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Archives of Virology

, Volume 153, Issue 4, pp 783–821 | Cite as

Geminivirus strain demarcation and nomenclature

  • C. M. Fauquet
  • R. W. Briddon
  • J. K. Brown
  • E. Moriones
  • J. Stanley
  • M. Zerbini
  • X. Zhou
Virology Division News

Abstract

Geminivirus taxonomy and nomenclature is growing in complexity with the number of genomic sequences deposited in sequence databases. Taxonomic and nomenclatural updates are published at regular intervals (Fauquet et al. in Arch Virol 145:1743–1761, 2000, Arch Virol 148:405–421, 2003). A system to standardize virus names, and corresponding guidelines, has been proposed (Fauquet et al. in Arch Virol 145:1743–1761, 2000). This system is now followed by a large number of geminivirologists in the world, making geminivirus nomenclature more transparent and useful. In 2003, 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% nucleotide (nt) identity threshold between full-length DNA-A component nucleotide sequences for begomovirus species. This threshold has been utilised since with general satisfaction. More recently, an article has been published to clarify the terminology used to describe virus entities below the species level [5]. The present publication is proposing demarcation criteria and guidelines to classify and name geminiviruses below the species level. Using the Clustal V algorithm (DNAStar MegAlign software), the distribution of pairwise sequence comparisons, for pairs of sequences below the species taxonomic level, identified two peaks: one at 85–94% nt identity that is proposed to correspond to “strain” comparisons and one at 92–100% identity that corresponds to “variant” comparisons. Guidelines for descriptors for each of these levels are proposed to standardize nomenclature under the species level. In this publication we review the status of geminivirus species and strain demarcation as well as providing updated isolate descriptors for a total of 672 begomovirus isolates. As a consequence, we have revised the status of some virus isolates to classify them as “strains”, whereas several others previously classified as “strains” have been upgraded to “species”. In all other respects, the classification system has remained robust, and we therefore propose to continue using it. An updated list of all geminivirus isolates and a phylogenetic tree with one representative isolate per species are provided.

Keywords

Genomic Component Demarcation Criterion Pairwise Sequence Comparison Begomovirus Species Tomato Golden Mosaic Virus 
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.

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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • C. M. Fauquet
    • 1
  • R. W. Briddon
    • 2
  • J. K. Brown
    • 3
  • E. Moriones
    • 4
  • J. Stanley
    • 5
  • M. Zerbini
    • 6
  • X. Zhou
    • 7
  1. 1.ILTAB/Danforth Plant Science CentreSt LouisUSA
  2. 2.National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
  3. 3.Department of Plant SciencesUniversity of ArizonaTucsonUSA
  4. 4.Estación Experimental “La Mayora”Consejo Superior de Investigaciones CientíficasMálagaSpain
  5. 5.John Innes CentreNorwichUK
  6. 6.Departamento de FitopatologiaUniversidade Federal de ViçosaViçosaBrazil
  7. 7.Institute of BiotechnologyZhejiang UniversityHangzhouChina

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