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.
Estacio´n Experimental ‘‘La Mayora’’,
Consejo Superior de Investigaciones Cientı´ficas,
29750 Algarrobo-Costa, Ma´laga, Spain
ILTAB/Danforth Plant Science Centre,
975 N. Warson Rd., St Louis, MO 63132, USA
e-mail: cmf@danforthcenter.org; iltab@danforthcenter.org
URL: www.danforthcenter.org/iltab/
National Institute for Biotechnology and Genetic Engineering,
Jhang Road, P.O. Box 577, Faisalabad, Pakistan
Department of Plant Sciences, University of Arizona,
Tucson, AZ 85721, USA
John Innes Centre, Colney Lane,
Norwich NR4 7UH, UK
Departamento de Fitopatologia,
Universidade Federal de Vic¸osa,
Vic¸osa, MG 36570-000, Brazil
Institute of Biotechnology, Zhejiang University,
Hangzhou 310029, China
Peer reviewed