data Table 4 Experimental infection of SPF piglets using intestine tissue homogenate
  10. Extended Data Table 5 Experimental animal infection of farm piglets using cultured SADS-CoV

Supplementary information

  1. Supplementary Information

    This file contains two supplementary tables. Supplementary table 1 contains a list of nucleotide variants among the 33 SADS-CoV genomes obtained from the four farms. Supplementary table 2 contains a list of PCR primers used in this study

  2. Reporting Summary

Source data

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DOI

https://doi.org/10.1038/s41586-018-0010-9

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