Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia

Journal of Virology

Volumn 79, Issue 2, 2005, Pages 884-895

  Woo, Patrick C Y ^a,b   Lau, Susanna K P ^a,b   Chu, Chung Ming ^c   Chan, Kwok Hung ^a   Tsoi, Hoi Wah ^a   Huang, Yi ^a   Wong, Beatrice H L ^a   Poon, Rosana W S ^a   Cai, James J ^a   Luk, Wei Kwang ^d   Poon, Leo L M ^a,b   Wong, Samson S Y ^a,b   Guan, Yi ^a,b   Peiris, J S Malik ^a,b   Yuen, Kwok Yung ^a,b  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b THE UNIVERSITY OF HONG KONG   (Hong Kong)

^c UNITED CHRISTIAN HOSPITAL   (Hong Kong)

^d TSEUNG KWAN O HOSPITAL   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN G; NUCLEOCAPSID PROTEIN;

ANTIBODY SPECIFICITY; ARTICLE; CORONAVIRUS; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC SCREENING; GENOME ANALYSIS; HUMAN; HUMAN CELL; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYADENYLATION; PRIORITY JOURNAL; RESPIRATORY TRACT INFECTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SEVERE ACUTE RESPIRATORY SYNDROME; VIRUS CHARACTERIZATION; VIRUS GENOME; VIRUS NUCLEOCAPSID; VIRUS PNEUMONIA;

AGED; AMINO ACID SEQUENCE; BASE SEQUENCE; BLOTTING, WESTERN; CORONAVIRUS; ENZYME-LINKED IMMUNOSORBENT ASSAY; GENES, POL; GENOME, VIRAL; HUMANS; MALE; MOLECULAR SEQUENCE DATA; NASOPHARYNX; OPEN READING FRAMES; PHYLOGENY; PNEUMONIA, VIRAL; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 19944427959     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.79.2.884-895.2005     Document Type: Article

References (51)

