Molecular epidemiology of human coronavirus OC43 reveals evolution of different genotypes over time and recent emergence of a novel genotype due to natural recombination

Journal of Virology

Volumn 85, Issue 21, 2011, Pages 11325-11337

  Lau, Susanna K P ^a,b   Lee, Paul ^a   Tsang, Alan K L ^a   Yip, Cyril C Y ^a   Tse, Herman ^a,b   Lee, Rodney A ^c   So, Lok Yee ^c   Lau, Yu Lung ^a   Chan, Kwok Hung ^a   Woo, Patrick C Y ^a,b   Yuen, Kwok Yung ^a,b  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b THE UNIVERSITY OF HONG KONG   (Hong Kong)

^c PAMELA YOUDE NETHERSOLE EASTERN HOSPITAL   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

RNA DIRECTED RNA POLYMERASE;

ADULT; AGED; ARTICLE; CHILD; CLINICAL ARTICLE; CONTROLLED STUDY; CORONAVIRUS; FEMALE; GENE SEQUENCE; GENOTYPE; HUMAN; HUMAN CORONAVIRUS OC43; LAST COMMON ANCESTOR; MALE; MOLECULAR CLOCK; MOLECULAR EPIDEMIOLOGY; MOLECULAR EVOLUTION; NASOPHARYNX; NONHUMAN; PHYLOGENY; PRESCHOOL CHILD; PRIORITY JOURNAL; SCHOOL CHILD; VIRUS GENE; VIRUS GENOME; VIRUS NUCLEOCAPSID; VIRUS RECOMBINATION; VIRUS STRAIN;

CLUSTER ANALYSIS; COMMON COLD; CORONAVIRUS INFECTIONS; CORONAVIRUS OC43, HUMAN; DNA-DIRECTED RNA POLYMERASES; EVOLUTION, MOLECULAR; GENOTYPE; HUMANS; MEMBRANE GLYCOPROTEINS; MOLECULAR EPIDEMIOLOGY; MOLECULAR SEQUENCE DATA; NASOPHARYNX; NUCLEOCAPSID PROTEINS; PHYLOGENY; RECOMBINATION, GENETIC; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; VIRAL ENVELOPE PROTEINS;

CORONAVIRUS;

EID: 80055111481     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.05512-11     Document Type: Article

References (60)

