Virus species and virus identification: Past and current controversies

Infection, Genetics and Evolution

Volumn 7, Issue 1, 2007, Pages 133-144

  Van Regenmortel, M H V ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

Geminiviruses; Pair wise sequence comparisons; Papillomaviruses; Picornaviruses; Polythetic class; Potyviruses; Quasi species; Species; Virus classification; Virus nomenclature; Virus species; Virus strain

Indexed keywords

ARTICLE; NOMENCLATURE; NONHUMAN; PRIORITY JOURNAL; SPECIES IDENTIFICATION; TAXONOMY; VIRUS CLASSIFICATION; VIRUS DIAGNOSIS; VIRUS IDENTIFICATION;

PAPILLOMAVIRIDAE;

EID: 33845250191     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2006.04.002     Document Type: Note

References (100)

1. Adams M.J., Antoniw J.F., and Fauquet C.M. Molecular criteria for genus and species discrimination within the family Potyviridae. Arch. Virol. 150 (2005) 459-479
2. Agut H. Back to Latin and tradition: a proposal for an official nomenclature of virus species. Arch. Virol. 147 (2002) 1465-1470
3. Albouy J., and Devergne J.C. Maladies à virus des plantes ornementales (1998), Editions INRA, Paris
4. Ball, L.A., 2005. The universal taxonomy of viruses in theory and practice. In: Fauquet, C.M., et al. (Eds.), Eighth ICTV Report. Elsevier, pp. 11-16.
5. Ball L.A., and Mayo M.A. Report from the 33rd Meeting of the ICTV executive committee. Arch. Virol. 149 (2004) 1259-1263
6. Bao Y., Federhen S., Leipe D., Pham V., Resenchuk S., Rozanov M., Tatusov R., and Tatusova T. Guest commentary. National Center for Biotechnology Information Viral Genomes Project. J. Virol. (2004) 7291-7298
7. Beckner M. The Biological Way of Thought (1959), Columbia University Press, New York
8. Bos L. The naming of viruses: an urgent call to order. Arch. Virol. 144 (1999) 631-636
9. Bos L. Structure and typography of virus names. Arch. Virol. 145 (2000) 429-432
10. Bos L. International naming of viruses a digest of recent developments. Arch. Virol. 147 (2002) 1471-1477
11. Bos L. Virus nomenclature; continuing topicality. Arch. Virol. 148 (2003) 1235-1246
12. Buchen-Osmond, C., Blaine, L. and Horzinek, M., 2000. The universal virus database of ICTV (ICTVdB). In: Van Regenmortel M.H.V., Fauquet, C.M., Bishop, D.H.L., et al. (Eds.), Seventh ICTV Report. San Diego Academic Press pp. 19-24.
13. Buck R.C., and Hull D.L. The logical structure of the Linnaean hierarchy. Syst. Zool. 15 (1966) 97-111
14. Calisher C.H., and Mahy B.W.J. Taxonomy: get it right or leave it alone. Am. J. Trop. Med. Hyg. 68 (2003) 505-506
15. Calisher C.H., Horzinek M.C., Mayo M.A., Ackermann H.W., and Maniloff J. Sequence analyses and a unifying system of virus taxonomy: consensus via consent. Arch. Virol. 140 (1995) 2093-2099
16. In: Claridge M.F., Dawah H.A., and Wilson M.R. (Eds). Species: The Units of Biodiversity (1997), Chapman and Hall, London
17. Colwell R.K. Niche: a bifurcation in the conceptual lineage of the term. In: Keller E.F., and Lloyd E.A. (Eds). Keywords in Evolutionary Biology (1992), Harvard University Press, Cambrigde, Mass 241-248
18. Damond F., Worobey M., Campa P., et al. Identification of a highly divergent HIV type 2 and proposal for a change in HIV type 2 classification. Aids Res. Hum. Retrovir. 20 (2004) 66-672
19. Dekker E.L., Dore I., Porta C., and Van Regenmortel M.H.V. Conformational specificity of monoclonal antibodies used in the diagnosis of tomato mosaic virus. Arch. Virol. 95 (1997) 191-203
20. De Villiers E.M., Fauquet C., Broker T.R., Bernard H.-U., and Zur Hausen H. Classification of papillomaviruses. Virology 324 (2004) 17-27
