1887

Abstract

Caliciviruses infect a wide range of mammalian hosts and include the genus , the major cause of food-borne viral gastroenteritis in humans. Using publicly available sequence data and phylogenetic analysis tools, the origins and virus–host co-phylogeny of these viruses were investigated. Here, evidence is presented in support of host switching by caliciviruses, but showing that zoonotic transfer does not appear to have occurred in the history of these viruses. The age or demography of the caliciviruses cannot yet be estimated with any firm degree of support, but further studies of this family, as new dated sequences become available, could provide key information of importance to human health and in understanding the emergence of food-borne disease.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.81635-0
2006-05-01
2019-12-06
Loading full text...

Full text loading...

/deliver/fulltext/jgv/87/5/1229.html?itemId=/content/journal/jgv/10.1099/vir.0.81635-0&mimeType=html&fmt=ahah

References

  1. Alroy, J. ( 1999; ). The fossil record of North American mammals: evidence for a Paleocene evolutionary radiation. Syst Biol 48, 107–118.[CrossRef]
    [Google Scholar]
  2. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., Rapp, B. A. & Wheeler, D. L. ( 2002; ). GenBank. Nucleic Acids Res 30, 17–20.[CrossRef]
    [Google Scholar]
  3. Berke, T., Golding, B., Jiang, X., Cubitt, D. W., Wolfaardt, M., Smith, A. W. & Matson, D. O. ( 1997; ). Phylogenetic analysis of the Caliciviruses. J Med Virol 52, 419–424.[CrossRef]
    [Google Scholar]
  4. Berry, E. S., Skilling, D. E., Barlough, J. E., Vedros, N. A., Gage, L. J. & Smith, A. W. ( 1990; ). New marine calicivirus serotype infective for swine. Am J Vet Res 51, 1184–1187.
    [Google Scholar]
  5. Bininda-Emonds, O. R. P., Gittleman, J. L. & Purvis, A. ( 1999; ). Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biol Rev Camb Philos Soc 74, 143–175.[CrossRef]
    [Google Scholar]
  6. Centers for Disease Control & Prevention ( 2003; ). Norovirus activity – United States, 2002. MMWR Morb Mortal Wkly Rep 52, 41–45.
    [Google Scholar]
  7. Chare, E. R., Gould, E. A. & Holmes, E. C. ( 2003; ). Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J Gen Virol 84, 2691–2703.[CrossRef]
    [Google Scholar]
  8. Charleston, M. A. ( 1998; ). Jungles: a new solution to the host/parasite phylogeny reconciliation problem. Math Biosci 149, 191–223.[CrossRef]
    [Google Scholar]
  9. Charleston, M. A. & Page, R. D. M. ( 1998; ). TreeMap 2.0β. Macintosh program for co-phylogenetic analysis, 2.0β edn. Available at http://evolve.zoo.ox.ac.uk/software.html?id=treemap
  10. Charleston, M. A. & Robertson, D. L. ( 2002; ). Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny. Syst Biol 51, 528–535.[CrossRef]
    [Google Scholar]
  11. Clarke, I. N. & Lambden, P. R. ( 1997; ). The molecular biology of caliciviruses. J Gen Virol 78, 291–301.
    [Google Scholar]
  12. Drake, J. W. & Holland, J. J. ( 1999; ). Mutation rates among RNA viruses. Proc Natl Acad Sci U S A 96, 13910–13913.[CrossRef]
    [Google Scholar]
  13. Felsenstein, J. ( 1989; ). phylip – Phylogeny Inference Package (Version 3.2). Cladistics 5, 164–166.
    [Google Scholar]
  14. Felsenstein, J. & Churchill, G. A. ( 1996; ). A hidden Markov model approach to variation among sites in rate of evolution. Mol Biol Evol 13, 93–104.[CrossRef]
    [Google Scholar]
  15. Food Standards Agency ( 2000; ). A Report of the Study of Infectious Intestinal Disease in England. London: The Stationery Office.
  16. Green, J., Vinje, J., Gallimore, C. I., Koopmans, M., Hale, A., Brown, D. W., Clegg, J. C. & Chamberlain, J. ( 2000; ). Capsid protein diversity among Norwalk-like viruses. Virus Genes 20, 227–236.[CrossRef]
    [Google Scholar]
  17. Hardy, M. E. & Estes, M. K. ( 1996; ). Completion of the Norwalk virus genome sequence. Virus Genes 12, 287–290.
    [Google Scholar]
  18. Hasegawa, M., Kishino, H. & Yano, T. ( 1985; ). Dating of the human–ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22, 160–174.[CrossRef]
