Open Access Open Access  Restricted Access Subscription or Fee Access

Classes, taxa and categories in hierarchical virus classification: a review of current debates on definitions and names of virus species

MARC H.V. VAN REGENMORTEL

Abstract


The species taxon was introduced in virus classification as late as 1991 when it was endorsed by the International Committee on Taxonomy of Viruses (ICTV). The official definition of virus species was as follows: “A virus species is a polythetic class of viruses that constitute a replicating lineage and occupy a particular ecological niche”. Its key feature was that it incorporated the notion of polythetic class also known as a cluster class. Whereas monothetic classes are defined by one or a few properties that are both necessary and sufficient for membership in the class, polythetic classes are defined by a variable set of statistically covariant properties, none of which is a defining property necessarily present in every member of the class. Since a virus species class is a conceptual construction, it cannot be described by its physical or material properties and can only be defined by listing certain properties of the viruses that are its members. Properties used for defining virus species are properties of viruses that can be altered by a few mutations, such as their natural host range, pathogenicity, mode of transmission and small differences in the viral genome. This means that these species-defining properties vary considerably in different members of the same virus species. Since higher taxa such as genera and families have more viruses as members than species taxa, they require fewer defining properties than species taxa which require more properties to meet the qualifications for membership. The logical principle that increasing the number of qualifications decreases membership invalidates the claim that a single property could be sufficient for defining a virus species.

The bionominalist school of thought which claims that species are individuals instead of classes is examined and it is concluded that bionominalism does not provide a useful framework for classifying viruses. Since large numbers of sequences of viral genomes have become available, many attempts are currently made to establish species solely on the basis of genome data obtained from putative members of a viral species. Since the nucleic acid sequence present in a virus particle is part of the phenotype of the virus, a virus classification based on nucleotide sequences is a phenotypic classification that relies on molecular sequences rather than on the morphological and biological properties of viruses. Since it is not possible to infer the phenotypic properties of a virus from its genome sequence, a genome-based classification which privileges phylogeny is actually a classification of viral genomes rather than a classification of viruses.

In recent years, it has been suggested that it should be possible to define a virus species monothetically by a single species-defining property such as a genome nucleotide motif and that the term ‘polythetic’ should therefore be removed from the official species definition. In 2013, the ICTV ratified the following new definition of virus species: “A virus species is a monophyletic group of viruses whose properties can be distinguished from those of other species by multiple criteria”. Since every virus species, genus or family could be considered to be a monophyletic group, this was actually a definition of ‘virus taxon’ instead of virus species. Many objections were raised against this new species definition and these are available on the ICTV website. A major concern was that ‘polythetic class’ in the earlier definition had been replaced by ‘group’ of viruses, because a group is a collection of viruses that are linked by a part-whole relation, whereas the term class implies the logical relations of class membership and class inclusion used in all hierarchical classifications. The authors of the new definition actually claimed that the term class should be used only to denote a category in the classification hierarchy, above the category order and below the category phylum. Examples were also given of the pernicious consequences that followed from the fact that new species could now be established on the basis of a single criterion of nucleotide sequence similarity in viral genomes.

In 1998, the ICTV introduced species names that differed from virus names only by typography, with the result that measles virus became officially a member of the species Measles virus (italicized, with a capital initial). This led to considerable confusion and the ICTV subsequently agreed that its Study Groups in charge of the taxonomy and nomenclature of individual virus families could propose non-Latinized binomial names (NLBNs) for species in certain virus genera. Such NLBNs, which had been used unofficially for 50 years, are obtained by replacing the terminal word ‘virus’ that occurs in all common English virus names with the name of the genus to which the virus belongs, which also ends in -virus. Measles virus thus became a member of the species Measles morbillivirus which was more easily recognized as a species name since binomial names in biology are associated with taxonomic species names. In the last four years, numerous species NLBNs have been introduced in several virus families.


