Advertisement

Archives of Virology

, Volume 150, Issue 10, pp 2151–2179 | Cite as

Revising the way we conceive and name viruses below the species level: A review of geminivirus taxonomy calls for new standardized isolate descriptors

  • C. M. Fauquet
  • J. Stanley
Article

Summary.

Geminivirus taxonomy and nomenclature is increasing in complexity with time, and the growing number of geminivirus sequences deposited in gene banks requires regular taxonomic updates and calls for new descriptors to identify virus isolates unambiguously. Fauquet et al. [1] proposed a system to standardize the names of the viruses, and corresponding guidelines have been followed since, rendering nomenclature much easier. Recently, due to difficulties inherent in species identification, the ICTV Geminiviridae Study Group proposed new species demarcation criteria, the most important of which being an 89% identity threshold between complete DNA-A component nucleotide sequences of begomoviruses. This threshold has been utilised since with general satisfaction. In this paper, we review the status of geminivirus species demarcation and nomenclature for a total of 389 isolates. A small number of corrections have been made to comply with the adopted demarcation criteria but otherwise the classification system has remained robust and therefore we propose to continue using it. However, the large numbers of geminivirus sequences that have become available have led us to recognize the need for a better description of virus isolates. The pairwise comparison distribution below the taxonomic level of species identified two peaks, one at 90–91% identity that may correspond to “strains” and one at 96–98% identity that may correspond to “variants”. Guidelines for descriptors for each of these levels are proposed to standardize nomenclature. As a consequence, we have revisited the status of some virus isolates to elevate them to “strains”. An updated list of all geminivirus isolates currently available is provided.

Keywords

Species Identification Good Description Virus Isolate Taxonomic Level Gene Bank 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Fauquet, CM, Maxwell, DP, Gronenborn, B, Stanley, J 2000Revised proposal for naming geminiviruses.Arch Virol14517431761CrossRefPubMedGoogle Scholar
  2. Fauquet CM (2002) The best sequence threshold criterion for geminivirus species demarcation. www.danforthcenter.org/iltab/geminiviridae/spdemGoogle Scholar
  3. Fauquet, CM, Bisaro, DM, Briddon, RW, Brown, J, Harrison, BD, Rybicki, EP, Stenger, DC, Stanley, J 2003Revision of taxonomic criteria for species demarcation in the family Geminiviridae, and an updated list of begomovirus species.Arch Virol148405421CrossRefPubMedGoogle Scholar
  4. Mayo, MA, Maniloff, J, van Regenmortel, MHV, Fauquet, CM 2002The Type Species in virus taxonomy.Arch Virol14712711274CrossRefGoogle Scholar
  5. Padidam, M, Sawyer, S, Fauquet, CM 1999Possible emergence of new geminiviruses by frequent recombination.Virology265218224PubMedGoogle Scholar
  6. Stanley J, Bisaro DM, Briddon RW, Brown JK, Fauquet CM, Harrison BD, Rybicki EP, Stenger DC (2005) Geminiviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds), Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 301–326Google Scholar
  7. van Regenmortel, MHV, Bishop, DHL, Fauquet, CM, Mayo, MA, Maniloff, J, Calisher, CH 1997Guidelines to the demarcation of virus species.Arch Virol14215051518PubMedGoogle Scholar

Copyright information

© Springer-Verlag/Wien 2005

Authors and Affiliations

  • C. M. Fauquet
    • 1
  • J. Stanley
    • 2
  1. 1.ILTAB/Donald Danforth Plant Science CenterSt. LouisU.S.A.
  2. 2.John Innes CenterNorwichU.K.

Personalised recommendations