Analysis of human coronavirus 229E spike and nucleoprotein genes demonstrates genetic drift between chronologically distinct strains Free

Abstract

Historically, coronaviruses have been recognized as a cause of minor respiratory infections in humans. However, the recent identification of three novel human coronaviruses, one causing severe acute respiratory syndrome (SARS), has prompted further examination of these viruses. Previous studies of geographically and chronologically distinct (HCoV-229E) isolates have found only limited variation within S gene nucleotide sequences. In contrast, analysis of the S genes of contemporary variants identified in Belgium revealed two distinct viruses circulating during 2003 and 2004. Here, the S and N gene sequences of 25 HCoV-229E variants identified in Victoria, Australia, between 1979 and 2004 in patients with symptomatic infections were determined. Phylogenetic analysis showed clustering of the isolates into four groups, with evidence of increasing divergence with time. Evidence of positive selection in the S gene was also established.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.81662-0
2006-05-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/jgv/87/5/1203.html?itemId=/content/journal/jgv/10.1099/vir.0.81662-0&mimeType=html&fmt=ahah

References

  1. Birch C. J., Clothier H. J., Seccull A., Tran T., Catton M. C., Lambert S. B., Druce J. D. 2005; Human coronavirus OC43 causes influenza-like illness in residents and staff of aged-care facilities in Melbourne, Australia. Epidemiol Infect 133:273–277 [CrossRef]
    [Google Scholar]
  2. Bonavia A., Zelus B. D., Wentworth D. E., Talbot P. J., Holmes K. V. 2003; Identification of a receptor-binding domain of the spike glycoprotein of human coronavirus HCoV-229E. J Virol 77:2530–2538 [CrossRef]
    [Google Scholar]
  3. Brian D. A., Baric R. S. 2005; Coronavirus genome structure and replication. Curr Top Microbiol Immunol 287:1–30
    [Google Scholar]
  4. Bush R. M. 2001; Predicting adaptive evolution. Nat Rev Genet 2:387–392
    [Google Scholar]
  5. Cavanagh D., Davis P. J., Mockett A. P. 1988; Amino acids within hypervariable region 1 of avian coronavirus IBV (Massachusetts serotype) spike glycoprotein are associated with neutralization epitopes. Virus Res 11:141–150 [CrossRef]
    [Google Scholar]
  6. Clothier H. J., Fielding J. E., Kelly H. A. 2005; An evaluation of the Australian Sentinel Practice Research Network (ASPREN) surveillance for influenza-like illness. Commun Dis Intell 29:231–247
    [Google Scholar]
  7. Corpet F. 1988; Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16:10881–10890 [CrossRef]
    [Google Scholar]
  8. Drosten C., Gunther S., Preiser W. & 23 other authors 2003; Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med 348:1967–1976 [CrossRef]
    [Google Scholar]
  9. Felsenstein J. 1993 phylip: phylogeny inference package (version 3.5c) Department of Genetics, University of Washington; Seattle, WA, USA:
    [Google Scholar]
  10. Hall T. A. 1999; bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
    [Google Scholar]
  11. Hays J. P., Myint S. H. 1998; PCR sequencing of the spike genes of geographically and chronologically distinct human coronaviruses 229E. J Virol Methods 75:179–193 [CrossRef]
    [Google Scholar]
  12. Holmes K. V. 2001; Coronaviruses. In Fields Virology . , 3rd edn. pp  1187–1203 Edited by Fields B. N., Knipe D. M., Howley P. M. Philadelphia: Lippincott Williams & Wilkins;
  13. Holmes K. V., Lai M. M. C. 1996; Coronaviridae : the viruses and their replication. In Fields Virology , 3rd edn. vol 1 pp  1075–1093 Edited by Fields B. N., Knipe D. M., Howley P. M. Philadelphia: Lippincott Raven;
    [Google Scholar]
  14. Kumar S., Tamura K., Nei M. 2004; mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163 [CrossRef]
    [Google Scholar]
  15. Lai M. M. 1990; Coronavirus: organization, replication and expression of genome. Annu Rev Microbiol 44:303–333 [CrossRef]
    [Google Scholar]
  16. McIntosh K. 1996; Coronaviruses. In Fields Virology . , 3rd edn. vol 1 pp  1095–1103 Edited by Fields B. N., Knipe D. M., Howley P. M. Philadelphia: Lippincott Raven;
  17. Navas-Martin S., Weiss S. R. 2003; SARS: lessons learned from other coronaviruses. Viral Immunol 16:461–474 [CrossRef]
    [Google Scholar]
  18. Nicholas K. B., Nicholas H. B., Jr. 1997; Genedoc: a tool for editing and annotating multiple sequence alignments. Distributed by author, 2·6·002 edn. http://www.psc.edu/biomed/genedoc
    [Google Scholar]
  19. Page R. D. M. 1996; treeview: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358
    [Google Scholar]
  20. Pene F., Merlat A., Vabret A., Rozenberg F., Buzyn A., Dreyfus F., Cariou A., Freymuth F., Lebon P. 2003; Coronavirus 229E-related pneumonia in immunocompromised patients. Clin Infect Dis 37:929–932 [CrossRef]
    [Google Scholar]
  21. Rest J. S., Mindell D. P. 2003; SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting. Infect Genet Evol 3:219–225 [CrossRef]
    [Google Scholar]
  22. Schmidt H. A., Strimmer K., Vingron M., von Haeseler A. 2002; treepuzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502–504 [CrossRef]
    [Google Scholar]
  23. Siddell S. G. 1995; The Coronaviridae : an introduction. In The Coronaviridae Edited by Siddell S. G. New York: Plenum Press;
    [Google Scholar]
  24. Snijder E. J., Bredenbeek P. J., Dobbe J. C. & 7 other authors 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 [CrossRef]
    [Google Scholar]
  25. Vabret A., Mourez T., Gouarin S., Petitjean J., Freymuth F. 2003; An outbreak of coronavirus OC43 respiratory infection in Normandy, France. Clin Infect Dis 36:985–989 [CrossRef]
    [Google Scholar]
  26. van der Hoek L., Pyrc K., Jebbink M. F. & 7 other authors 2004; Identification of a new human coronavirus. Nat Med 10:368–373 [CrossRef]
    [Google Scholar]
  27. Vijgen L., Keyaerts E., Lemey P., Moes E., Li S., Vandamme A. M., Van Ranst M. 2005; Circulation of genetically distinct contemporary human coronavirus OC43 strains. Virology 337:85–92 [CrossRef]
    [Google Scholar]
  28. Woo P. C., Lau S. K., Chu C. M. & 12 other authors 2005; Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol 79:884–895 [CrossRef]
    [Google Scholar]
  29. Yang Z., Bielawski J. P. 2000; Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496–503 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.81662-0
Loading
/content/journal/jgv/10.1099/vir.0.81662-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed