1887

Chapter 75 : Taxonomy and Classification of Viruses

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

Taxonomy and Classification of Viruses, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555816728/9781555814632_Chap75-1.gif /docserver/preview/fulltext/10.1128/9781555816728/9781555814632_Chap75-2.gif

Abstract:

This chapter discusses about taxonomy and classification of viruses. For viruses, the process of comparative analysis plays a critical role in increasing our overall knowledge of the molecular biology, pathogenesis, epidemiology, and evolution of poorly understood or newly isolated viruses. This knowledge enhances our ability to respond to new threats by supporting the development of diagnostics, vaccines, and other antiviral therapies. In fact, it is likely that viruses have multiple independent evolutionary origins that cannot be easily or completely separated from the evolution of their hosts, as they cannot reproduce or evolve separately from their hosts. Therefore, viruses might be better represented as individual twigs arising from branches spread throughout the rest of the tree. In addition to distinct evolutionary histories, viruses differ from other domains of life in the variety of possible coding molecules they utilize to store their genetic programs. For viruses, the Virology Division of the International Union of Microbiological Societies has charged the International Committee on Taxonomy of Viruses (ICTV) with the task of developing, refining, and maintaining a universal viral taxonomy. As categorized according to the 2009 ICTV taxonomy, viruses that infect humans fall into 4 orders: the , , , and . The ICTV produces an extensive amount of information during the process of classifying and naming viruses that is published regularly in the ICTV reports.

Citation: Lefkowitz E. 2011. Taxonomy and Classification of Viruses, p 1265-1275. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch75

Key Concept Ranking

Hepatitis C virus
0.5254237
Horizontal Gene Transfer
0.42971087
0.5254237
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

Taxonomic demarcation via sequence similarity. (A) PASC was carried out on the viral DNA-dependent DNA polymerase gene (the vaccinia virus E9L gene homolog) for every completely sequenced poxvirus genome. Each protein was aligned to every other protein, and the percent identity of each pairwise comparison was then included in a histogram plot of all possible comparisons. Peaks are identified across the top of the figure according to the taxa represented by particular pairwise sequence comparisons. (B) Phylogenetic reconstruction of the family of viruses based on their DNA polymerase protein sequences. Subfamily and genera demarcations are identified. Terminal nodes are labeled according to genus. Sequences belonging to one of the genera labeled either group A or B coincide with the A and B comparison peaks at the top of panel A. (C) Phylogenetic prediction based on the multiple nucleic acid sequence alignment of the core genomic region of each representative orthopoxvirus species or strain. BR, strain Brighton Red; GRI, strain GRI-90. Reprinted with modification from ( ) with permission of the publisher.

Citation: Lefkowitz E. 2011. Taxonomy and Classification of Viruses, p 1265-1275. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch75
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

Virion morphology. Depiction of the shapes and sizes of viruses of families that include animal, zoonotic, and human pathogens. The virions are drawn to scale, but artistic license has been used in representing their structure. In some, the cross-sectional structure of capsid and envelope are shown, with a representation of the genome; with the very small virions, only their size and symmetry are depicted. RT, reverse transcribing; +, positive-sense genome; -, negativesense genome. Reprinted with modification from ( ) with permission of the publisher.