1. Abraham, S., T. E. Kienzle, W. Lapps, and D. A. Brian. 1990. Deduced sequence of the bovine coronavirus spike protein and identification of the internal proteolytic cleavage site. Virology 176:296-301.
2. Apweiler, R., et al. 2001. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29:37-40.
3. Birch, C. J., et al. 2005. Human coronavirus OC43 causes influenza-like illness in residents and staff of aged-care facilities in Melbourne, Australia. Epidemiol. Infect. 133:273-277.
4. Brian, D. A., and R. S. Baric. 2005. Coronavirus genome structure and replication. Curr. Top. Microbiol. Immunol. 287:1-30.
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. Decaro, N., et al. 2009. Recombinant canine coronaviruses related to transmissible gastroenteritis virus of Swine are circulating in dogs. J. Virol. 83: 1532-1537.
7. Drummond, A. J., and A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
8. Esposito, S., et al. 2006. Impact of human coronavirus infections in otherwise healthy children who attended an emergency department. J. Med. Virol. 78:1609-1615.
9. Fouchier, R. A., et al. 2004. A previously undescribed coronavirus associated with respiratory disease in humans. Proc. Natl. Acad. Sci. U. S. A. 101:6212-6216.
10. Fu, K., and R. S. Baric. 1992. Evidence for variable rates of recombination in the MHV genome. Virology 189:88-102.
11. Gerna, G., et al. 2006. Impact of human metapneumovirus and human cytomegalovirus versus other respiratory viruses on the lower respiratory tract infections of lung transplant recipients. J. Med. Virol. 78:408-416.
12. Gill, E. P., et al. 1994. Development and application of an enzyme immunoassay for coronavirus OC43 antibody in acute respiratory illness. J. Clin. Microbiol. 32:2372-2376.
13. Guan, Y., et al. 2003. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science 302:276-278.
14. 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.
15. 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.
16. 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.
17. Keane, T. M., C. J. Creevey, M. M. Pentony, T. J. Naughton, and J. O. Mclnerney. 2006. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 6:29.
18. Krempl, C., B. Schultze, and G. Herrler. 1995. Analysis of cellular receptors for human coronavirus OC43. Adv. Exp. Med. Biol. 380:371-374.
19. Kuypers, J., et al. 2007. Clinical disease in children associated with newly described coronavirus subtypes. Pediatrics 119:e70-e76.
20. Langereis, M. A., A. L. van Vliet, W. Boot, and R. J. de Groot. 2010. Attachment of mouse hepatitis virus to O-acetylated sialic acid is mediated by hemagglutinin-esterase and not by the spike protein. J. Virol. 84:8970-8974.
21. Lau, S. K. P., et al. 2010. 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.
22. Lau, S. K., et al. 2010. 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, selflimiting infection that allows recombination events. J. Virol. 84:2808-2819.
23. Lau, S. K., et al. 2006. Coronavirus HKU1 and other coronavirus infections in Hong Kong. J. Clin. Microbiol. 44:2063-2071.
24. Lau, S. K., et al. 2005. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc. Natl. Acad. Sci. U. S. A. 102:14040-14045.
25. Lau, S. K., et al. 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.
26. Li, W., et al. 2005. Bats are natural reservoirs of SARS-like coronaviruses. Science 310:676-679.
27. Lin, C. W., K. H. Lin, T. H. Hsieh, S. Y. Shiu, and J. Y. Li. 2006. Severe acute respiratory syndrome coronavirus 3C-like protease-induced apoptosis. FEMS Immunol. Med. Microbiol. 46:375-380.
28. Makino, S., J. G. Keck, S. A. Stohlman, and M. M. Lai. 1986. High-frequency RNA recombination of murine coronaviruses. J. Virol. 57:729-737.
29. McIntosh, K., et al. 1970. Seroepidemiologic studies of coronavirus infection in adults and children. Am. J. Epidemiol. 91:585-592.
30. McIntosh, K., W. B. Becker, and R. M. Chanock. 1967. Growth in sucklingmouse brain of "IBV-like" viruses from patients with upper respiratory tract disease. Proc. Natl. Acad. Sci. U. S. A. 58:2268-2273.
31. 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.
32. Patrick, D. M., et al. 2006. An outbreak of human coronavirus OC43 infection and serological cross-reactivity with SARS coronavirus. Can. J. Infect. Dis. Med. Microbiol. 17:330-336.
33. Peiris, J. S., et al. 2003. Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet 361:1319-1325.
34. Pyrc, K., et al. 2010. Culturing the unculturable: human coronavirus HKU1 infects, replicates, and produces progeny virions in human ciliated airway epithelial cell cultures. J. Virol. 84:11255-11263.
35. Pyrc, K., M. F. Jebbink, B. Berkhout, and L. van der Hoek. 2004. Genome structure and transcriptional regulation of human coronavirus NL63. Virol. J. 1:7.
36. Pyrc, K., et al. 2006. Mosaic structure of human coronavirus NL63, one thousand years of evolution. J. Mol. Biol. 364:964-973.
37. Rota, P. A., et al. 2003. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300:1394-1399.
38. Sloots, T. P., et al. 2006. Evidence of human coronavirus HKU1 and human bocavirus in Australian children. J. Clin. Virol. 35:99-102.
39. St.-Jean, J. R., et al. 2004. Human respiratory coronavirus OC43: genetic stability and neuroinvasion. J. Virol. 78:8824-8834.
40. Suchard, M. A., R. E. Weiss, and J. S. Sinsheimer. 2001. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 18:1001-1013.
41. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
42. Tang, X. C., et al. 2006. Prevalence and genetic diversity of coronaviruses in bats from China. J. Virol. 80:7481-7490.
43. Vabret, A., et al. 2006. Inter- and intra-variant genetic heterogeneity of human coronavirus OC43 strains in France. J. Gen. Virol. 87:3349-3353.
44. Vabret, A., T. Mourez, S. Gouarin, J. Petitjean, and F. Freymuth. 2003. An outbreak of coronavirus OC43 respiratory infection in Normandy, France. Clin. Infect. Dis. 36:985-989.
45. van der Hoek, L., et al. 2004. Identification of a new human coronavirus. Nat. Med. 10:368-373.
46. van der Most, R. G., L. Heijnen, W. J. Spaan, and R. J. de Groot. 1992. Homologous RNA recombination allows efficient introduction of site-specific mutations into the genome of coronavirus MHV-A59 via synthetic co-replicating RNAs. Nucleic Acids Res. 20:3375-3381.
47. Vijgen, L., et al. 2005. Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event. J. Virol. 79:1595-1604.
48. Vijgen, L., et al. 2005. Circulation of genetically distinct contemporary human coronavirus OC43 strains. Virology 337:85-92.
49. Vijgen, L., et al. 2006. Evolutionary history of the closely related group 2 coronaviruses: porcine hemagglutinating encephalomyelitis virus, bovine coronavirus, and human coronavirus OC43. J. Virol. 80:7270-7274.
50. Woo, P. C., et al. 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.
51. Woo, P. C., et al. 2004. False-positive results in a recombinant severe acute respiratory syndrome-associated coronavirus (SARS-CoV) nucleocapsid enzyme-linked immunosorbent assay due to HCoV-OC43 and HCoV-229E rectified by Western blotting with recombinant SARS-CoV spike polypeptide. J. Clin. Microbiol. 42:5885-5888.
52. Woo, P. C., et al. 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.
53. Woo, P. C., et al. 2005. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J. Virol. 79:884-895.
54. Woo, P. C., et al. 2009. Comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group 3c coronavirus. J. Virol. 83:908-917.
55. Woo, P. C., et al. 2004. Relative rates of non-pneumonic SARS coronavirus infection and SARS coronavirus pneumonia. Lancet 363:841-845.
56. Woo, P. C., et al. 2005. Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia. J. Infect. Dis. 192:1898-1907.
57. Woo, P. C., et al. 2006. Molecular diversity of coronaviruses in bats. Virology 351:180-187.
58. Wu, C. H., et al. 2009. Glycogen synthase kinase-3 regulates the phosphorylation of severe acute respiratory syndrome coronavirus nucleocapsid protein and viral replication. J. Biol. Chem. 284:5229-5239.
59. Yokomori, K., et al. 1995. Neuropathogenicity of mouse hepatitis virus JHM isolates differing in hemagglutinin-esterase protein expression. J. Neurovirol. 1:330-339.
60. Yoo, D., et al. 1992. Synthesis and processing of the haemagglutinin-esterase glycoprotein of bovine coronavirus encoded in the E3 region of adenovirus. J. Gen. Virol. 73:2591-2600.