Virus Species

Genetics and Evolution of Infectious Diseases

Volumn , Issue , 2011, Pages 3-19

  Van Regenmortel, Marc H V ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84872262220     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-384890-1.00001-7     Document Type: Chapter

References (89)

1. Adams M.J., Antoniw J.F., Bar-Joseph M. The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Arch. Virol. 2004, 149:1045-1060.
2. Agut H. Back to Latin and tradition: a proposal for an official nomenclature of virus species. Arch. Virol. 2002, 147:1465-1470.
3. Albouy J., Devergne J.C. Maladies à Virus des Plantes Ornementales 1998, Editions INRA, Paris.
4. Ball L.A. The universal taxonomy of viruses in theory and practice. Eighth ICTV Report 2005, 11-16. Elsevier. C.M. Fauquet (Ed.).
5. Ball L.A., Mayo M.A. Report from the 33rd Meeting of the ICTV executive committee. Arch. Virol. 2004, 149:1259-1263.
6. Bao Y., Kapustin Y., Tatusova T. Virus classification by Pairwise Sequence Comparison (PASC). Desk Encyclopedia of General Virology 2010, 95-100. Academic Press, Elsevier, Oxford. M.H.V. Van Regenmortel, B. Mahy (Eds.).
7. Baum D., Donoghue M. Choosing among alternative "phylogenetic" species concepts. Syst. Biol. 1995, 20:560-573.
8. Beckner M. The Biological Way of Thought 1959, Columbia University Press, New York, NY.
9. Bos L. The naming of viruses: an urgent call to order. Arch. Virol. 1999, 144:631-636.
10. Bos L. Plant Viruses, Unique and Intriguing Pathogens-A Textbook of Plant Virology 1999, Backhuys Publishers, Leiden.
11. Bos L. Coming to grips with the naming of viruses; continuing discord, or a way out. Arch. Virol. 2007, 152:649-653.
12. Buck R.C., Hull D.L. The logical structure of the Linnaean hierarchy. Syst. Zool. 1966, 15:97-111.
13. Bunge M. Philosophical Dictionary 2003, Prometheus Books, Amherst, NY.
14. Calisher C.H., Van Regenmortel M.H.V. Should all other biologists follow the lead of virologists and stop italicizing the names of living organisms? A proposal. Zootaxa 2009, 2113:63-68.
15. Calisher C.H., Horzinek M.C., Mayo M.A., Ackermann H.W., Maniloff J. Sequence analyses and a unifying system of virus taxonomy: consensus via consent. Arch. Virol. 1995, 140:2093-2099.
16. Calisher C.H., Mahy B.M.J. Taxonomy: get it right or leave it alone. Am. J. Trop. Med. Hyg. 2003, 68:505-506.
17. Carstens E.B., Ball L.A. Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2008). Arch. Virol. 2009, 154:1181-1188.
18. Claridge M.F. Species are real biological entities. Contemporary Debates in Philosophy of Biology 2010, 91-109. Wiley-Blackwell, Chichester. F.J. Ayala, R. Arp (Eds.).
19. de Queiroz K. Species concepts and species delimitation. Syst. Biol. 2007, 56:879-886.
20. Domingo E., Holland J.J. RNA virus mutations and fitness for survival. Ann. Rev. Microbiol. 1997, 51:151-178.
21. Doolittle W.F., Bapteste E. Pattern pluralism and the Tree of Life hypothesis. Proc. Natl. Acad. Sci. (USA) 2007, 104:2043-2049.
22. Drebot M.A., Henchal E., Hjelle B., LeDuc J.W., Repik P.M., Roehrig J.T., Schmaljohn C.S., Shope R.E., Tesch R.B., Weaver S.C., Calisher C.H. Improved clarity of meaning from the use of both formal species names and common (vernacular) virus names in virological literature. Arch. Virol. 2002, 147:2465-2471.
23. Ebach M.C., Holdrege C. More taxonomy, not DNA barcoding. Bioscience 2005, 55:822-823.
24. Eigen M. On the nature of viral quasispecies. Trends Microbiol. 1996, 4:216-218.
25. Ereshefsky M. Darwin's solution to the species problem. Synthese 2009, 10.1007/s11229-009-9538-4.
26. Ereshefsky M. Mystery of mysteries: Darwin and the species problem. Cladistics 2010, 26:1-13.
27. Fauquet C.M., Stanley J. Revising the way we conceive and name viruses below the species level: a review of geminivirus taxonomy calls for new standardized isolate descriptors. Arch. Virol. 2005, 150:2151-2179.
28. Fauquet C.M., Mayo M.A., Maniloff J., Desselberger U., Ball L.A. Virus Taxonomy, Classification and Nomenclature of Viruses, Eighth Report of the ICTV 2005, Elsevier, San Diego, CA.