21. Dijkstra J., and Khan J.A. The current naming of plant viruses: a critical appraisal. Arch. Virol. 147 (2002) 2251-2253
22. Domingo E. Quasispecies theory in virology. J. Virol. 76 (2002) 463-465
23. Domingo E., and Holland J.J. RNA virus mutations and fitness for survival. Ann. Rev. Microbiol. 51 (1997) 151-178
24. Domingo E., Holland J.J., Biebricher C., and Eigen M. Quasispecies: the concept and the word. In: Gibbs A.J., Calisher C.H., and Garcia-Arenal F. (Eds). Molecular Basis of Virus Evolution (1995), Cambridge University Press, Cambridge 171
25. 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., and 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. 147 (2002) 2465-2471
26. Dupré J. The Disorder of Things. Metaphysical Foundations of the Disunity of Science (1993), Harvard Univ. Press, Cambridge, MA
27. Eigen M. New concepts for dealing with the evolution of nucleic acids. Cold Spring Harbor Symp. Quant. Biol. 52 (1987) 307-319
28. Eigen M. On the nature of viral quasispecies. Trends Microbiol. 4 (1996) 216-218
29. Ereshefsky M. Eliminative pluralism. In: Hull D.L., and Ruse M. (Eds). The Philosophy of Biology (1998), University press, Oxford 348-368
30. Fauquet C.M., and Fargette D. International Committee on Taxonomy of Viruses and the 3, 142 unassigned species. Virology Journal. 2 (2005) 64-73
31. Fauquet C.M., and Martelli G.P. Updated ICTV list of names and abbreviations of viruses, viroids and satellites infecting plants. Arch. Virol. 140 (1995) 393-413
32. Fauquet C.M., and Pringle C.R. Abbreviations for vertebrate virus species names. Arch. Virol. 144 (1999) 1865-1880
33. Fauquet C.M., and 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. 150 (2005) 2151-2179
34. Fauquet C.M., Bisaro D.M., Briddon R.W., Brown J.K., Harrison B.D., Rybicki E.P., Stenger D.C., and Stanley J. Revision of taxonomic criteria for species demarcation in the family Geminiviridae, and an updated list of begomovirus species. Arch. Virol. 148 (2003) 405-421
35. Fauquet C.M., Mayo, M.A., Maniloff, J. Desselberger, U., Ball, L.A., 2005. Virus Taxonomy. Classification and Nomenclature of Viruses. Eighth Report of the ICTV, Elsevier, San Diego.
36. Fenner F. The Classification and Nomenclature of Viruses. Second Report of the International Committee on Taxonomy of Viruses. Intervirology 7 (1976) 1-115
37. Ghiselin M.T. A radical solution to the species problem. Syst. Zool. 23 (1974) 536-544
38. Ghiselin M.T. "Definition" "character" and other equivocal terms. Syst. Zool. 33 (1984) 104-110
39. Ghiselin M.T. Metaphysics and the Origin of Species (1997), New York State University Press, New York
40. Gibbs A. Virus nomenclature descending into chaos. Arch. Virol. 145 (2000) 1505-1507
41. Gibbs A.J. Virus nomenclature, what next?. Arch. Virol. 148 (2003) 1645-1653
42. Gibbs A.J., Armstrong J.S., and Gibbs M.J. A type of nucleotide motif that distinguishes tobamovirus species more efficiently than nucleotide signatures. Arch. Virol. 149 (2004) 1941-1954
43. Gibbs A., and Harrison B. Plant Virology. The Principles (1976), Edward Arnold, London pp. 292
44. Hanage W.P., Fraser C., and Spratt B.G. Fuzzy species among recombinogenic bacteria. BMC Biol. 3 (2005) 6-17
45. Holland J.J., De la Torre J.C., and Steinhauer D.A. RNA virus populations as quasispecies. In: Holland J.J. (Ed). Genetic Diversity of RNA Viruses (1992), Springer-Verlag, New York
46. Holmes E.C., and Moya A. Is the quasispecies concept relevant to RNA viruses?. J. Virol. 76 (2002) 460-462
47. Hull D.L. Are species really individuals?. Syst. Zool. 25 (1976) 174-191
