Letter | Published:

Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor

Nature volume 503, pages 535538 (28 November 2013) | Download Citation

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Abstract

The 2002–3 pandemic caused by severe acute respiratory syndrome coronavirus (SARS-CoV) was one of the most significant public health events in recent history1. An ongoing outbreak of Middle East respiratory syndrome coronavirus2 suggests that this group of viruses remains a key threat and that their distribution is wider than previously recognized. Although bats have been suggested to be the natural reservoirs of both viruses3,4,5, attempts to isolate the progenitor virus of SARS-CoV from bats have been unsuccessful. Diverse SARS-like coronaviruses (SL-CoVs) have now been reported from bats in China, Europe and Africa5,6,7,8, but none is considered a direct progenitor of SARS-CoV because of their phylogenetic disparity from this virus and the inability of their spike proteins to use the SARS-CoV cellular receptor molecule, the human angiotensin converting enzyme II (ACE2)9,10. Here we report whole-genome sequences of two novel bat coronaviruses from Chinese horseshoe bats (family: Rhinolophidae) in Yunnan, China: RsSHC014 and Rs3367. These viruses are far more closely related to SARS-CoV than any previously identified bat coronaviruses, particularly in the receptor binding domain of the spike protein. Most importantly, we report the first recorded isolation of a live SL-CoV (bat SL-CoV-WIV1) from bat faecal samples in Vero E6 cells, which has typical coronavirus morphology, 99.9% sequence identity to Rs3367 and uses ACE2 from humans, civets and Chinese horseshoe bats for cell entry. Preliminary in vitro testing indicates that WIV1 also has a broad species tropism. Our results provide the strongest evidence to date that Chinese horseshoe bats are natural reservoirs of SARS-CoV, and that intermediate hosts may not be necessary for direct human infection by some bat SL-CoVs. They also highlight the importance of pathogen-discovery programs targeting high-risk wildlife groups in emerging disease hotspots as a strategy for pandemic preparedness.

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Accessions

Data deposits

Sequences of three bat SL-CoV genomes, bat SL-CoV RBD and R. sinicus ACE2 genes have been deposited in GenBank under accession numbers KC881005KC881007 (genomes from SL-CoV RsSHC014, Rs3367 and W1V1, respectively), KC880984KC881003 (bat SL-CoV RBD genes) and KC881004 (R. sinicus ACE2), respectively.

References

  1. 1.

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

  2. 2.

    , , , & Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N. Engl. J. Med. 367, 1814–1820 (2012)

  3. 3.

    et al. Coronaviruses in bats from Mexico. J. Gen. Virol. 94, 1028–1038 (2013)

  4. 4.

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

  5. 5.

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

  6. 6.

    et al. Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences. J. Virol. 84, 11336–11349 (2010)

  7. 7.

    et al. Detection of novel SARS-like and other coronaviruses in bats from Kenya. Emerg. Infect. Dis. 15, 482–485 (2009)

  8. 8.

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

  9. 9.

    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)

  10. 10.

    et al. Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus. J. Virol. 82, 1819–1826 (2008)

  11. 11.

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

  12. 12.

    , , , & A 193-amino acid fragment of the SARS coronavirus S protein efficiently binds angiotensin-converting enzyme 2. J. Biol. Chem. 279, 3197–3201 (2004)

  13. 13.

    et al. Synthetic recombinant bat SARS-like coronavirus is infectious in cultured cells and in mice. Proc. Natl Acad. Sci. USA 105, 19944–19949 (2008)

  14. 14.

    et al. Host range, prevalence, and genetic diversity of adenoviruses in bats. J. Virol. 84, 3889–3897 (2010)

  15. 15.

    et al. Generic detection of coronaviruses and differentiation at the prototype strain level by reverse transcription-PCR and nonfluorescent low-density microarray. J. Clin. Microbiol. 45, 1049–1052 (2007)

  16. 16.

    et al. Evolutionary relationships between bat coronaviruses and their hosts. Emerg. Infect. Dis. 13, 1526–1532 (2007)

  17. 17.

    et al. Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans. J. Gen. Virol. 91, 1058–1062 (2010)

  18. 18.

    et al. Full-length genome sequences of two SARS-like coronaviruses in horseshoe bats and genetic variation analysis. J. Gen. Virol. 87, 3355–3359 (2006)

  19. 19.

    et al. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26, 2462–2463 (2010)

  20. 20.

