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Identification of a new human coronavirus

Nature Medicine volume 10, pages 368–373 (2004)Cite this article

Abstract

Three human coronaviruses are known to exist: human coronavirus 229E (HCoV-229E), HCoV-OC43 and severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV). Here we report the identification of a fourth human coronavirus, HCoV-NL63, using a new method of virus discovery. The virus was isolated from a 7-month-old child suffering from bronchiolitis and conjunctivitis. The complete genome sequence indicates that this virus is not a recombinant, but rather a new group 1 coronavirus. The in vitro host cell range of HCoV-NL63 is notable because it replicates on tertiary monkey kidney cells and the monkey kidney LLC-MK2 cell line. The viral genome contains distinctive features, including a unique N-terminal fragment within the spike protein. Screening of clinical specimens from individuals suffering from respiratory illness identified seven additional HCoV-NL63-infected individuals, indicating that the virus was widely spread within the human population.

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Figure 1: The VIDISCA method.
Figure 2: Detection of HCoV-NL63 in winter months of 2002 and 2003.
Figure 3: Phylogenetic analysis of RT-PCR sequences of the 1a gene from HCoV-NL63-positive patients.
Figure 4: HCoV-NL63 genome organization and phylogenetic analysis.

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References

  1. Stohlman, S.A. & Hinton, D.R. Viral induced demyelination. Brain Pathol. 11, 92–106 (2001).

    Article  CAS  PubMed  Google Scholar 

  2. Jubelt, B. & Berger, J.R. Does viral disease underlie ALS? Lessons from the AIDS pandemic. Neurology 57, 945–946 (2001).

    Article  CAS  PubMed  Google Scholar 

  3. Shingadia, D., Bose, A. & Booy, R. Could a herpesvirus be the cause of Kawasaki disease? Lancet Infect. Dis. 2, 310–313 (2002).

    Article  CAS  PubMed  Google Scholar 

  4. Bachem, C.W. et al. Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J. 9, 745–753 (1996).

    Article  CAS  PubMed  Google Scholar 

  5. Holmes, K.V. & Lai, M.M.C. Coronaviridae. in Fields Virology (eds. Fields, B.N. et al.) 1075–1093 (Lippincott-Raven Publishers, Philadelphia, 1996).

    Google Scholar 

  6. Guy, J.S., Breslin, J.J., Breuhaus, B., Vivrette, S. & Smith, L.G. Characterization of a coronavirus isolated from a diarrheic foal. J. Clin. Microbiol. 38, 4523–4526 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Tyrrell, D.A.J. & Bynoe, M.L. Cultivation of novel type of common-cold virus in organ cultures. Br. Med. J. 1, 1467–1470 (1965).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Hamre, D. & Procknow, J.J. A new virus isolated from the human respiratory tract. Proc. Soc. Exp. Biol. Med. 121, 190–193 (1966).

    Article  CAS  PubMed  Google Scholar 

  9. Almeida, J.D. & Tyrrell, D.A. The morphology of three previously uncharacterized human respiratory viruses that grow in organ culture. J. Gen. Virol. 1, 175–178 (1967).

    Article  CAS  PubMed  Google Scholar 

  10. Thiel, V., Herold, J., Schelle, B. & Siddell, S.G. Infectious RNA transcribed in vitro from a cDNA copy of the human coronavirus genome cloned in vaccinia virus. J. Gen. Virol. 82, 1273–1281 (2001).

    Article  CAS  PubMed  Google Scholar 

  11. McIntosh, K., Dees, J.H., Becker, W.B., Kapikian, A.Z. & Chanock, R.M. Recovery in tracheal organ cultures of novel viruses from patients with respiratory disease. Proc. Natl. Acad. Sci. USA 57, 933–940 (1967).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Hendley, J.O., Fishburne, H.B. & Gwaltney, J.M., Jr. Coronavirus infections in working adults. Eight-year study with 229 E and OC 43. Am Rev. Respir. Dis. 105, 805–811 (1972).

    CAS  PubMed  Google Scholar 

  13. Mounir, S., Labonte, P. & Talbot, P.J. Characterization of the nonstructural and spike proteins of the human respiratory coronavirus OC43: comparison with bovine enteric coronavirus. Adv. Exp. Med. Biol. 342, 61–67 (1993).

    Article  CAS  PubMed  Google Scholar 

  14. Kunkel, F. & Herrler, G. Structural and functional analysis of the surface protein of human coronavirus OC43. Virol. 195, 195–202 (1993).

    Article  CAS  Google Scholar 

  15. Bradburne, A.F., Bynoe, M.L. & Tyrrell, D.A. Effects of a “new” human respiratory virus in volunteers. Br. Med. J. 3, 767–769 (1967).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Peiris, J.S. et al. Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study. Lancet 361, 1767–1772 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Lai, M.M. SARS virus: the beginning of the unraveling of a new coronavirus. J. Biomed. Sci. 10, 664–675 (2003).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  19. Martina, B.E. et al. Virology: SARS virus infection of cats and ferrets. Nature 425, 915 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  22. Snijder, E.J. et al. Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J. Mol. Biol. 331, 991–1004 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Hamparian, V.V. Rhinoviruses. in Diagnostic Procedures for Viral, Rickettsial and Chlamydial Infection. (eds. Lennette, E.H. & Schmidt, N.J.) 562 (American Public Health Association, Washington DC, 1979).

    Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  25. Chen, L.L., Ou, H.Y., Zhang, R. & Zhang, C.T. ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes. Biochem. Biophys. Res. Commun. 307, 382–388 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Sawicki, S.G. & Sawicki, D.L. Coronaviruses use discontinuous extension for synthesis of subgenome-length negative strands. Adv. Exp. Med. Biol. 380, 499–506 (1995).

    Article  CAS  PubMed  Google Scholar 

  27. van Marle, G. et al. Arterivirus discontinuous mRNA transcription is guided by base pairing between sense and antisense transcription-regulating sequences. Proc. Natl. Acad. Sci. USA 96, 12056–12061 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Lole, K.S. et al. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. 73, 152–160 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Mounir, S. & Talbot, P.J. Human coronavirus OC43 RNA 4 lacks two open reading frames located downstream of the S gene of bovine coronavirus. Virol. 192, 355–360 (1993).

    Article  CAS  Google Scholar 

  30. Duarte, M. et al. Sequence analysis of the porcine epidemic diarrhea virus genome between the nucleocapsid and spike protein genes reveals a polymorphic ORF. Virol. 198, 466–476 (1994).

    Article  CAS  Google Scholar 

  31. Godet, M., Grosclaude, J., Delmas, B. & Laude, H. Major receptor-binding and neutralization determinants are located within the same domain of the transmissible gastroenteritis virus (coronavirus) spike protein. J. Virol. 68, 8008–8016 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Krempl, C. et al. Characterization of the sialic acid binding activity of transmissible gastroenteritis coronavirus by analysis of haemagglutination-deficient mutants. J. Gen. Virol. 81, 489–496 (2000).

    Article  CAS  PubMed  Google Scholar 

  33. Bonavia, A., Zelus, B.D., Wentworth, D.E., Talbot, P.J. & Holmes, K.V. Identification of a receptor-binding domain of the spike glycoprotein of human coronavirus HCoV-229E. J. Virol. 77, 2530–2538 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  35. Vaughn, E.M., Halbur, P.G. & Paul, P.S. Sequence comparison of porcine respiratory coronavirus isolates reveals heterogeneity in the S, 3, and 3-1 genes. J. Virol. 69, 3176–3184 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. McIntosh, K. et al. Coronavirus infection in acute lower respiratory tract disease of infants. J. Infect. Dis. 130, 502–507 (1974).

    Article  CAS  PubMed  Google Scholar 

  37. Pene, F. et al. Coronavirus 229E-related pneumonia in immunocompromised patients. Clin. Infect. Dis. 37, 929–932 (2003).

    Article  PubMed  Google Scholar 

  38. Boivin, G. et al. Human metapneumovirus infections in hospitalized children. Emerg. Infect. Dis. 9, 634–640 (2003).

    Article  PubMed  PubMed Central  Google Scholar 

  39. Myint, S., Johnston, S., Sanderson, G. & Simpson, H. Evaluation of nested polymerase chain methods for the detection of human coronaviruses 229E and OC43. Mol. Cell. Probes 8, 357–364 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Stephensen, C.B., Casebolt, D.B. & Gangopadhyay, N.N. Phylogenetic analysis of a highly conserved region of the polymerase gene from 11 coronaviruses and development of a consensus polymerase chain reaction assay. Virus Res. 60, 181–189 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Boom, R. et al. A rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28, 495–503 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank G. Koen and H. van Eijk for the images of the CPE, W. van Est for artwork, W. Pauw for providing patient specimens, and A. de Ronde for critical reading of the manuscript.

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Authors and Affiliations

  1. Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, Amsterdam, 1105 AZ, The Netherlands

    Lia van der Hoek, Krzysztof Pyrc, Maarten F Jebbink, Katja C Wolthers & Ben Berkhout

  2. Public Health Laboratory, Municipal Health Service, Nieuwe Achtergracht 100, Amsterdam, 1018 WT, The Netherlands

    Wilma Vermeulen-Oost, Ron J M Berkhout & Joke Spaargaren

  3. Department of Medical Microbiology/Clinical Virology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, Amsterdam, 1105 AZ, The Netherlands

    Pauline M E Wertheim-van Dillen

  4. Pediatric Department, Slotervaart Hospital, Louwesweg 6, Amsterdam, 1066 EC, The Netherlands

    Jos Kaandorp

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Correspondence to Ben Berkhout.

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Competing interests

L.v.d.H. is listed as the inventor on a European and a US patent application, held by Primagen Holding b.v., entitled “Coronavirus nucleic acid, protein, and methods for the generation of vaccine, medicaments and diagnostics.”

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van der Hoek, L., Pyrc, K., Jebbink, M. et al. Identification of a new human coronavirus. Nat Med 10, 368–373 (2004). https://doi.org/10.1038/nm1024

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