1. Apweiler, R., T. K. Attwood, A. Bairoch, A. Bateman, E. Birney, M. Biswas, P. Bucher, L. Cerutti, F. Corpet, M. D. Croning, R. Durbin, L. Falquet, W. Fleischmann, J. Gouzy, H. Hermjakob, N. Hulo, I. Jonassen, D. Kahn, A. Kanapin, Y. Karavidopoulou, R. Lopez, B. Marx, N. J. Mulder, T. M. Oinn, M. Pagni, F. Servant, C. J. Sigrist, and E. M. Zdobnov. 2001. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29:37-40.
2. Bateman, A., E. Birney, L. Cerruti, R. Durbin, L. Etwiller, S. R. Eddy, S. Griffiths-Jones, K. L. Howe, M. Marshall, and E. L. Sonnhammer. 2002. The Pfam protein families database. Nucleic Acids Res. 30:276-280.
3. Combet, C., C. Blanchet, C. Geourjon, and G. Deléage. 2000. NPS@: network protein sequence analysis. Trends Biochem. Sci. 25:147-150.
4. Eickmann, M., S. Becker, H. D. Klenk, H. W. Doerr, K. Stadler, S. Censini, S. Guidotti, V. Masignani, M. Scarselli, M. Mora, C. Donati, J. H. Han, H. C. Song, S. Abrignani, A. Covacci, and R. Rappuoli. 2003. Phylogeny of the SARS coronavirus. Science 302:1504-1505.
5. Fischer, F., D. Peng, S. T. Hingley, S. R. Weiss, and P. S. Masters. 1997. The internal open reading frame within the nucleocapsid gene of mouse hepatitis virus encodes a structural protein that is not essential for viral replication. J. Virol. 71:996-1003.
6. Fouchier, R. A., N. G. Hartwig, T. M. Bestebroer, B. Niemever, J. C. de Jong, J. H. Simon, and A. D. Osterhaus. 2004. A previously undescribed coronavirus associated with respiratory disease in humans. Proc. Natl. Acad. Sci. USA 101:6212-6216.
7. Gattiker, A., E. Gasteiger, and A. Bairoch. 2002. ScanProsite: a reference implementation of a PROSITE scanning tool. Appl. Bioinformatics 1:107-108.
8. Goebel, S. J., B. Hsue, T. F. Dombrowski, and P. S. Masters. 2004. Characterization of the RNA components of a putative molecular switch in the 3′ untranslated region of the murine coronavirus genome. J. Virol. 78:669-682.
9. Guan, Y., B. J. Zheng, Y. Q. He, X. L. Liu, Z. X. Zhuang, C. L. Cheung, S. W. Luo, P. H. Li, L. J. Zhang, Y. J. Guan, K. M. Butt, K. L. Wong, K. W. Chan, W. Lim, K. F. Shortridge, K. Y. Yuen, J. S. Peiris, and L. L. Poon. 2003. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science 302:276-278.
10. Herold, J., S. G. Siddell, and A. E. Gorbalenya. 1999. A human RNA viral cysteine proteinase that depends upon a unique Zn2+-binding finger connecting the two domains of a papain-like fold. J. Biol. Chem. 274:14918-14925.
11. Hofmann, K., and W. Stoffel. 1993. TMbase - a database of membrane spanning proteins segments. Biol. Chem. Hoppe-Seyler 374:166.
12. Jendrach, M., V. Thiel, and S. Siddell. 1999. Characterization of an internal ribosome entry site within mRNA 5 of murine hepatitis virus. Arch. Virol. 144:921-933.
13. Kanjanahaluethai, A., D. Jukneliene, and S. C. Baker. 2003. Identification of the murine coronavirus MP1 cleavage site recognized by papain-like proteinase 2. J. Virol. 77:7376-7382.
14. Klausegger, A., B. Strobl, G. Regl, and A. Kaser. 1999. Identification of a coronavirus hemagglutinin-esterase with a substrate specificity different from those of influenza C virus and bovine coronavirus. J. Virol. 73:3737-3743.
15. Krempl, C., B. Schultze, and G. Herrler. 1995. Analysis of cellular receptors for human coronavirus OC43. Adv. Exp. Med. Biol. 380:371-374.
16. Lai, M. M., and D. Cavanagh. 1997. The molecular biology of coronaviruses. Adv. Virus Res. 48:1-100.
17. Lai, M. M., R. S. Baric, P. R. Brayton, and S. A. Stohlman. 1984. Characterization of leader RNA sequences on the virion and mRNAs of mouse hepatitis virus, a cytoplasmic RNA virus. Proc. Natl. Acad. Sci. USA 81:3626-3630.
18. Macfarlane, J. T., A. Colville, A. Guion, R. M. Macfarlane, and D. H. Rose. 1993. Prospective study of aetiology and outcome of adult lower-respiratory-tract infections in the community. Lancet 341:511-514.