48. Hull D.L. The ideal species concept and why we can not get it. In: Claridge M.F., Dawah H.A., and Wilson M.R. (Eds). Species: The Units of Biodiversity (1997), Chapman and Hall, London 381-424
49. Hull R., Milne R.G., and Van Regenmortel M.H.V. A list of proposed standard acronyms for plant viruses and viroids. Arch. Virol. 120 (1991) 151-164
50. Jelcic I., Hotz-Wagenblatt A., Hunziker A., Zur Hausen H., and De Villiers E.-M. Isolation of multiple TT virus genotypes from spleen biopsy tissue from a hodgkin's disease patient: genome reorganization and diversity in the hypervariable region. J. Virology. 78 (2004) 7498-7507
51. Kingsbury D.W. Species classification problems in virus taxonomy. Intervirology 24 (1985) 62-70
52. Kitcher P. Species. Philos. Sci. 51 (1984) 308-333
53. Lovtrup S. The evolutionary species: Fact or fiction?. Syst. Zool. 28 (1979) 386-392
54. Mahner M., and Bunge M. Foundations of Biophilosophy (1997), Springer-Verlag, Berlin
55. Matthews R.E.F. Classification and nomenclature of viruses. Third Report of the International Committee on Taxonomy of Viruses. Intervirology 12 (1979) 132-296
56. Matthews R.E.F. Classification and nomenclature of viruses. Fourth Report of the International Committee on Taxonomy of Viruses. Intervirology 17 (1982) 1-200
57. Matthews R.E.F. The history of viral taxonomy. In: Matthews R.E.F. (Ed). A Critical Appraisal of Viral Taxonomy (1983), CRC Press, Boca Raton, Florida 1-35
58. Matthews R.E.F. Viral taxonomy for the non-virologist. Ann. Rev. Microbiol. 39 (1985) 451-474
59. Mayden R.L. A hierarchy of species concepts: the denouement in the saga of the species problem. In: Claridge M.F., Dawah H.A., and Wilson M.R. (Eds). Species: The Units of Biodiversity (1997), Chapman and Hall, London 381-424
60. Mayo M.A. ICTV at the Paris ICV: results of the plenary session and the binomial ballot. Arch. Virol. 147 (2002) 2254-2260
61. Mayo M.A., and Horzinek M.C. A revised version of the International Code of Virus Classification and Nomenclature. Arch. Virol. 143 (1998) 1645-1654
62. Mayo M.A., Maniloff J., Van Regenmortel M.H.V., and Fauquet C.M. The type species in virus taxonomy. Arch. Virol. 147 (2002) 1271-1274
63. Mayr E. The Growth of Biological Thought; Diversity. Evolution and Inheritance (1982), Harvard University Press, Cambridge, MA
64. McNeill D., and Freiberger P. Fuzzy Logic (1993), Simon and Schuster, New York
65. Milne R.G. The species problem in plant virology. Microbiol. Sci. 1 (1984) 113-122
66. Mischler B.D., and Donoghue M.J. Species concepts: a case for pluralism. Syst. Zool. 31 (1982) 491-503
67. Murphy F.A. Viral taxonomy. In: Fields B.N., Knipe D.M., Howley P.M., et al. (Eds). Fields Virology. 3nd ed. (1996), Lippincott-Raven Publishers, Philadelphia 15-57
68. 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. (Eds), 1995. Virus Taxonomy. Sixth Report of the ICTV, Springer, Vienna.
69. Oberste M.S., Maher K., Kilpatrick D.R., and Pallansch M.A. Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification. J. Virol. 73 (1999) 1941-1948
70. Padidam M., Sawyer S., and Fauquet C.M. Possible emergence of new geminiviruses by frequent recombination. Virology 265 (1999) 218-225
71. Patthy L. Protein Evolution (1999), Blackwell Science, Oxford
72. Pigliucci M. Species as family resemblance concepts: the (dis-)solution of the species problem?. Bioessays 25 (2003) 596-602
73. Pringle, C.R., 1991. The 20th Meeting of the Executive Committee of the ICTV. Virus species, higher taxa, a universal database and other matters. Arch. Virol. 119, 303-304.
74. Quine W.V. Classes versus properties. Quiddities (1987), Belknap Press, Cambridge, MA pp. 2-24