Keywords


Virus taxonomy, Linnaean hierarchy, International Committee on Taxonomy of Viruses (ICTV), bionominalism, polythetic class, virus identification, viral phenotype, DNA barcoding, viral genomes, species-defining properties, begomoviruses,

Full Text:

PDF (248KB)

References


Adams, M. J., Lefkowitz, E. J., King, A. M. Q. & Carstens, E. B. (2013) Recently agreed changes to the International Code of Virus Classification and Nomenclature. Archives of Virology, 158: 2633–2639.

Anonymous [International Commission on Zoological Nomenclature] (1999) International code of zoological nomenclature. Fourth edition. London (International Trust for zoological Nomenclature). <http://www.iczn.org/> [accessed 6 November 2015].

Anonymous [International Committee on Taxonomy of Viruses] (2002) The Universal Virus Database of the International Committee on Taxonomy of Viruses. <http://web.archive.org/web/20070611143548/ http:// phene.cpmc.columbia.edu/index.htm> [accessed 18 Feburary 2016].

Albouy, J. & Devergne, J. C. (1998) Maladies à virus des plantes ornementales. Paris (Éditions de l’INRA). Agut, H. (2002) Back to Latin and tradition: a proposal for an official nomenclature of virus species. Archives of Virology, 147: 1465–1470.

Baldwin, J. T. & Lessmann, O. (1998) What is Russell’s paradox? Scientific American, 17 August 1998. Ball, L. A. (2005) The universal taxonomy of viruses in theory and practice. In: C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger & L. A. Ball (ed.), Virus taxonomy. Eight Report of the International Committee on Taxonomy of Viruses. Amsterdam (Elsevier Academic Press): 3–8. <http://dx.doi.org/10.1016/b978-0-12-249951-7.50003-1>

Ball, L. A. & Mayo, M. A. (2004) Report from the 33rd Meeting of the ICTV executive committee. Archives of Virology, 149: 1259–1263. <http://dx.doi.org/10.1007/s00705-004-0338-3>

Bao, Y., Kapustin, Y. & Tatusova, T. (2010) Virus classification by Pairwise Sequence Comparison (PASC). In: M. H. V. Van Regenmortel & B. Mahy (ed.), Desk encyclopedia of general virology, Oxford (Academic Press, Elsevier): 95–100.

Beckner, M. (1959) The biological way of thought. New York (Columbia University Press).

Bernier, R. (1984) The species as an individual: facing essentialism. Systematic Zoology, 33: 460–469. <http:// dx.doi.org/10.2307/2413097>

Blachowicz, J. (2009) How science textbooks treat scientific method: a philosopher’s perspective. British Journal for the Philosophy of Science, 60: 303–344. http://dx.doi.org/10.1093/bjps/axp011

Bos, L. (1999a) Plant viruses, unique and intriging pathogens – A textbook of plant virology. Leiden (Backhuys Publishers).

Bos, L. (1999b) The naming of viruses: an urgent call to order. Archives of Virology, 144: 631–636. <http://dx.doi.org/ 10.1007/s007050050532>

Bos, L. (2000) Structure and typography of virus names. Archives of Virology, 145: 429–432. <http://dx.doi.org/ 10.1007/s007050050035>

Bos, L. (2002) International naming of viruses. A digest of recent developments. Archives of Virology, 147: 1471–1477. <http://dx.doi.org/10.1007/s007050200044>

Bos, L. (2003) Virus nomenclature; continuing topicality. Archives of Virology, 148: 1235–1246. <http://dx.doi.org/ 10.1007/s00705-003-0129-2>

Brown, J. K., Zerbini, F. M., Navas-Castillo, J., Morlones, E., Ramos-Sobrinho, R., Silva, J. C. F., Fiallo-Olivé, E., Briddon, R. W., Fernandez-Zepeda, C., Idris, A., Malathi,V. G., Martin, D. P., Rivera-Bustamante, R., Ueda, S. & Varsani, A. (2015) Revision of Begomovirus taxonomy based on pairwise sequence comparisons. Archives of Virology, 160: 1593–1619. <http: dx.doi.org/10.1007/s00705-015-2398-y>

