Comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group 3c coronavirus

Journal of Virology

Volumn 83, Issue 2, 2009, Pages 908-917

  Woo, Patrick C Y ^a,b   Lau, Susanna K P ^a,b   Lam, Carol S F ^b   Lai, Kenneth K Y ^b   Huang, Yi ^b   Lee, Paul ^b   Luk, Geraldine S M ^c   Dyrting, Kitman C ^c   Chan, Kwok Hung ^b   Yuen, Kwok Yung ^a,b  

^a THE UNIVERSITY OF HONG KONG   (Hong Kong)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

^c Agriculture Fisheries and Conservation Department   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

CHYMOTRYPSIN; HELICASE; NUCLEOCAPSID PROTEIN; RNA DIRECTED RNA POLYMERASE;

ARTICLE; AVIAN INFECTIOUS BRONCHITIS VIRUS; CORONAVIRUS; GENE SEQUENCE; MAMMAL; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN ANALYSIS; SPIKE;

ANIMALS; BASE SEQUENCE; BIRD DISEASES; BIRDS; CLUSTER ANALYSIS; CORONAVIRUS; CORONAVIRUS INFECTIONS; EPIDEMIOLOGY, MOLECULAR; GENOME, VIRAL; HONG KONG; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, VIRAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SYNTENY; VIRAL PROTEINS;

AVES; AVIAN INFECTIOUS BRONCHITIS VIRUS; CORONAVIRUS; MAMMALIA; PRIONAILURUS BENGALENSIS;

EID: 58149487608     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.01977-08     Document Type: Article

References (50)

