1887

Abstract

Species definitions of viruses are frequently descriptive, with assignments often being based on their disease manifestations, host range, geographical distribution and transmission routes. This method of categorizing viruses has recently been challenged by technology advances, such as high-throughput sequencing. These have dramatically increased knowledge of viral diversity in the wider environment that dwarfs the current catalogue of viruses classified by the International Committee for the Taxonomy of Viruses (ICTV). However, because such viruses are known only from their sequences without phenotypic information, it is unclear how they might be classified consistently with much of the existing taxonomy framework. This difficulty exposes deeper incompatibilities in how species are conceptualized. The original species assignments based on disease or other biological attributes were primarily descriptive, similar to principles used elsewhere in biology for species taxonomies. In contrast, purely sequence-based classifications rely on genetic metrics such as divergence thresholds that include or exclude viruses in individual species categories. These different approaches bring different preconceptions about the nature of a virus species, the former being more easily conceptualized as a category with a part/whole relationship of individuals and species, while species defined by divergence thresholds or other genetic metrics are essentially logically defined groups with specific inclusion and exclusion criteria. While descriptive species definitions match our intuitive division of viruses into natural kinds, rules-based genetic classifications are required for viruses known from sequence alone, whose incorporation into the ICTV taxonomy is essential if it is to represent the true diversity of viruses in nature.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.001010
2018-03-01
2019-12-09
Loading full text...

Full text loading...

/deliver/fulltext/jgv/99/3/277.html?itemId=/content/journal/jgv/10.1099/jgv.0.001010&mimeType=html&fmt=ahah