Brunt, A., Crabtree, K. & Gibbs, A. (1990) Viruses of tropical plants. Wallingford (CAB International). Buchen-Osmond, C., Blaine, L. & Horzinek, M. C. (2000) The Universal Virus Database of ICTV (ICTVdB). In: M. H. V. Van Regenmortel, C. M. Fauquet, D. H. L. Bishop, E. B. Carstens, M. K. Estes, S. M., Lemon, J. Maniloff, M. A. Mayo, D. J. McGeoch, C. R. Pringle & R. B. Wickner (ed.), The Seventh Report of the International Committee on Taxonomy of Viruses, Academic Press, Elsevier Science & Technology Books. Buck, R. C. & Hull, D. L. (1966) The logical structure of the Linnaean hierarchy. Systematic Zoology, 15: 97–111. <http://dx.doi.org/10.2307/2411628>

Bukreyev, A. A., Chandran, K., Dolnik, O., Dye, J. M., Ebihara, H., Leroy, E. M., Mühlberger, E., Netesov, S. V., Patterson, J. L., Paweska, J. T., Saphire, E. O., Smither, S. J., Takada, A., Towner, J. S., Volchkov, V. E., Warren, T. K. & Kuhn, J. H. (2014) Discussions and decisions of the 2012–2014 International Committee on Taxonomy of Viruses (ICTV) Filoviridae Study Group, January 2012–June 2013. Archives of Virology, 159: 821–830. <http:// dx.doi.org/10.1007/s00705-013-1846-9>

Calisher, C. H., Horzinek, M., Mayo, M. A., Ackermann, H. W. & Maniloff, J. (1995) Sequence analyses and a unifying system of virus taxonomy: consensus via consent. Archives of Virology, 140: 2093–2099. <http://dx.doi.org/ 10.1007/BF01322696>

Calisher, C. H. & Mahy, B. M. J. (2003) Taxonomy: get it right or leave it alone. The American Society of tropical Medicine & Hygiene, 68: 505–506.

Calisher, C. H. & Van Regenmortel, M. H. V. (2009) Should all other biologists follow the lead of virologists and stop italicizing the names of living organisms? A proposal. Zootaxa, 2113: 63–68.

Claridge, M. F. (2010) Species are real biological entities. In: F. J. Ayala & R. Arp (ed.), Contemporary debates in philosophy of biology, Chichester, UK (Wiley-Blackwell): 91–109.

Colwell, R. K. (1992) Niche: a bifurcation in the conceptual lineage of the term. In: E. F. Keller & E. A. Lloyd (ed.), Keywords in evolutionary biology, Cambridge, Mass. (Harvard University Press): 241–248.

De Queiroz, K. & Donoghue, M. J. (1988) Phylogenetic systematics and the species problem. Cladistics, 4: 317–338. <http://dx.doi.org/10.1111/j.1096-0031.1988.tb00518.x>

Dekker, E. L., Dore, I., Porta, C. & Van Regenmortel, M. H. V. (1997) Conformational specificity of monoclonal antibodies used in the diagnosis of tomato mosaic virus. Archives of Virology, 95: 191–203.

Drebot, M. A., Henchal, E., Hjelle, B., Le Duc, J. W., Repik, P. M., Roehrig, J. T., Schmaljohn, C. S., Shope, R. E., Tesh, R. B., Weaver, S. C. & Calisher, C. H. (2002) Improved clarity of meaning from the use of both formal species names and common (vernacular) virus names in virological literature. Archives of Virology, 147: 2465–2471. <http://dx.doi.org/10.1007/s00705-002-0938-8>

Dubois, A. (2011) Species and ‘strange species’ in zoology: do we need a ‘unified concept of species’. Comptes rendus Palevol., 10: 77–94. <http://dx.doi.org/10.1016/j.crpv.2011.01.002>