29. Fauquet C.M., Briddo R.W., Brown J.K., Moriones E., Stanley J., Zerbini M., et al. Geminivirus strain demarcation and nomenclature. Arch. Virol. 2008, 153:783-821.
30. Fenner F. The classification and nomenclature of viruses. Second report of the International Committee on Taxonomy of Viruses. Intervirology 1976, 7:1-115.
31. Francki R.I.B. Plant virus taxonomy. Handbook of Plant Virus Infections and Comparative Diagnosis 1981, 3-16. Elsevier, Amsterdam. E. Kurstak (Ed.).
32. Fristrup K. Character: current usages. Keywords in Evolutionary Biology 1992, 45-51. Harvard University Press, Cambridge, MA. E.F. Keller, E.A. Lloyd (Eds.).
33. Ghiselin M.T. A radical solution to the species problem. Syst. Zool. 1974, 23:536-544.
34. Ghiselin M.T. Metaphysics and the Origin of Species 1997, New York State University Press, New York, NY.
35. Gibbs A.J. Virus nomenclature, what next?. Arch. Virol. 2003, 148:1645-1653.
36. Gibbs A., Gibbs M.J. A broader definition of the "virus species". Arch. Virol. 2006, 148:1645-1653.
37. Hebert P.D.N., Gregory T.R. The promise of DNA barcoding for taxonomy. Syst. Biol. 2005, 54:852-859.
38. Holland J.J., De la Torre J.C., Steinhauer D.A. RNA virus populations as quasispecies. Genetic Diversity of RNAViruses 1992, Springer-Verlag, New York, NY. J.J. Holland (Ed.).
39. Holmes E.C., Moya A. Is the quasi-species concept relevant to RNA viruses?. J. Virol. 2002, 76:460-462.
40. Hull D.L. Are species really individuals?. Syst. Zool 1976, 25:174-191.
41. Hull D.L. Science as a Process 1988, The University of Chicago Press, Chicago, IL.
42. Hull D. Individual. Keywords in Evolutionary Biology 1992, 181-187. Harvard University Press, Cambridge, MA. E. Fox-Keller, E. Lloyd (Eds.).
43. Inglis W.G. Characters: the central mystery of taxonomy and systematics. Biol. J. Linn. Soc. 1991, 44:121-139.
44. Kuhn J.H., Jahrling P.B. Clarification and guidance on the proper usage of virus and virus species names. Arch. Virol. 2010, 155:445-453.
45. Lewontin R.C. Genotype and phenotype. Keywords in Evolutionary Biology 1992, 137-144. Harvard University Press, Cambridge, MA. E. Fox Keller, E.A. Lloyd (Eds.).
46. Lopez-Garcia P., Moreira D. Yet viruses cannot be included in the tree of life. Nat. Rev. Microbiol. 2009, 7:615-617. (August 2009) doi: 10.1038/nrmicro2108-c7.
47. Mahner M., Bunge M. Foundations of Biophilosophy 1997, Springer-Verlag, Berlin.
48. Matthews R.E.F. Classification and nomenclature of viruses. Fourth report of the International Committee on Taxonomy of Viruses. Intervirology 1982, 17:1-200.
49. Matthews R.E.F. The history of viral taxonomy. A Critical Appraisal of Viral Taxonomy 1983, 1-35. CRC Press, Boca Raton, FL. R.E.F. Matthews (Ed.).
50. Matthews R.E.F. Viral taxonomy for the non-virologist. Ann. Rev. Microbiol. 1985, 39:451-474.
51. Mayden R.L. A hierarchy of species concepts: the denouement in the saga of the species problem. Species: The Units of Biodiversity 1997, 381-424. Chapman and Hall, London. M.F. Claridge, H.A. Dawah, M.R. Wilson (Eds.).
52. Mayo M.A. ICTV at the Paris ICV: results of the plenary session and the binomial ballot. Arch. Virol. 2002, 147:2254-2260.
53. Mayo M.A., Haenni A.-L. Report from the 36th and 37th meetings of the Executive Committee of the ICTV. Arch. Virol. 2006, 151:1031-1037.
54. Mayo M.A., Horzinek M.C. A revised version of the International Code of Virus Classification and Nomenclature. Arch. Virol. 1998, 143:1645-1654.
55. Mayo M.A., Maniloff J., Van Regenmortel M.H.V., Fauquet C.M. The type species in virus taxonomy. Arch. Virol. 2002, 147:1271-1274.
56. Mayr E. Populations, Species and Evolution 1970, Harvard University Press, Cambridge, MA.
57. Milne R.G. The species problem in plant virology. Microbiol. Sci. 1984, 1:113-122.
58. Moreira D., Brochier-Armanet C. Giant viruses, giant chimeras: the multiple evolutionary histories of Mimivirus genes. BMC Evol. Biol. 2008, 8:e12.
59. Moreira D., Lopez-Garcia P. Ten reasons to exclude viruses from the tree of life. Nat. Rev. Microbiol. 2009, 7:306-311.