References

  1. Woese CR. Bacterial evolution. Microbiol Rev 1987;51:221–271[PubMed]
    [Google Scholar]
  2. Cain AJ. Linnaeus's Ordines naturales. Arch Nat Hist 1993;20:405–415 [CrossRef]
    [Google Scholar]
  3. Darwin C. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life London: John Murray; 1859
    [Google Scholar]
  4. Mayr E. Systematics and the Origin of Species from the Viewpoint of a Zoologist New York: Columbia University Press; 1942
    [Google Scholar]
  5. Mayden RL. A hierarchy of species concepts: the denouement in the saga of the species problem. In Claridge MF, Dawah HA, Wildon MR. (editors) Species: The Units of Biodiversity London: Chapman and Hall; 1997; pp.381–424
    [Google Scholar]
  6. Parker CT, Tindall BJ, Garrity GM. International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2015; [CrossRef][PubMed]
    [Google Scholar]
  7. Edwards RA, Rohwer F. Viral metagenomics. Nat Rev Microbiol 2005;3:504–510 [CrossRef][PubMed]
    [Google Scholar]
  8. Suttle CA. Marine viruses-major players in the global ecosystem. Nat Rev Microbiol 2007;5:801–812 [CrossRef][PubMed]
    [Google Scholar]
  9. Konstantinidis KT, Rosselló-Móra R. Classifying the uncultivated microbial majority: a place for metagenomic data in the Candidatus proposal. Syst Appl Microbiol 2015;38:223–230 [CrossRef][PubMed]
    [Google Scholar]
  10. Hedlund BP, Dodsworth JA, Staley JT. The changing landscape of microbial biodiversity exploration and its implications for systematics. Syst Appl Microbiol 2015;38:231–236 [CrossRef][PubMed]
    [Google Scholar]
  11. Hibbett DS, Taylor JW. Fungal systematics: is a new age of enlightenment at hand?. Nat Rev Microbiol 2013;11:129–133 [CrossRef][PubMed]
    [Google Scholar]
  12. Simmonds P, Adams MJ, Benkő M, Breitbart M, Brister JR et al. Consensus statement: Virus taxonomy in the age of metagenomics. Nat Rev Microbiol 2017;15:161–168 [CrossRef][PubMed]
    [Google Scholar]
  13. Wildy P. Classification and nomenclature of viruses. First report of the International Committee on Nomenclature of Viruses. Monog virol 1971;5:1–81[Crossref]
    [Google Scholar]
  14. Ninth Report of the International Committee on Taxonomy of Viruses London: Academic Press; 2009
    [Google Scholar]
  15. Durzyńska J, Goździcka-Józefiak A. Viruses and cells intertwined since the dawn of evolution. Virol J 2015;12:169 [CrossRef][PubMed]
    [Google Scholar]
  16. Koonin EV, Senkevich TG, Dolja VV. The ancient Virus World and evolution of cells. Biol Direct 2006;1:29 [CrossRef][PubMed]
    [Google Scholar]
  17. Brüssow H. The not so universal tree of life or the place of viruses in the living world. Philos Trans R Soc Lond B Biol Sci 2009;364:2263–2274 [CrossRef][PubMed]
    [Google Scholar]
  18. Hey J. The mind of the species problem. Trends Ecol Evol 2001;16:326–329 [CrossRef][PubMed]
    [Google Scholar]
  19. Mishler BD. Species are not uniquely real biological entities. In Ayala FJ, Arp R. (editors) Contemporary Debates in Philosophy of Biology Blackwell; 2010; pp.110–122
    [Google Scholar]
  20. Claridge RF. Species are real biological entities. In Ayala FJ, Arp R. (editors) Contemporary Debates in Philosophy of Biology Blackwell; 2010; pp.91–109
    [Google Scholar]
  21. Ghiselin MT. A radical solution to the species problem. Syst Zool 1974;23:536–544 [CrossRef]
    [Google Scholar]
  22. Hull DL. Are species really individuals?. Syst Zool 1976;25:174–191 [CrossRef]
    [Google Scholar]
  23. van Regenmortel MHV. Classes, taxa and categories in a heirarchical virus classification: a review of current debates of definitions and names of species. Bionomia2016: (in press)
    [Google Scholar]
  24. van Regenmortel MHV. Viruses are real, virus species are man-made, taxonomic constructions. Arch Virol 2003;148:2481–2488 [CrossRef][PubMed]
    [Google Scholar]
  25. Hurford JR. Animals approach human cognition. The Origins of Meaning Oxford: Oxford University Press; 2007; pp.20–64
    [Google Scholar]
  26. Bos L. Virus nomenclature; continuing topicality. Arch Virol 2003;148:1235–1246 [CrossRef][PubMed]
    [Google Scholar]
  27. Hennig W. Phylogenetic Systematics Champaign/Urbana, IL: University of Illinois Press; 1966
    [Google Scholar]
  28. Stuessy TF. Plant Taxonomy. The Systematic Evaluation of Comparative Data New York: Columbia University Press; 1990
    [Google Scholar]
  29. Cronquist A. Once again, what is a species?. In Knutson LV. (editor) BioSystematics in Agriculture Montclair, NJ: Allenheld Osmun; 1988; pp.3–20
    [Google Scholar]
