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Infect Genet Evol. 2007 Jan;7(1):133-44. Epub 2006 May 19.
Virus species and virus identification: past and current controversies.
Van Regenmortel MH.
Ecole Supérieure de Biotechnologie de Strasbourg, CNRS, Boulevard Sebastien Brandt, 67400 ILLKIRCH Cedex 2, France. vanregen@esbs.u-strasbg.fr
The basic concepts used in virus classification are analyzed. A cleardistinction is drawn between viruses that are real, concrete objects studied by virologists and virus species that are man-made taxonomic constructions that exist only in the mind. Classical views regarding the nature of biological species are reviewed and the concept of species used in virology is explained. The use of pair-wise sequence comparisons between the members of a virus family for delineatingspecies and genera is reviewed. The difference between the process of virus identification using one or a few diagnostic properties and the process of creating virus taxa using a combination of many properties is emphasized. The names of virus species in current use are discussed as well as a binomial system that may be introduced in the future.

Intervirology. 1990;31(5):241-54.
Virus species,a much overlooked but essential concept in virus classification.
Van Regenmortel MH.

Infect Genet Evol. 2007 Jan;7(1):133-44. Epub 2006 May 19.
Virus species and virus identification: past and current controversies.
Van Regenmortel MH.
Ecole Supérieure de Biotechnologie de Strasbourg, CNRS, Boulevard Sebastien Brandt, 67400 ILLKIRCH Cedex 2, France.vanregen@esbs.u-strasbg.fr
The basic concepts used in virus classification are analyzed. A clear distinction is drawn between viruses that are real, concrete objects studied by virologists and virus species that are man-made taxonomic constructions that exist only in the mind. Classical views regarding the nature of biological species are reviewed and the concept of species used in virology is explained.The use of pair-wise sequence comparisons between the members of a virus family for delineating species and genera is reviewed. The difference between the process of virus identification using one or a few diagnostic properties and the process of creating virus taxa using a combination of many properties is emphasized. The names of virus species in current use are discussed as well as a binomialsystem that may be introduced in the future.

Intervirology. 1976;7(1-2):1-115.
Classification and nomenclature of viruses. Second report of the International Committee on Taxonomy of Viruses. Fenner F.

Crit Rev Biochem Mol Biol. 1993;28(5):375-430.
Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences.
KooninEV, Dolja VV.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894.
Despite the rapid mutational change that is typical of positive-strand RNA viruses, enzymes mediating the replication and expression of virus genomes contain arrays of conserved sequence motifs. Proteins with such motifs include RNA-dependentRNA polymerase, putative RNA helicase, chymotrypsin-like and papain-like proteases, and methyltransferases. The genes for these proteins form partially conserved modules in large subsets of viruses. A concept of the virus genome as a relatively evolutionarily stable "core" of housekeeping genes accompanied by a much more flexible "shell" consisting mostly of genes coding for virion components andvarious accessory proteins is discussed. Shuffling of the "shell" genes including genome reorganization and recombination between remote groups of viruses is considered to be one of the major factors of virus evolution. Multiple alignments for the conserved viral proteins were constructed and used to generate the respective phylogenetic trees. Based primarily on the tentative phylogeny for the...
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