19. Makino, S., S. A. Stohlman, and M. M. Lai. 1986. Leader sequences of murine coronavirus mRNAs can be freely reassorted: evidence for the role of free leader RNA in transcription. Proc. Natl. Acad. Sci. USA 83:4204-4208.
20. Marra, M. A., S. J. Jones, C. R. Astell, R. A. Holt, A. Brooks-Wilson, Y. S. Butterfield, J. Khattra, J. K. Asano, S. A. Barber, S. Y. Chan, A. Cloutier, S. M. Coughlin, D. Freeman, N. Girn, O. L. Griffith, S. R. Leach, M. Mayo, H. McDonald, S. B. Montgomery, P. K. Pandoh, A. S. Petrescu, A. G. Robertson, J. E. Schein, A. Siddiqui, D. E. Smailus, J. M. Stott, G. S. Yang, F. Plummer, A. Andonov, H. Artsob, N. Bastien, K. Bernard, T. F. Booth, D. Bowness, M. Czub, M. Drebot, L. Fernando, R. Flick, M. Garbutt, M. Gray, A. Grolla, S. Jones, H. Feldmann, A. Meyers, A. Kabani, Y. Li, S. Normand, U. Stroher, G. A. Tipples, S. Tyler, R. Vogrig, D. Ward, B. Watson, R. C. Brunham, M. Krajden, M. Petric, D. M. Skowronski, C. Upton, and R. L. Roper. 2003. The genome sequence of the SARS-associated coronavirus. Science 300:1399-1404.
21. Nielsen, H., J. Engelbrecht, S. Brunak, and G. von Heijne. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10:1-6.
22. Nussenzweig, V., and R. S. Nussenzweig. 1985. Circumsporozoite proteins of malaria parasites. Cell 42:401-403.
23. Peiris, J. S., C. M. Chu, V. C. Cheng, K. S. Chan, I. F. Hung, L. L. Poon, K. I. Law, B. S. Tang, T. Y. Hon, C. S. Chan, K. H. Chan, J. S. Ng, B. J. Zheng, W. L. Ng, R. W. Lai, Y. Guan, K. Y. Yuen, and the HKU/UCH SARS Study Group. 2003. Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study. Lancet 361:1767-1772.
24. Peiris, J. S., K. Y. Yuen, A. D. Osterhaus, and K. Stohr. 2003. The severe acute respiratory syndrome. N. Engl. J. Med. 349:2431-2441.
25. Peiris, J. S., S. T. Lai, L. L. Poon, Y. Guan, L. Y. Yam, W. Lim, J. Nicholls, W. K. Yee, W. W. Yan, M. T. Cheung, V. C. Cheng, K. H. Chan, D. N. Tsang, R. W. Yung, T. K. Ng, K. Y. Yuen, and the SARS Study Group. 2003. Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet 361:1319-1325.
26. Popova, R., and X. Zhang. 2002. The spike but not the hemagglutinin/esterase protein of bovine coronavirus is necessary and sufficient for viral infection. Virology 294:222-236.
27. Riski, H., and T. Hovi. 1980. Coronavirus infections of man associated with diseases other than the common cold. J. Med. Virol. 6:259-265.
28. Rota, P. A., M. S. Oberste, S. S. Monroe, W. A. Nix, R. Campagnoli, J. P. Icenogle, S. Penaranda, B. Bankamp, K. Maher, M. H. Chen, S. Tong, A. Tamin, L. Lowe, M. Frace, J. L. DeRisi, Q. Chen, D. Wang, D. D. Erdman, T. C. Peret, C. Burns, T. G. Ksiazek, P. E. Rollin, A. Sanchez, S. Liffick, B. Holloway, J. Limor, K. McCaustland, M. Olsen-Rasmussen, R, Fouchier, S. Gunther, A. D. Osterhaus, C. Drosten, M. A. Pallansch, L. J. Anderson, and W. J. Bellini. 2003. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300:1394-1399.
29. Ruiz, M., S. Ewig, M. A. Marcos, J. A. Martinez, F. Arancibia, J. Mensa, and A. Torres. 1990. Etiology of community-acquired pneumonia: impact of age, comorbidity, and severity. Am. J. Respir. Crit. Care Med. 160:397-405.
30. Schwarz, B., E. Routledge, and S. G. Siddell. 1990. Murine coronavirus nonstructural protein ns2 is not essential for virus replication in transformed cells. J. Virol. 64:4784-4791.
31. Snijder, E. J., P. J. Bredenbeek, J. C. Dobbe, V. Thiel, J. Ziebuhr, L. L. Poon, Y. Guan, M. Rozanov, W. J. Spaan, and A. E. Gorbalenya. 2003. 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.
32. Sonnhammer, E. L., G. von Heijne, and A. Krogh. 1998. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6:175-182.
33. Suzuki, H., and F. Taguchi. 1996. Analysis of the receptor-binding site of murine coronavirus spike protein. J. Virol. 70:2632-2636.
34. Thiel, V., and S. G. Siddell. 1994. Internal ribosome entry in the coding region of murine hepatitis virus mRNA 5. J. Gen. Virol. 75:3041-3046.
35. Vabret, A., T. Mourez, S. Gouarin, J. Petitiean, and F. Freymuth. 2003. An outbreak of coronavirus OC43 respiratory infection in Normandy, France. Clin. Infect. Dis. 36:985-989.