Ebach, M. C. & Holdrege, C. (2005) More taxonomy, not DNA barcoding, Bioscience, 55: 822–823. <http://dx.doi.org/ 10.1641/0006-3568(2005)055[0823:MTNDB]2.0.CO;2>

Ereshefsky, M. (2009) Darwin’s solution to the species problem. Synthese. <http://dx.doi.org/10.1007/s11229-009- 9538-4>

Fauquet, C. M. (2010) Taxonomy, classification and nomenclature of viruses. In: B. W. J. Mahy & M. H. V. Van Regenmortel (ed.), Desk encyclopedia of general virology, San Diego (Elsevier): 80–95.

Fauquet, C. M., Bisaro, D. M., Briddon, R. W., Brown, J. K., Harrison, B. D., Rybicki, E. P., Stenger, D. C. & Stanley, J. (Study Group Chair) (2003) Virology Division News: revision of taxonomic criteria for species demarcation in the family Geminiviridae, and an updated list of begomovirus species. Archives of Virology, 148 : 405–421. <http:// dx.doi.org/10.1007/s00705-002-0957-5>

Fauquet, C. M., Briddo, R. W., Brown, J. K., Moriones, E., Stanley, J., Zerbini, M. & Zhou, X. (2008) Geminivirus strain demarcation and nomenclature. Archives of Virology, 153: 783–821. <http://dx.doi.org/10.1007/s00705-008-0037-6>

Fauquet, C. M. & Stanley, J. (2005) Revising the way we conceive and name viruses below the species level: a review of geminivirus taxonomy calls for new standardized isolate descriptors. Archives of Virology, 150: 2151–2179.

Fenner, F. (1976) The classification and nomenclature of viruses. Second Report of the International Committee on Taxonomy of Viruses. Intervirology, 7: 1–115. <http://dx.doi.org/10.1159/000149938>

Francki, R. I. B., Fauquet, C. M., Knudson, D. L. & Brown, F. (1991) Fifth Report of the International Committee on Taxonomy of Viruses. Archives of Virology, Supplementa, 2: 450. <http://dx.doi.org/10.1007/978-3-7091-9163-7>

Fristrup, K. (1992) Character: current usages. In: E. F. Keller & E. A. Lloyd (ed.), Keywords in evolutionary biology, Cambridge, MA (Harvard University Press): 45–51.

Ghiselin, M. T. (1974) A radical solution to the species problem. Systematic Zoology, 23: 536–544. <http://dx.doi.org/ 10.2307/2412471>

Gibbs, A. J. (2000) Virus nomenclature descending into chaos. Archives of Virology, 145: 1505–1507. <http:// dx.doi.org/10.1007/s007050070108>

Gibbs, A. J. (2003) Virus nomenclature: where next ? Archives of Virology, 148: 1645–1653. <http://dx.doi.org/10.1007/ s00705-003-0150-5>

Gibbs, A. J., Armstrong, J. S. & Gibbs, M. J. (2004) A type of nucleotide motif that distinguishes tobamovirus species more efficiently than nucleotide signatures. Archives of Virology, 149: 1941–1954.

Gibbs, A. J. & Gibbs, M. J. (2006) A broader definition of the ‘virus species’. Archives of Virology, 151: 1419–1422. <http://dx.doi.org/10.1007/s00705-006-0775-2>

Gibbs, A. J. & Harrison, B. (1976) Plant virology. The principles. London (Edward Arnold).

Gorbalenya, A. E. (2010) Phylogeny of viruses. In: B. W. J. Mahy & M. H. V. Van Regenmortel (ed.), Desk encyclopedia of general virology, San Diego (Elsevier): 66–69.

