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A Chatterji, M Padidam, RN Beachy, CM Fauquet (1999)
Identification of replication specificity determinance in tomato leaf curl virus from New DelhiJ Virol, 73
A. Chatterji, U. Chatterji, R. Beachy, C. Fauquet (2000)
Sequence parameters that determine specificity of binding of the replication-associated protein to its cognate site in two strains of tomato leaf curl virus-New Delhi.Virology, 273 2
A. Chatterji, M. Padidam, R. Beachy, C. Fauquet (1999)
Identification of Replication Specificity Determinants in Two Strains of Tomato Leaf Curl Virus from New DelhiJournal of Virology, 73
CM Fauquet, DM Bisaro, RW Briddon, J Brown, BD Harrison, EP Rybicki, DC Stenger, J Stanley (2003)
Revision of taxonomic criteria for species demarcation in the family Geminiviridae, and an updated list of begomovirus speciesArch Virol, 148
C. Fauquet, D. Maxwell, Bruno Gronenborn, John Stanley (2000)
Revised proposal for naming geminivirusesArchives of Virology, 145
C. Fauquet, J. Stanley (2005)
Revising the way we conceive and name viruses below the species level: A review of geminivirus taxonomy calls for new standardized isolate descriptorsArchives of Virology, 150
J Stanley, DM Bisaro, RW Briddon, JK Brown, CM Fauquet, BD Harrison, EP Rybicki, DC Stenger (2005)
Virus taxonomy, viiith report of the ICTV
M. Padidam, S. Sawyer, C. Fauquet (1999)
Possible emergence of new geminiviruses by frequent recombination.Virology, 265 2
C. Fauquet, D. Bisaro, R. Briddon, Judith Brown, B. Harrison, E. Rybicki, D. Stenger, J. Stanley (2003)
Virology division news: Revision of taxonomic criteria for species demarcation in the family Geminiviridae, and an updated list of begomovirus speciesArchives of Virology, 148
(2005)
Ball LA (eds) Virus Taxonomy, viiith report of the ICTV
M. Regenmortel, D. Bishop, C. Fauquet, M. Mayo, J. Maniloff, C. Calisher (1997)
Guidelines to the demarcation of virus speciesArchives of Virology, 142
M. Boulton, D. King, J. Donson, J. Davies (1991)
Point substitution in a promoter-like region and the V1 gene affect the host range and symptoms of maize streak virus.Virology, 183 1
MA Mayo, J Maniloff, MHV Regenmortel, CM Fauquet (2002)
The Type Species in virus taxonomyArch Virol, 147
(2002)
The best sequence threshold criterion for geminivirus species demarcation
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.
Archives of Virology – Springer Journals
Published: Apr 1, 2008
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