36. van den Hoogen, B. G., J. C. de Jong, J. Groen, T. Kuiken, R. de Groot, R. A. Fouchier, and A. D. Osterhaus. 2001. A newly discovered human pneumovirus isolated from young children with respiratory tract disease. Nat. Med. 7:719-724.
37. van der Hoek, L., K. Pyre, M. F. Jebbink, W. Vermeulen-Oost, R. J. Berkhout, K. C. Wolthers, P. M. Wertheim-Van Dillen, J. Kaandorp, J. Spaargaren, and B. Berkhout. 2004. Identification of a new human coronavirus. Nat. Med. 10:368-373.
38. Vlasak, R., W. Luytjes, J. Leider, W. Spaan, and P. Palese. 1988. The E3 protein of bovine coronavirus is a receptor-destroying enzyme with acetylesterase activity. J. Virol. 62:4686-4690.
39. Vlasak, R., W. Luytjes, W. Spaan, and P. Palese. 1988. Human and bovine coronaviruses recognize sialic acid-containing receptors similar to those of influenza C viruses. Proc. Natl. Acad. Sci. USA 85:4526-4529.
40. Wenzel, R. P., J. O. Hendley, J. A. Davies, and J. M. Gwaltney, Jr. 1974. Coronavirus infections in military recruits. Three-year study with coronavirus strains OC43 and 229E. Am. Rev. Respir. Dis. 109:621-624.
41. Wessner, D. R., P. C. Shick, J. H. Lu, C. B. Cardellichio, S. E. Gagneten, N. Beauchemin, K. V. Holmes, and G. S. Dveksler. 1998. Mutational analysis of the virus and monoclonal antibody binding sites in MHVR, the cellular receptor of the murine coronavirus mouse hepatitis virus strain A59. J. Virol. 72:1941-1948.
42. Williams, G. D., R. Y. Chang, and D. A. Brian. 1999. A phylogenetically conserved hairpin-type 3′ untranslated region pseudoknot functions in coronavirus RNA replication. J. Virol. 73:8349-8355.
43. Williams, R. K., G. S. Jiang, and K. V. Holmes. 1991. Receptor for mouse hepatitis virus is a member of the carcinoembryonic antigen family of glycoproteins. Proc. Natl. Acad. Sci. USA 88:5533-5536.
44. Woo, P. C., S. K. Lau, B. H. Wong, H. W. Tsoi, A. M. Fung, K. H. Chan, V. K. Tam, J. S. Peiris, and K. Y. Yuen. 2004. Detection of specific antibodies to severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein for serodiagnosis of SARS coronavirus pneumonia. J. Clin. Microbiol. 42:2306-2309.
45. Woo, P. C., S. K. Lau, H. W. Tsoi, K. H. Chan, B. H. Wong, X. Y. Che, V. K. Tam, S. C. Tam, V. C. Cheng, I. F. Hung, S. S. Wong, B. J. Zheng, Y. Guan, and K. Y. Yuen. 2004. Relative rates of non-pneumonic SARS coronavirus infection and SARS coronavirus pneumonia. Lancet 363:841-845.
46. Woo, P. C., S. S. Chiu, W. H. Seto, and M. Peiris. 1997. Cost-effectiveness of rapid diagnosis of viral respiratory tract infections in pediatric patients. J. Clin. Microbiol. 35:1579-1581.
47. Yang, H. J., S. J. Park, K. I. Im, and T. S. Yong. 2000. Identification of a Clonorchis sinensis gene encoding a vitellaria antigenic protein containing repetitive sequences. Mol. Biochem. Parasitol. 111:213-216.
48. Yeh, S. H., H. Y. Wang, C. Y., Tsai, C. L. Kao, J. Y. Yang, H. W. Liu, I. J. Su, S. F. Tsai, D. S. Chen, P. J. Chen, and the National Taiwan University SARS Research Team. 2004. Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan: molecular epidemiology and genome evolution. Proc. Natl. Acad. Sci. USA 101:2542-2547.
49. Yokomori, K., L. R. Banner, and M. M. Lai. 1991. Heterogeneity of gene expression of the hemagglutinin-esterase (HE) protein of murine coronaviruses. Virology 183:647-657.
50. Yokomori, K., M. Asanaka, S. A. Stohlman, S. Makino, R. A. Shubin, W. Gilmore, L. P. Weiner, F. I. Wang, and M. M. Lai. 1995. Neuropathogenicity of mouse hepatitis virus JHM isolates differing in hemagglutinin-esterase protein expression. J. Neurovirol. 1:330-339.
51. Zhong, N. S., B. J. Zheng, Y. M. Li, L. L. Poon, Z. H. Xie, K. H. Chan, P. H. Li, S. Y. Tan, Q. Chang, J. P. Xie, X. Q. Liu, J. Xu, D. X. Li, K. Y. Yuen, J. S. Peiris, and Y. Guan. 2003. Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People's Republic of China, in February, 2003. Lancet 362:1353-1358.