75. Robertson D.L., Anderson J.A., Bradac J.K., et al. HIV-1 nomenclature proposal. Science 288 (2000) 55-57
76. Rossello-Mora R., and Amann R. The species concept of prokaryotes. FEMS Microbiol. Rev. 25 (2001) 39-67
77. Schaefer J.A., and Wilson C.C. The fuzzy structure of populations. Can. J. Zool. 80 (2002) 2235-2241
78. Smith D.B., McAllister J., Casino C., and Simmonds P. Virus "quasispecies": making a mountain out of a molehill?. J. Gen. Virol. 78 (1997) 1511-1519
79. Stanley, J., Bisaro, D.M., Bridden, R.W., et al., 2005. Family: Geminiviridae. In: Fauquet, C.M., et al (Eds.), Eighth ICTV Report, Elsevier, Academic Press, San Diego, pp. 301-326.
80. Tamames J., Ouzounis C., Sander C., and Valencia A. Genomes with distinct function composition. FEBS Lett. 389 (1996) 96-101
81. Van Regenmortel M.H.V. Serology and Immunochemistry of Plant Viruses (1982), Academic Press, New York 302 pp
82. Van Regenmortel M.H.V. Applying the species concept to plant viruses. Arch. Virol. 104 (1989) 1-17
83. Van Regenmortel M.H.V. Virus species, a much overlooked but essential concept in virus classification. Intervirology 31 (1990) 241-254
84. Van Regenmortel M.H.V. From absolute to exquisite specificity. Reflections on the fuzzy nature of species, specificity and antigenic sites. J. Immun. Meth. 216 (1998) 37-48
85. Van Regenmortel M.H.V. How to write the names of virus species. Arch. Virol. 144 (1999) 1041-1042
86. Van Regenmortel, M.H.V., 2000a. Introduction to the species concept in virus taxonomy. In: Van Regenmortel, M.H.V., Fauquet, C.M., Bishop, D.H.L., Carstens, E.B., Estes, M.K., Lemon, S.M., McGeogh, D.J., Maniloff, J., Mayo, M.A., Pringle, C.R, Wickner, R.B., (Eds.), Virus Taxonomy. Seventh ICTV Report. San Diego: Academic Press, pp. 3-16.
87. Van Regenmortel M.H.V. On the relative merits of italics, Latin and binomial nomenclature in virus taxonomy. Arch. Virol. 145 (2000) 433-441
88. Van Regenmortel M.H.V. Perspectives on binomial names of virus species. Arch. Virol. 146 (2001) 1637-1640
89. Van Regenmortel M.H.V. Viruses are real, virus species are man-made taxonomic constructions. Arch. Virol. 148 (2003) 2481-2488
90. Van Regenmortel, M.H.V., 2006. Virologists, taxonomy and the demands of logic. Arch. Virol. 151, in press.
91. Van Regenmortel M.H.V., and Fauquet C.M. Only italicized species names of viruses have a taxonomic meaning. Arch. Virol. 147 (2002) 2247-2250
92. Van Regenmortel M.H.V., and Mahy B.W.J. Emerging issues in virus taxonomy. Emerg. Infect. Dis. 10 (2004) 8-13
93. Van Regenmortel M.H.V., Maniloff J., and Calisher C.H. The concept of virus species. Arch. Virol. 120 (1991) 313-314
94. Van Regenmortel M.H.V., Bishop D.H.L., Fauquet C.M., Mayo M.A., Maniloff J., and Calisher C.H. Guidelines to the demarcation of virus species. Arch. Virol. 142 (1997) 1505-1518
95. Van Regenmortel, M.H.V., Fauquet, C.M., Bishop, D.H.L., Carstens, E.B., Estes, M.K., Lemon, S.M., McGeogh, D.J., Maniloff,J., Mayo, M.A., Pringle, C.R, Wickner, R.B. (Eds), 2000a. Taxonomy of viruses. Seventh ICTV Report. San Diego: Academic Press.
96. Van Regenmortel M.H.V., Mayo M.A., Fauquet C.M., and Maniloff J. Virus nomenclature: consensus versus chaos. Arch. Virol. 145 (2000) 2227-2232
97. Villarreal L.P. Viruses and The Evolution of Life (2005), ASM Press, Washington DC pp. 395
98. Wiley E. The evolutionary species concept reconsidered. Syst. Zool. 27 (1978) 17-26
99. Wittgenstein L. Philosophical Investigations (1953), Macmillan, New-York
100. Zanotto P.M., de A., Gibbs M.J., Gould E.A., and Holmes E.C. A reevaluation of the higher taxonomy of viruses based on RNA polymerases. J. Virol. 70 (1996) 6083-6096