60. Virus Taxonomy. Sixth Report of the ICTV 1995, Springer, Vienna. F.A. Murphy, C.M. Fauquet, D.H.L. Bishop, S.A. Ghabrial, A.W. Jarvis, G.P. Martelli (Eds.).
61. Padidam M., Sawyer S., Fauquet C.M. Possible emergence of new geminiviruses by frequent recombination. Virology 1999, 265:218-225.
62. Pigliucci M. Species as family resemblance concepts: the (dis-)solution of the species problem?. Bioessays 2003, 25:596-602.
63. Pringle C.R. The 20th meeting of the executive committee of the ICTV. Virus species, higher taxa, a universal database and other matters. Arch. Virol. 1991, 119:303-304.
64. Pringle C.R. The order Mononegavirales. Arch. Virol. 1997, 142:2321-2326.
65. Raoult D., Forterre P. Redefining viruses: lessons from Mimivirus. Nat. Rev. Microbiol. 2008, 6:315-319.
66. Raoult D., Audic S., Robert C., Abergel C., Renesto P., Ogata H., et al. The 1.2-megabase genome sequence of Mimivirus. Science 2004, 306:1344-1350.
67. Sanjuan R. Quasispecies. Desk Encyclopedia of General Virology 2010, 42-48. Academic Press, Elsevier, Oxford. B.W.J. Mahy, M.H.V. Van Regenmortel (Eds.).
68. Schaefer J.A., Wilson C.C. The fuzzy structure of populations. Can. J. Zool. 2002, 80:2235-2241.
69. Smith D.B., McAllister J., Casino C., Simmonds P. Virus "quasi-species": making a mountain out of a molehill?. J. Gen. Virol. 1997, 78:1511-1519.
70. Stamos D.N. The Species Problem. Biological Species, Ontology and the Metaphysics of Biology 2003, Lexington Books, Oxford.
71. Van Regenmortel M.H.V. Applying the species concept to plant viruses. Arch. Virol. 1989, 104:1-17.
72. Van Regenmortel M.H.V. From absolute to exquisite specificity. Reflections on the fuzzy nature of species, specificity and antigenic sites. J. Immunol. Meth. 1998, 216:37-48.
73. Van Regenmortel M.H.V. Introduction to the species concept in virus taxonomy. Virus Taxonomy. Seventh Report of the International Committee on Taxonomy of Viruses 2000, 3-16. Academic Press, San Diego, CA. M.H.V. Van Regenmortel, C. Fauquet, D.H.L. Bishop, E.B. Carstens, M.K. Estes, S.M. Lemon (Eds.).
74. Van Regenmortel M.H.V. On the relative merits of italics, Latin and binomial nomenclature in virus taxonomy. Arch. Virol. 2000, 145:433-441.
75. Van Regenmortel M.H.V. Perspectives on binomial names of virus species. Arch. Virol. 2001, 146:1637-1640.
76. Van Regenmortel M.H.V. Viruses are real, virus species are man-made taxonomic constructions. Arch. Virol. 2003, 148:2481-2488.
77. Van Regenmortel M.H.V. Virologists, taxonomy and the demand of logic. Arch. Virol. 2006, 151:1251-1255.
78. Van Regenmortel M.H.V. Virus species and virus identification: past and current controversies. Infect. Gen. Evol. 2007, 7:133-144.
79. Van Regenmortel M.H.V. Logical puzzles and scientific controversies: the nature of species, viruses and living organisms. Syst. Appl. Microbiol. 2010, 33:1-6.
80. Van Regenmortel M.H.V. The nature of viruses. Desk Encyclopedia of General Virology 2010, 23-29. Academic Press, Elsevier, Oxford. B.W.J. Mahy, M.H.V. Van Regenmortel (Eds.).
81. Van Regenmortel M.H.V., Fauquet C.M. Only italicised species names of viruses have a taxonomic meaning. Arch. Virol. 2002, 147:2247-2250.
82. Van Regenmortel M.H.V., Bishop D.H.L., Fauquet C.M., Mayo M.A., Maniloff J., Calisher C.H. Guidelines to the demarcation of virus species. Arch. Virol. 1997, 142:1505-1518.
83. Villarreal L.P. Viruses and The Evolution of Life 2005, ASM Press, Washington, DC.
84. Waugh J. DNA barcoding in animal species: progress, potential and pitfalls. Bioessays 2007, 29:188-197.
85. Species Concepts and Phylogenetic Theory: A Debate 2000, Columbia University Press, New York, NY. Q. Wheeler, R. Meier (Eds.).
86. Wheeler Q.D., Valdecasas A.G. Taxonomy: myths and misconceptions. An. Jard. Bot. Madr. 2007, 64:237-241.
87. Wimmer E. The test-tube synthesis of a chemical called poliovirus: the simple synthesis of a virus has far-reaching societal implications. EMBO Rep. 2006, 7:S3-S9.
88. Wittgenstein L. Philosophical Investigations 1953, Macmillan, New York, NY.
89. Wolkowicz R., Schaechter M. What makes a virus a virus?. Nat. Rev. Microbiol. 2008, 6:643.