Citation: Lefkowitz E. 2011. Taxonomy and Classification of Viruses, p 1265-1275. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch75
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555816728.chap75
1. Adams, M. J.,, J. F. Antoniw,, M. Bar-Joseph,, A. A. Brunt,, T. Candresse,, G. D. Foster,, G. P. Martelli,, R. G. Milne,, S. K. Zavriev,, and C. M. Fauquet. 2004. The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Arch. Virol. 149:10451060.
2. Adams, M. J.,, J. F. Antoniw,, and C. M. Fauquet. 2005. Molecular criteria for genus and species discrimination within the family Potyviridae. Arch. Virol. 150:459479.
3. Baltimore, D. 1971. Expression of animal virus genomes. Bacteriol. Rev. 35:235241.
4. Bao, Y.,, Y. Kapustin,, and T. Tatusova,. 2008. Virus classification by pairwise sequence comparison (PASC), p. 342348. In B. W. J. Mahy, and M. H. V. Van Regenmortel (ed.), Encyclopedia of Virology. Elsevier, Boston, MA.
5. Baxevanis, A. D. 2008. Searching NCBI databases using Entrez. Curr. Protoc. Bioinformatics 1:1.3.
6. Benson, D. A.,, I. Karsch-Mizrachi,, D. J. Lipman,, J. Ostell,, and E. W. Sayers. 2009. GenBank. Nucleic Acids Res. 37:D26D31.
7. Briese, T.,, J. T. Paweska,, L. K. McMullan,, S. K. Hutchison,, C. Street,, G. Palacios,, M. L. Khristova,, J. Weyer,, R. Swanepoel,, M. Egholm,, S. T. Nichol,, and W. I. Lipkin. 2009. Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog. 5:e1000455.
8. Buchen-Osmond, C. 1997. Further progress in ICTVdB, a universal virus database. Arch. Virol. 142:17341739.
9. Buechen-Osmond, C.,, and M. Dallwitz. 1996. Towards a universal virus database—progress in the ICTVdB. Arch. Virol. 141:392399.
10. Carstens, E. B. 2009. Report from the 40th meeting of the Executive Committee of the International Committee of Taxonomy of Viruses. Arch. Virol. 155:133146.
11. Carstens, E. B.,, and L. A. Ball. 2009. Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2008). Arch. Virol. 154:11811188.
12. Davison, A. J.,, R. Eberle,, B. Ehlers,, G. S. Hayward,, D. J. McGeoch,, A. C. Minson,, P. E. Pellett,, B. Roizman,, M. J. Studdert,, and E. Thiry. 2009. The order Herpesvirales. Arch. Virol. 154:171177.
13. Delwart, E. L. 2007. Viral metagenomics. Rev. Med. Virol. 17:115131.
14. Domingo, E.,, C. R. Parrish,, and J. J. Holland. 2008.Origin and Evolution of Viruses, 2nd ed. Academic Press, San Diego, CA.
15. Edwards, R. A.,, and F. Rohwer. 2005. Viral metagenomics. Nat. Rev. Microbiol. 3:504510.
16. Fauquet, C. M.,, M. A. Mayo,, J. Maniloff,, U. Desselberger,, and L. A. Ball (ed.). 2005. Virus Taxonomy. Eighth Report of the International Committee on Taxonomy of Viruses. Academic Press, San Diego, CA.
17. Fields, B. N.,, D. M. Knipe,, and P. M. Howley. 2007. Fields Virology, 5th ed. Wolters Kluwer Health/Lippincott Williams & Wilkins, Philadelphia, PA.
18. Gibbs, A. J.,, C. H. Calisher,, and F. Garcia-Arenal. 1995. Molecular Basis of Virus Evolution. Cambridge University Press, Cambridge, England.
19. Gorbalenya, A. E.,, L. Enjuanes,, J. Ziebuhr,, and E. J. Snijder. 2006. Nidovirales: evolving the largest RNA virus genome. Virus Res. 117:1737.
20. Henchal, E. A.,, and J. R. Putnak. 1990. The dengue viruses. Clin. Microbiol. Rev. 3:376396.
21.International Commission on Zoological Nomenclature. 1999. International Code of Zoological Nomenclature (Code International de Nomenclature Zoologique), 4th ed. International Trust for Zoological Nomenclature, London, United Kingdom.
22.International Committee on Nomenclature of Viruses, and P. Wildy. 1971. Classification and Nomenclature of Viruses. First Report of the International Committee on Nomenclature of Viruses. S. Karger, Basel, Switzerland.