  30. van Regenmortel MHV, Maniloff J, Calisher C. The concept of virus species. Arch Virol 1991;120:313–317 [CrossRef][PubMed]
    [Google Scholar]
  31. van Regenmortel MHV. Applying the species concept to plant viruses. Arch Virol 1989;104:1–17 [CrossRef][PubMed]
    [Google Scholar]
  32. Beckner L. The Biological Way of Thought New York: Columbia University Press; 1959
    [Google Scholar]
  33. Gibbs AJ, Gibbs MJ. A broader definition of 'the virus species'. Arch Virol 2006;151:1419–1422 [CrossRef][PubMed]
    [Google Scholar]
  34. Wiley EO. The evolutionary species concept reconsidered. Syst Zool 1978;27:17–26 [CrossRef]
    [Google Scholar]
  35. Vauclair J. Animal Cognition: An Introduction to Modern Comparative Psychology London: Harvard University Press; 1996
    [Google Scholar]
  36. Hauser MD. Wild Minds: What Animals Really Think New York: Henty Holt; 2000
    [Google Scholar]
  37. Jackendoff R. Reference and truth. Foundations of Language New York: Oxford University Press; 1999; pp.294–322
    [Google Scholar]
  38. Rosch EH. Natural categories. Cogn Psychol 1973;4:328–350 [CrossRef]
    [Google Scholar]
  39. Lakoff G. Women, Fire and Dangerous Things: What Categories Reveal About the Mind Chicago: University of Chicago Press; 1987;[Crossref]
    [Google Scholar]
  40. Nosofsky RM. Generalized context model: an exemplar model of classification. formal approaches to categorization. In Pothos EM, Wills AJ. (editors) Formal Approaches in Classification Cambridge: Cambridge Universtiy Press; 2011; pp.18–39[Crossref]
    [Google Scholar]
  41. Wittgenstein L. Philosophische Unterschungen. In Hacker PMS, Schulte J. (editors) Philosophical Investigations, the German Text with an English Translation Oxford: Blackwell; 2009; pp.1–181
    [Google Scholar]
  42. Roehrig JT, Layton M, Smith P, Campbell GL, Nasci R et al. The emergence of West Nile virus in North America: ecology, epidemiology, and surveillance. Curr Top Microbiol Immunol 2002;267:223–240[PubMed]
    [Google Scholar]
  43. Bos L. Coming to grips with the naming of viruses; continuing discord, or a way out?. Arch Virol 2007;152:649–653 [CrossRef][PubMed]
    [Google Scholar]
  44. Martelli GP. Classification and nomenclature of plant viruses: state of the art. Plant Disease 1992;76:436–442 [CrossRef]
    [Google Scholar]
  45. Smith DB, Simmonds P, Jameel S, Emerson SU, Harrison TJ et al. Consensus proposals for classification of the family Hepeviridae. J Gen Virol 2014;95:2223–2232 [CrossRef][PubMed]
    [Google Scholar]
  46. Sneath PHA. Phenetic taxonomy at the species level and above. Taxon 1976;25:437–450 [CrossRef]
    [Google Scholar]
  47. de Queiroz K. The general lineage concept of species and the defining properties of the species category. In Wilson RA. (editor) Species MA: MIT Press; 1999; pp.49–89
    [Google Scholar]
  48. Tanaka K, Lapointe R, Barney WE, Makkay AM, Stoltz D et al. Shared and species-specific features among ichnovirus genomes. Virology 2007;363:26–35 [CrossRef][PubMed]
    [Google Scholar]
  49. Rosario K, Breitbart M. Exploring the viral world through metagenomics. Curr Opin Virol 2011;1:289–297 [CrossRef][PubMed]
    [Google Scholar]
  50. Roossinck MJ. Plant virus metagenomics: biodiversity and ecology. Annu Rev Genet 2012;46:359–369 [CrossRef][PubMed]
    [Google Scholar]
  51. Simmonds P. Methods for virus classification and the challenge of incorporating metagenomic sequence data. J Gen Virol 2015;96:1193–1206 [CrossRef][PubMed]
    [Google Scholar]
  52. Adams MJ, Lefkowitz EJ, King AM, Harrach B, Harrison RL et al. 50 years of the International Committee on Taxonomy of Viruses: progress and prospects. Arch Virol 2017;162:1441–1446 [CrossRef][PubMed]
    [Google Scholar]
  53. Katzourakis A, Gifford RJ. Endogenous viral elements in animal genomes. PLoS Genet 2010;6:e1001191 [CrossRef][PubMed]
    [Google Scholar]
  54. Acevedo A, Andino R. Library preparation for highly accurate population sequencing of RNA viruses. Nat Protoc 2014;9:1760–1769 [CrossRef][PubMed]
    [Google Scholar]
  55. Whitfield ZJ, Andino R. Characterization of viral populations by using circular sequencing. J Virol 2016;90:8950–8953 [CrossRef][PubMed]
    [Google Scholar]
  56. Kumar A, Murthy S, Kapoor A. Evolution of selective-sequencing approaches for virus discovery and virome analysis. Virus Res 2017;239:172–179 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/jgv.0.001010
Loading
/content/journal/jgv/10.1099/jgv.0.001010
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error