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. Brian, D. A., and R. S. Baric. 2005. Coronavirus genome structure and replication. Curr. Top. Microbiol. Immunol. 287:1-30.
4. Cao, J., C. C. Wu, and T. L. Lin. 2008. Complete nucleotide sequence of polyprotein gene 1 and genome organization of turkey coronavirus. Virus Res. 136:43-49.
5. Cheng, V. C., S. K. Lau, P. C. Woo, and K. Y. Yuen. 2007. Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection. Clin. Microbiol. Rev. 20:660-694.
6. Chu, D. K., J. S. Peiris, H. Chen, Y. Guan, and L. L. Poon. 2008. Genomic characterizations of bat coronaviruses (1A, 1B and HKU8) and evidence for co-infections in Miniopterus bats. J. Gen. Virol. 89:1282-1287.
7. Circella, E., A. Camarda, V. Martella, G. Bruni, A. Lavazza, and C. Buonavoglia. 2007. Coronavirus associated with an enteric syndrome on a quail farm. Avian Pathol. 36:251-258.
8. Dominguez, S. R., T. J. O'Shea, L. M. Oko, and K. V. Holmes. 2007. Detection of group 1 coronaviruses in bats in North America. Emerg. Infect. Dis. 13:1295-1300.
9. Dong, B. Q., W. Liu, X. H. Fan, D. Vijaykrishna, X. C. Tang, F. Gao, L. F. Li, G. J. Li, J. X. Zhang, L. Q. Yang, L. L. Poon, S. Y. Zhang, J. S. Peiris, G. J. Smith, H. Chen, and Y. Guan. 2007. Detection of a novel and highly divergent coronavirus from Asian leopard cats and Chinese ferret badgers in Southern China. J. Virol. 81:6920-6926.
10. Ellis, T. M., R. B. Bousfield, L. A. Bissett, K. C. Dyrting, G. S. Luk, S. T. Tsim, K. Sturm-Ramirez, R. G. Webster, Y. Guan, and J. S. Peiris. 2004. Investigation of outbreaks of highly pathogenic H5N1 avian influenza in waterfowl and wild birds in Hong Kong in late 2002. Avian Pathol. 33:492-505.
11. Fouchier, R. A., N. G. Hartwig, T. M. Bestebroer, B. Niemeyer, 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.
12. Gloza-Rausch, F., A. Ipsen, A. Seebens, M. Göttsche, M. Panning, J. Felix Drexler, N. Petersen, A. Annan, K. Grywna, M. Müller, S. Pfefferle, and C. Drosten. 2008. Detection and prevalence patterns of group I coronaviruses in bats, northern Germany. Emerg. Infect. Dis. 14:626-631.
13. Gomaa, M. H., J. R. Barta, D. Ojkic, and D. Yoo. 2008. Complete genomic sequence of turkey coronavirus. Virus Res. 135:237-246.
14. Gough, R. E., S. E. Drury, F. Culver, P. Britton, and D. Cavanagh. 2006. Isolation of a coronavirus from a green-cheeked Amazon parrot (Amazon viridigenalis Cassin) Avian Pathol. 35:122-126.
15. 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.
16. Hasoksuz, M., K. Alekseev, A. Vlasova, X. Zhang, D. Spiro, R. Halpin, S. Wang, E. Ghedin, and L. J. Saif. 2007. Biologic, antigenic, and full-length genomic characterization of a bovine-like coronavirus isolated from a giraffe. J. Virol. 81:4981-4990.
17. Herrewegh, A. A., I. Smeenk, M. C. Horzinek, P. J. Rottier, and R. J. de Groot. 1998. Feline coronavirus type II strains 79-1683 and 79-1146 originate from a double recombination between feline coronavirus type I and canine coronavirus. J. Virol. 72:4508-4514.
18. Hofmann, K. S. 1993. TMbase: a database of membrane spanning proteins segments. Biol. Chem. Hoppe-Seyler 374:166.
19. Huang, Y., S. K. Lau, P. C. Woo, and K. Y. Yuen. 2008. CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes. Nucleic Acids Res. 36:D504-D511.
20. Jonassen, C. M., T. Kofstad, I. L. Larsen, A. Lovland, K. Handeland, A. Follestad, and A. Lillehaug. 2005. Molecular identification and characterization of novel coronaviruses infecting graylag geese (Anser anser), feral pigeons (Columbia livia) and mallards (Anas platyrhynchos). J. Gen. Virol. 86:1597-1607.
21. Lai, M. M., and D. Cavanagh. 1997. The molecular biology of coronaviruses. Adv. Virus. Res. 48:1-100.
22. Lau, S. K., P. C. Woo, K. S. Li, Y. Huang, H. W. Tsoi, B. H. Wong, S. S. Wong, S. Y. Leung, K. H. Chan, and K. Y. Yuen. 2005. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc. Natl. Acad. Sci. USA 102:14040-14045.
23. Lau, S. K., P. C. Woo, C. C. Yip, H. Tse, H. W. Tsoi, V. C. Cheng, P. Lee, B. S. Tang, C. H. Cheung, R. A. Lee, L. Y. So, Y. L. Lau, K. H. Chan, and K. Y. Yuen. 2006. Coronavirus HKU1 and other coronavirus infections in Hong Kong. J. Clin. Microbiol. 44:2063-2071.
24. Lau, S. K., P. C. Woo, K. S. Li, Y. Huang, M. Wang, C. S. Lam, H. Xu, R. Guo, K. H. Chan, B. J. Zheng, and K. Y. Yuen. 2007. 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.
25. Li, K. S., Y. Guan, J. Wang, G. J. Smith, K. M. Xu, L. Duan, A. P. Rahardjo, P. Puthavathana, C. Buranathai, T. D. Nguyen, A. T. Estoepangestie, A. Chaisingh, P. Auewarakul, H. T. Long, N. T. Hanh, R. J. Webby, L. L. Poon, H. Chen, K. F. Shortridge, K. Y. Yuen, R. G. Webster, and J. S. Peiris. 2004. Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia. Nature 430:209-213.