Greuter, W., Garrity, G., Hawksworth, D. L., Jahn, R., Kirkn P. M., Knapp, S., McNeill, J., Michel, E., Patterson, D. J., Pyle, R. & Tindall, B. R. J. (2011) Draft BioCode (2011). Principles and Rules regulating the naming of organisms. New draft, revised in November 2010. Bionomina, 3: 26–44. <http://dx.doi.org/10.11646/bionomina.3.1.3>

Hebert, P. D. N. & Gregory, T. R. (2005) The promise of DNA barcoding for taxonomy. Systematic Biology, 54: 852–859. <http://dx.doi.org/10.1080/10635150500354886>

Hull, D. L. (1976) Are species really individuals? Systematic Zoology, 25: 174–191. <http://dx.doi.org/10.2307/ 2412744>

Hull, D. L. (1988) Science as a process. Chicago (The University of Chicago Press). <http://dx.doi.org/10.7208/chicago/ 9780226360492.001.0001>

Inglis, W. G. (1991) Characters: the central mystery of taxonomy and systematics. Biological Journal of the Linnean Society, 44: 121–139. <http://dx.doi.org/10.1111/j.1095-8312.1991.tb00611.x>

King, A. (2012) Comments to proposed modification to code rule 3.21 (defining virus species). ICTV Discussions. <http://talk.ictvonline.org/discussions/ictv1/f/63/t/3930.aspx/> [Accessed on 6 November 2015].

King, A., Adams, M., Lefkowitz, E. & Carstens, E. (2012a) ICTV Proposal 2011.002sg. In: 2011.002auG. A.v9.statute_and_code_changes.pdf (page 15) <http://talk.ictvonline.org/files/ictv_official_taxonomy_updates _since_the_8th_report/m/general-2008/4444.aspx> [Accessed on 6 November 2015].

King, A., Lefkowitz, E., Adams, M. J. & Carstens, E. (ed.) (2012b) Virus taxonomy. Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press. ISBN: 978-0-12-384684-6.

Kingsbury, D. W. (1985) Species classification problems in virus taxonomy. Intervirology, 24: 62–70. <http:// dx.doi.org/10.1159/000149621>

Krupovic, M. & Bamford, D. H. (2010) Order to the viral universe. Journal of Virology, 84: 12476–12479. <http:// dx.doi.org/10.1128/JVI.01489-10>

Krupovic, M. & Bamford, D. H. (2011) Double-stranded DNA viruses: 20 families and only five different architectural principles for virus assembly. Current Opinion in Virology, 1: 118–124. <http://dx.doi.org/10.1016/ j.coviro.2011.06.001>

Kuhn, J. H., Dürrwald, R., Bao, Y., Briese, T., Carbone, K., Clawson, A. N., de Risi, J. L., Garten, W., Jahrling, P. B., Kolodziejek, J., Rubbenstroth, D., Schwemmle, M., Stenglein, M., Tomonaga, K., Weissenböck, H. & Nowotny, N. (2015) Taxonomic reorganization of the family Bornaviridae. Archives of Virology, 160: 621–632. <http:// dx.doi.org/10.1007/s00705-014-2276-z>

Kuhn, J. H. & Jahrling, P. B. (2010) Clarification and guidance on the proper usage of virus and virus species names. Archives of Virology, 145: 445–453. <http://dx.doi.org/10.1007/s00705-010-0600-9>

Lapage, S. P., Sneath, P. H. A., Lessel, E. F., Skerman, V. B. D., Seeliger, H. P. R. & Clark, W. A. (ed.) (1992) International code of nomenclature of bacteria. Washington, DC (ASM Press).

Lewontin, R. C. (1992) Genotype and phenotype. In: E. Fox Keller & E. A. Lloyd (ed.), Keywords in evolutionary biology, Cambridge (Harvard University Press): 137–144.

Mahner, M. & Bunge, M. (1997) Foundations of biophilosophy. Berlin (Springer-Verlag). <http://dx.doi.org/10.1007/ 978-3-662-03368-5>

Matthews, R. E. F. (1971) Plant virology. San Diego (Academic Press).

Matthews, R. E. F. (1979) Classification and nomenclature. Third Report of the International Committee on Taxonomy of Viruses. Intervirology, 7: 1–115.