    , , , & Mechanisms of host receptor adaptation by severe acute respiratory syndrome coronavirus. J. Biol. Chem. 287, 8904–8911 (2012)

  21. 21.

    et al. Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2. EMBO J. 24, 1634–1643 (2005)

  22. 22.

    et al. Ecoepidemiology and complete genome comparison of different strains of severe acute respiratory syndrome-related Rhinolophus bat coronavirus in China reveal bats as a reservoir for acute, self-limiting infection that allows recombination events. J. Virol. 84, 2808–2819 (2010)

  23. 23.

    et al. Coexistence of different genotypes in the same bat and serological characterization of Rousettus bat coronavirus HKU9 belonging to a novel Betacoronavirus subgroup. J. Virol. 84, 11385–11394 (2010)

  24. 24.

    et al. Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proc. Natl Acad. Sci. USA 102, 2430–2435 (2005)

  25. 25.

    et al. Middle East respiratory syndrome coronavirus in bats, Saudi Arabia. Emerg. Infect. Dis. 19, 11 (2013)

  26. 26.

    et al. Is the discovery of the novel human betacoronavirus 2c EMC/2012 (HCoV-EMC) the beginning of another SARS-like pandemic? J. Infect. 65, 477–489 (2012)

  27. 27.

    et al. Close relative of human Middle East respiratory syndrome coronavirus in bat, South Africa. Emerg. Infect. Dis. 19, 1697–1699 (2013)

  28. 28.

    et al. Prediction and prevention of the next pandemic zoonosis. Lancet 380, 1956–1965 (2012)

  29. 29.

    et al. Angiotensin-converting enzyme 2 (ACE2) proteins of different bat species confer variable susceptibility to SARS-CoV entry. Arch. Virol. 155, 1563–1569 (2010)

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Acknowledgements

We acknowledge financial support from the State Key Program for Basic Research (2011CB504701 and 2010CB530100), National Natural Science Foundation of China (81290341 and 31321001), Scientific and technological basis special project (2013FY113500), CSIRO OCE Science Leaders Award, National Institute of Allergy and Infectious Diseases (NIAID) award number R01AI079231, a National Institutes of Health (NIH)/National Science Foundation (NSF) ‘Ecology and Evolution of Infectious Diseases’ award from the NIH Fogarty International Center (R01TW005869), an award from the NIH Fogarty International Center supported by International Influenza Funds from the Office of the Secretary of the Department of Health and Human Services (R56TW009502), and United States Agency for International Development (USAID) Emerging Pandemic Threats PREDICT. The contents are the responsibility of the authors and do not necessarily reflect the views of NIAID, NIH, NSF, USAID or the United States Government. We thank X. Che from Zhujiang Hospital, Southern Medical University, for providing human SARS patient sera.

Author information

Author notes

    • Xing-Yi Ge
    • , Jia-Lu Li
    •  & Xing-Lou Yang

    These authors contributed equally to this work.

Affiliations

  1. Center for Emerging Infectious Diseases, State Key Laboratory of Virology, Wuhan Institute of Virology of the Chinese Academy of Sciences, Wuhan 430071, China

    • Xing-Yi Ge
    • , Jia-Lu Li
    • , Xing-Lou Yang
    • , Ben Hu
    • , Wei Zhang
    • , Cheng Peng
    • , Yu-Ji Zhang
    • , Chu-Ming Luo
    • , Bing Tan
    • , Ning Wang
    • , Yan Zhu
    •  & Zheng-Li Shi
  2. EcoHealth Alliance, New York, New York 10001, USA

    • Aleksei A. Chmura
    • , Guangjian Zhu
    • , Jonathan H. Epstein
    •  & Peter Daszak
  3. One Health Institute, School of Veterinary Medicine, University of California, Davis, California 95616, USA

    • Jonna K. Mazet
  4. CSIRO Australian Animal Health Laboratory, Geelong, Victoria 3220, Australia

    • Gary Crameri
    •  & Lin-Fa Wang
  5. College of Life Sciences, East China Normal University, Shanghai 200062, China

    • Shu-Yi Zhang
  6. Emerging Infectious Diseases Program, Duke-NUS Graduate Medical School, Singapore 169857

    • Lin-Fa Wang

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Contributions

Z.-L.S. and P.D. designed and coordinated the study. X.-Y.G., J.-L. L. and X.-L.Y. conducted majority of experiments and contributed equally to the study. A.A.C., B.H., W.Z., C.P., Y.-J.Z., C.-M.L., B.T., N.W. and Y.Z. conducted parts of the experiments and analyses. J.H.E., J.K.M. and S.-Y.Z. coordinated the field study. X.-Y.G., J.-L.L., X.-L.Y., B.T. and G.-J.Z. collected the samples. G.C. and L.-F.W. designed and supervised part of the experiments. All authors contributed to the interpretations and conclusions presented. Z.-L.S. and X-Y.G. wrote the manuscript with significant contributions from P.D. and L-F.W. and input from all authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Peter Daszak or Zheng-Li Shi.

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DOI

https://doi.org/10.1038/nature12711

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