26. Li, W., Z. Shi, M. Yu, W. Ren, C. Smith, J. H. Epstein, H. Wang, G. Crameri, Z. Hu, H. Zhang, J. Zhang, J. McEachern, H. Field, P. Daszak, B. T. Eaton, S. Zhang, and L. F. Wang. 2005. Bats are natural reservoirs of SARS-like coronaviruses. Science 310:676-679.
27. Liu, S., J. Chen, J. Chen, X. Kong, Y. Shao, Z. Han, L. Feng, X. Cai, S. Gu, and M. Liu. 2005. Isolation of avian infectious bronchitis coronavirus from domestic peafowl (Pavo cristatus) and teal (Anas). J. Gen. Virol. 86:719-725.
28. Mardani, K., A. H. Noormohammadi, P. Hooper, J. Ignjatovic, and G. F. Browning. 2008. Infectious bronchitis viruses with a novel genomic organization. J. Virol. 82:2013-2024.
29. 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.
30. Mihindukulasuriya, K. A., G. Wu, J. St. Leger, R. W. Nordhausen, and D. Wang. 2008. Identification of a novel coronavirus from a beluga whale by using a panviral microarray. J. Virol. 82:5084-5088.
31. Nuttall, P. A., and K. A. Harrap. 1982. Isolation of a coronavirus during studies on puffinosis, a disease of the Manx shearwater (Puffinus puffinus). Arch. Virol. 73:1-13.
32. 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, and K. Y. Yuen. 2003. Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet 361:1319-1325.
33. Poon, L. L., D. K. Chu, K. H. Chan, O. K. Wong, T. M. Ellis, Y. H. Leung, S. K. Lau, P. C. Woo, K. Y. Suen, K. Y. Yuen, Y. Guan, and J. S. Peiris. 2005. Identification of a novel coronavirus in bats. J. Virol. 79:2001-2009.
34. Robertson, M. P., H. Igel, R. Baertsch, D. Haussler, M. Ares, Jr., and W. G. Scott. 2005. The structure of a rigorously conserved RNA element within the SARS virus genome. PLoS Biol. 3:e5.
35. 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.
36. 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.
37. 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.
38. Stavrinides, J., and D. S. Guttman. 2004. Mosaic evolution of the severe acute respiratory syndrome coronavirus. J. Virol. 78:76-82.
39. Tang, X. C., J. X. Zhang, S. Y. Zhang, P. Wang, X. H. Fan, L. F. Li, G. Li, B. Q. Dong, W. Liu, C. L. Cheung, K. M. Xu, W. J. Song, D. Vijaykrishna, L. L. Poon, J. S. Peiris, G. J. Smith, H. Chen, and Y. Guan. 2006. Prevalence and genetic diversity of coronaviruses in bats from China. J. Virol. 80:7481-7490.
40. van der Hoek, L., K. Pyrc, 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.
41. Woo, P. C., Y. Huang, S. K. Lau, H. W. Tsoi, and K. Y. Yuen. 2005. In silico analysis of ORF1ab in coronavirus HKU1 genome reveals a unique putative cleavage site of coronavirus HKU1 3C-like protease. Microbiol. Immunol. 49:899-908.
42. Woo, P. C., S. K. Lau, C. M. Chu, K. H. Chan, H. W. Tsoi, Y. Huang, B. H. Wong, R. W. Poon, J. J. Cai, W. K. Luk, L. L. Poon, S. S. Wong, Y. Guan, J. S. Peiris, and K. Y. Yuen. 2005. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J. Virol. 79:884-895.
43. Woo, P. C., S. K. Lau, K. S. Li, R. W. Poon, B. H. Wong, H. W. Tsoi, B. C. Yip, Y. Huang, K. H. Chan, and K. Y. Yuen. 2006. Molecular diversity of coronaviruses in bats. Virology 351:180-187.
44. Woo, P. C., S. K. Lau, and K. Y. Yuen. 2006. Infectious diseases emerging from Chinese wet-markets: zoonotic origins of severe respiratory viral infections. Curr. Opin. Infect. Dis. 19:401-407.
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. K. Lau, H. W. Tsoi, Y. Huang, R. W. Poon, C. M. Chu, R. A. Lee, W. K. Luk, G. K. Wong, B. H. Wong, V. C. Cheng, B. S. Tang, A. K. Wu, R. W. Yung, H. Chen, Y. Guan, K. H. Chan, and K. Y. Yuen. 2005. Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia. J. Infect. Dis. 192:1898-1907.
47. Woo, P. C., S. K. Lau, C. C. Yip, Y. Huang, H. W. Tsoi, K. H. Chan, and K. Y. Yuen. 2006. Comparative analysis of 22 coronavirus HKU1 genomes reveals a novel genotype and evidence of natural recombination in coronavirus HKU1. J. Virol. 80:7136-7145.
48. Woo, P. C., M. Wang, S. K. Lau, H. Xu, R. W. Poon, R. Guo, B. H. Wong, K. Gao, H. W. Tsoi, Y. Huang, K. S. Li, C. S. Lam, K. H. Chan, B. J. Zheng, and K. Y. Yuen. 2007. Comparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features. J. Virol. 81:1574-1585.
49. Zhang, J., J. S. Guy, E. J. Snijder, D. A. Denniston, P. J. Timoney, and U. B. Balasuriya. 2007. Genomic characterization of equine coronavirus. Virology 369:92-104.
50. Ziebuhr, J. 2004. Molecular biology of severe acute respiratory syndrome coronavirus. Curr. Opin. Microbiol. 7:412-419.