Matthews, R. E. F. (1982) Classification and nomenclature of viruses. Fourth Report of the International Committee on Taxonomy of Viruses. Intervirology, 17: 1–200. <http://dx.doi.org/10.1159/000149278>

Matthews, R. E. F. (1983) The history of viral taxonomy. In: R. E. F. Matthews (ed.), A critical appraisal of viral taxonomy, Boca Raton, Florida (CRC Press): 1–35.

Matthews, R .E. F. (1985a) Viral taxonomy. Microbiological Sciences, 2: 74–75.

Matthews, R. E. F. (1985b) Viral taxonomy for the non-virologist. Annual Review of Microbiology, 39: 451–474. <http:/ /dx.doi.org/10.1146/annurev.mi.39.100185.002315>

Mayo, M. A. (2002) ICTV at the Paris ICV: results of the plenary session and the binomial ballot. Archives of Virology, 147: 2254–2260. <http://dx.doi.org/10.1007/s007050200052>

Mayo, M. A. & Horzinek, M. C. (1998) A revised version of the International Code of Virus Classification and Nomenclature. Archives of Virology, 143: 1645–1654. <http://dx.doi.org/10.1007/s007050050406>

Mayo, M. A. & Van Regenmortel, M. H. V. (2000) ICTV and the Virology Division News. Archives of Virology, 145: 1985–1988. <http://dx.doi.org/10.1007/s007050070071>

Mayr, E. (1970) Populations, species and evolution. Cambridge, Mass. (Harvard University Press). Mayr, E. (1982) The growth of biological thought. Diversity, evolution and inheritance. Cambridge, MA (Harvard University Press).

McNeill, J., Barrie, F. R., Buck, W. R., Demoulin, V., Greuter, W., Hawksworth, D. L., Herendeen, P. S., Knapp, S., Marhold, K., Prado, J., Prud’homme Van Reine, W. F., Smith, G. F. & Wiersema, J. H. (ed.) (2012) International code of nomenclature for algae, fungi, and plants (Melbourne Code). Koeltz Scientific Books. < http://www.iapttaxon. org/nomen/main.php/> [Accessed on 6 November 2015].

Milne, R. G. (1984) The species problem in plant virology. Microbiological Sciences, 1: 113–122. Mishler, B. D. (2010) Species are not uniquely real biological entities. In: F. J. Ayala & R. Arp (ed.), Contemporary debates in philosophy of Biology, Chichester, UK (Wiley-Blackwell): 110–122.

Moss, L. (2001) Deconstructing the gene and reconstructing molecular developmental systems. In: S. Oyama, P. Griffiths & R. Gray (ed.), Cycles of contigency – Developmental systems and evolution, Cambridge (MIT Press): 85–97.

Moss, L. (2003) What genes can’t do. Cambridge, Massachusetts (MIT Press).

Murphy, F. A., Fauquet, C. M., Bishop, D. H. L., Ghabrial, S. A., Jarvis, A. W., Martelli, G. P., Mayo, M. A. & Summers, M. D. (ed.) (1995) Virus taxonomy. Sixth Report of the International Committee on Taxonomy of Viruses.

Vienna (Springer). Neumann-Held, E. M. (2001) Let’s talk about genes: the process molecular gene concept and its context. In: S. Oyama, P. Griffiths & R. Gray (ed.), Cycles of contigency – Developmental systems and evolution, Cambridge (MIT Press): 69–84.

Nola, R. & Sankey, H. (2007) Theories of scientific method. Stocksfield (Acumen Publishers). Padidam, M., Sawyer, S., Fauquet, C. M. (1999) Possible emergence of new geminiviruses by frequent recombination. Virology, 265: 218–225. <http://dx.doi.org/10.1006/viro.1999.0056>

Pigliucci, M. (2003) Species as family resemblance concepts: the (dis-) solution of the species problem? BioEssays, 25: 596–602. <http://dx.doi.org/10.1002/bies.10284>

Ponomarenko, J. V. & Van Regenmortel, M. H. V. (2009) B cell epitope prediction. In: J. Gu & P. E. Bourne (ed.), Structural bioinformatics, Second edition, John Wiley & Sons Inc. pp. 849–879.