    [Google Scholar]
  19. Holmes, E. C. ( 2003; ). Molecular clocks and the puzzle of RNA virus origins. J Virol 77, 3893–3897.[CrossRef]
    [Google Scholar]
  20. Jenkins, M. J., Rambaut, A., Pybus, O. G. & Holmes, E. C. ( 2002; ). Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J Mol Evol 54, 156–165.[CrossRef]
    [Google Scholar]
  21. Kingman, J. F. C. ( 1982; ). On the genealogy of large populations. J Appl Probab 19A, 27–43.
    [Google Scholar]
  22. Koopmans, M. & Duizer, E. ( 2004; ). Foodborne viruses: an emerging problem. Int J Food Microbiol 90, 23–41.[CrossRef]
    [Google Scholar]
  23. Kumar, S. & Hedges, S. B. ( 1998; ). A molecular timescale for vertebrate evolution. Nature 392, 917–920.[CrossRef]
    [Google Scholar]
  24. Lui, F.-G. R., Miyamoto, M. M., Freire, N. P., Ong, P. Q., Tennant, M. R., Young, T. S. & Gugel, K. F. ( 2001; ). Molecular and morphological supertrees for eutherian (placental) mammals. Science 291, 1786–1789.[CrossRef]
    [Google Scholar]
  25. Maddison, D. R., Maddison, W. P., Schulz, K. S., Wheeler, T. & Frumkin, J. ( 2001; ). Tree of life web project. Available at: http://tolweb.org.
  26. Meslin, F. X., Stohr, K. & Heymann, D. ( 2000; ). Public health implications of emerging zoonoses. Rev Sci Tech 19, 310–317.
    [Google Scholar]
  27. Murphy, W. J., Elzirik, E., Johnson, W. E., Zhang, Y. P., Ryder, O. A. & O'Brien, S. J. ( 2001; ). Molecular phylogenetics and the origins of placental mammals. Nature 409, 614–618.[CrossRef]
    [Google Scholar]
  28. Pybus, O. G. & Rambaut, A. ( 2002; ). genie: estimating demographic history from molecular phylogenies. Bioinformatics 18, 1404–1405.[CrossRef]
    [Google Scholar]
  29. Rambaut, A. ( 2000; ). Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood estimates. Bioinformatics 16, 395–399.[CrossRef]
    [Google Scholar]
  30. Schou, S. & Hansen, A. K. ( 2000; ). Marburg and Ebola virus infections in laboratory non-human primates: a literature review. Comp Med 50, 108–123.
    [Google Scholar]
  31. Slifko, T. R., Smith, H. V. & Rose, J. B. ( 2000; ). Emerging parasite zoonoses associated with water and food. Int J Parasitol 30, 1379–1393.[CrossRef]
    [Google Scholar]
  32. Smith, A. W., Skilling, D. E., Cherry, N., Mead, J. H. & Matson, D. O. ( 1998; ). Calicivirus emergence from ocean reservoirs: zoonotic and interspecies movements. Emerg Infect Dis 4, 13–20.[CrossRef]
    [Google Scholar]
  33. Stavrinides, J. & Guttman, D. S. ( 2004; ). Mosaic evolution of the severe acute respiratory syndrome coronavirus. J Virol 78, 76–82.[CrossRef]
    [Google Scholar]
  34. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. ( 1997; ). The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef]
    [Google Scholar]
  35. Twiddy, S. S., Pybus, O. G. & Holmes, E. C. ( 2003; ). Comparative population dynamics of mosquito-borne flaviviruses. Infect Genet Evol 3, 87–95.[CrossRef]
    [Google Scholar]
  36. van Regenmortel, M. H. V., Fauquet, C. M., Bishop, D. H. L. & 8 other editors ( 2000; ). Virus Taxonomy: Classification and Nomenclature of Viruses: Seventh Report of the International Committee on Taxonomy of Viruses. San Diego: Academic Press.
  37. Yuen, K. Y., Chan, P. K. S., Peiris, M. & 8 other authors ( 1998; ). Clinical features and rapid viral diagnosis of human disease associated with avian influenza A H5N1 virus. Lancet 351, 467–471.[CrossRef]
    [Google Scholar]
  38. Yusmin, K., Peeters, M., Pybus, O. G., Bhattacharya, T., Delaporte, E., Mulanga, C., Muldoon, M., Theiler, J. & Korber, B. ( 2001; ). Using human immunodeficiency virus type 1 sequences to infer historical features of the acquired immune deficiency syndrome epidemic and human immunodeficiency virus evolution. Philos Trans R Soc Lond B Biol Sci 356, 855–866.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.81635-0
Loading
/content/journal/jgv/10.1099/vir.0.81635-0
Loading

Data & Media loading...

Supplements

Phylogenetic trees used in TipDate analysis

IMAGE

DNAML tree for Dataset 1 (Norviruses only).

IMAGE

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error