Arch Virol (2005) 150: 2151–2179
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
and J. Stanley
ILTAB/Donald Danforth Plant Science Center, St. Louis, MO, U.S.A.
John Innes Center, Norwich, U.K.
Received March 30, 2005; accepted May 5, 2005
Published online August 19, 2005
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.  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.
Geminiviruses have circular single stranded DNA genomes in one or two components (DNA-A
and DNA-B), they are transmitted by insects and can infect monocotyledonous or dicotyle-
Claude Fauquet is a Secretary of the International Committee on Taxonomy of Viruses (ICTV) and John
Stanley is the Chair of the ICTV Geminiviridae Study Group. However, the views in the article are those of
the authors and not necessarily policy of the ICTV, although the ideas presented in the paper will form the
basis of discussions by the ICTV Executive Committee in the near future.