Pringle, C. R. (1991) The 20th meeting of the executive committee of the ICTV. Virus species, higher taxa, a universal database and other matters. Archives of Virology, 119: 303–304. <http://dx.doi.org/10.1007/BF01310680>

Quine, W. V. (1960) Word and object. Cambridge (MIT Press).

Quine, W. V. (1990) Classes versus properties. In: Quiddities: an intermittently philosophical dictionary, London (Penguin Books): 22–24.

Quine,W. V. & Ullian, J. S. (1978) The web of belief. New-York (McGraw-Hill): 44.

Radoshitzky, S. R., Bào, Y., Buchmeier, M. J., Charrel, R. N., Clawson, A. N., Clegg, C. S., De Risi, J. L., Emonet, S., Gonzalez, J. P., Kuhn, J. H., Lukashevich, I. S., Peters, C. J., Romanowski, V., Salvato, M. S., Stenglein, M. D. & de la Torre, J. C. (2015) Past, present, and future of arenavirus taxonomy. Archives of Virology, 160: 1851–1874. <http://dx.doi.org/10.1007/s00705-015-2418-y>

Ruse, M. (1987) Biological species: natural kinds, individuals, or what? The British Journal for the Philosophy of Science, 38: 225–242. <http://dx.doi.org/10.1093/bjps/38.2.225>

Van Regenmortel, M. H. V. (1989) Applying the species concept to plant viruses. Archives of Virology, 104: 1–17. <http://dx.doi.org/10.1007/BF01313804>

Van Regenmortel, M. H. V. (1990) Virus species: a much overlooked but essential concept in virus classification Intervirology, 31 : 241–254.

Van Regenmortel, M. H. V. (2000) Introduction to the species concept. In: M. H. V. Van Regenmortel, C. M. Fauquet, D. H. L. Bishop, E. B. Carstens, M. K. Estes, S. M., Lemon, J. Maniloff, M. A. Mayo, D. J. McGeoch, C. R. Pringle & R. B. Wickner (2000) Virus taxonomy. Seventh Report of the International Committee on Taxonomy of Viruses, New York & San Diego (Academic Press): 3–16.

Van Regenmortel, M. H. V. (2001) Perspectives on binomial names of virus species. Archives of Virology, 146: 1637–1640. <http://dx.doi.org/10.1007/s007050170086>

Van Regenmortel, M. H. V. (2003) Viruses are real, virus species are man-made taxonomic constructions. Archives of Virology, 148: 2483–2490. <http://dx.doi.org/10.1007/s00705-003-0246-y>

Van Regenmortel, M. H. V. (2006) Virologists, taxonomy and the demands of logic. Archives of Virology, 159: 1251–1255. <http://dx.doi.org/10.1007/s00705-006-0786-z>

Van Regenmortel, M. H. V. (2007) Virus species and virus identification: past and current controversies. Infection, Genetics & Evolution, 7: 133–144. <http://dx.doi.org/10.1016/j.meegid.2006.04.002>

Van Regenmortel, M. H. V. (2010a) Logical puzzles and scientific controversies: the nature of species, viruses and living organisms. Systematic & applied Microbiology, 33: 1–6. <http://dx.doi.org/10.1016/j.syapm.2009.11.001>

Van Regenmortel, M. H. V. (2010b) Virus species. In: B. W. J. Mahy & M. H. V. Van Regenmortel (ed.), Desk encyclopedia of general virology, San Diego (Elsevier): 37–41.

Van Regenmortel, M. H. V. (2011) Virus species. In: M. Tibayrenc (ed.), Genetics and evolution of infectious diseases, London, Burlington (Elsevier): 3–19. <http://dx.doi.org/10.1016/B978-0-12-384890-1.00001-7>

Van Regenmortel, M. H. V. (2016) The metaphor that viruses are living is alive and well, but it is no more than a metaphor. Studies in History & Philosophy of biological and biomedical Sciences, 59: 117–124.

Van Regenmortel, M. H. V., Ackermann, H.-W., Calisher, C. H., Dietzgen, R. G., Horzinek, M., Keil, G. M., Mahy, B. W. J., Martelli, G. P., Murphy, F. A., Pringle, C., Rima, B. K., Skern, T., Vetten, H.-J. & Weaver, S. C. (2013) Virus species polemics: 14 senior virologists oppose a proposed change to the ICTV definition of virus species. Archives of Virology, 158: 1115–1119. <http://dx.doi.org/10.1007/s00705-012-1583-5>

Van Regenmortel, M. H. V., Bishop, D. H. L., Fauquet, C. M., Mayo, M. A., Maniloff, J. & Calisher, C. H. (1997) Guidelines to the demarcation of virus species. Archives of Virology, 142: 1505–1518.

Van Regenmortel, M. H. V., Burke, D. S., Calisher, C. H., Dietzgen, R. G., Fauquet, C. M., Ghabrial, S. A., Jahrling, P. B., Johnson, K. M., Holbrook, M. R., Horzinek, M. C., Keil, G. M., Kuhn, J. H., Mahy, B. W., Martelli, G. P., Pringle, C., Rybicki, E. P., Skern, T., Tesh, R. B., Wahl-Jensen, V., Walker, P. J. & Weaver, S. C. (2010) A proposal to change existing virus species names to non-Latinized binomials. Archives of Virology, 155: 1909–1919. <http://dx.doi.org/10.1007/s00705-010-0831-9>

Van Regenmortel, M. H. V. & Fauquet, C. M. (2002) Only italicized species names of viruses have a taxonomic meaning. Archives of Virology, 147: 2247–2250. <http://dx.doi.org/10.1007/s007050200050>

Van Regenmortel, M. H. V. & Mahy, B. W. J. (2004) Emerging issues in viral taxonomy. Emerging infectious Diseases, 10: 8–13. <http://dx.doi.org/10.3201/eid1001.030279>

Van Regenmortel, M. H. V., Mayo, M. A., Fauquet, C. M. & Maniloff, J. (2000) Virus nomenclature: consensus versus chaos. Archives of Virology, 145: 2227–2232. <http://dx.doi.org/10.1007/s007050070053>

Van Rijsbergen, K. (1979) Information retrieval. Second edition. London (Butterworths).

Varsani, A., Martin, D. P., Navas-Castillo, J., Moriones, E., Hernandez-Zepeda, C., Idris, A., Zerbini, F. M. & Brown, J. K. (2014) Revisiting the classification of curtoviruses based on genome-wide pairwise identity. Archives of Virology, 159: 1873–1882. http://dx.doi.org/10.1007/s00705-014-1982-x

Vetten, H. J. & Haenni, A.-L. (2006) Taxon-specific suffixes for vernacular. Archives of Virology, 151: 1249–1250. <http://dx.doi.org/10.1007/s00705-006-0743-x>

Villarreal, L. P. (2010) Evolution of viruses. In: B. W. J. Mahy & M. H. V. Van Regenmortel (ed.), Desk encyclopedia of general virology, San Diego (Elsevier): 70–80.

Wildy, P. (1971) Classification and nomenclature of First Report of the International Committee on Nomenclature of Viruses. Monographs in Virology, 5, Basel (Karger).

Wolf, U. (1995) The genetic contribution to the phenotype. Human Genetics, 95: 127–148. <http://dx.doi.org/10.1007/ BF00209392>




DOI: http://dx.doi.org/10.11646/bionomina.10.1.1

Refbacks

  • There are currently no refbacks.


 

ISSN 1179-7649 (print);   ISSN 1179-7657 (online)

Published by Magnolia Press, Auckland, New Zealand