23. InternationalCommitteeonTaxonomyofViruses, M. H. V. Van Regenmortel, and International Union of Microbiological Societies, Virology Division. 2000. Virus Taxonomy: Classification and Nomenclature of Viruses. Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press, San Diego, CA.
24. Koonin, E. V.,, T. G. Senkevich,, and V. V. Dolja. 2009. Compelling reasons why viruses are relevant for the origin of cells. Nat. Rev. Microbiol. 7:615. (Author’s reply, 7:615.).
25. Koonin, E. V.,, T. G. Senkevich,, and V. V. Dolja. 2006. The ancient virus world and evolution of cells. Biol. Direct. 1:29.
26. Koonin, E. V.,, Y. I. Wolf,, K. Nagasaki,, and V. V. Dolja. 2008. The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Nat. Rev. Microbiol. 6:925939.
27. Labonte, J. M.,, K. E. Reid,, and C. A. Suttle. 2009. Phylogenetic analysis indicates evolutionary diversity and environmental segregation of marine podovirus DNA polymerase gene sequences. Appl. Environ. Microbiol. 75:36343640.
28. Lapage, S. P.,, P. H. A. Sneath,, E. F. Lessel,, V. B. D. Skerman,, H. P. R. Seeliger,, and W. A. Clark (ed.). 1992. International Code of Nomenclature of Bacteria. American Society for Microbiology, Washington, DC.
29. Lavigne, R.,, D. Seto,, P. Mahadevan,, H. W. Ackermann,, and A. M. Kropinski. 2008. Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Res. Microbiol. 159:406414.
30. Lefkowitz, E. J.,, C. Wang,, and C. Upton. 2006. Poxviruses: past, present and future. Virus Res. 117:105118.
31. Le Gall, O.,, P. Christian,, C. M. Fauquet,, A. M. King,, N. J. Knowles,, N. Nakashima,, G. Stanway,, and A. E. Gorbalenya. 2008. Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T53 virion architecture. Arch. Virol. 153:715727.
32. Lima-Mendez, G.,, J. Van Helden,, A. Toussaint,, and R. Leplae. 2008. Reticulate representation of evolutionary and functional relationships between phage genomes. Mol. Biol. Evol. 25:762777.
33. Linné, C. V.,, M. S. J. Engel-Ledeboer,, and H. Engel,. 1964. Carolus Linnaeus Systema Naturae, 1735. B. de Graff, Nieuwkoop, The Netherlands.
34. Monier, A.,, J. M. Claverie,, and H. Ogata. 2008. Taxonomic distribution of large DNA viruses in the sea. Genome Biol. 9:R106.
35. Mushegian, A. 2008. Gene content of LUCA, the last universal common ancestor. Front. Biosci. 13:46574666.
36. Odom, M. R.,, R. C. Hendrickson,, and E. J. Lefkowitz. 2009. Poxvirus protein evolution: family wide assessment of possible horizontal gene transfer events. Virus Res. 144:233249.
37. Polaszek, A. 2005. A universal register for animal names. Nature 437:477.
38. Pruitt, K. D.,, T. Tatusova,, and D. R. Maglott. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35:D61D65.
39. Robertson, D. L.,, J. P. Anderson,, J. A. Bradac,, J. K. Carr,, B. Foley,, R. K. Funkhouser,, F. Gao,, B. H. Hahn,, M. L. Kalish,, C. Kuiken,, G. H. Learn,, T. Leitner,, F. McCutchan,, S. Osmanov,, M. Peeters,, D. Pieniazek,, M. Salminen,, P. M. Sharp,, S. Wolinsky,, and B. Korber. 2000. HIV-1 nomenclature proposal. Science 288:5556.
40. Schleifer, K. H. 2008. The International Union of Microbiological Societies, IUMS. Res. Microbiol. 159:4548.
41. Schoenfeld, T.,, M. Patterson,, P. M. Richardson,, K. E. Wommack,, M. Young,, and D. Mead. 2008. Assembly of viral metagenomes from yellowstone hot springs. Appl. Environ. Microbiol. 74:41644174.
42. Simmonds, P.,, J. Bukh,, C. Combet,, G. Deleage,, N. Enomoto,, S. Feinstone,, P. Halfon,, G. Inchauspe,, C. Kuiken,, G. Maertens,, M. Mizokami,, D. G. Murphy,, H. Okamoto,, J. M. Pawlotsky,, F. Penin,, E. Sablon,, I. T. Shin,, L. J. Stuyver,, H. J. Thiel,, S. Viazov,, A. J. Weiner,, and A. Widell. 2005. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 42:962973.
43. Villarreal, L. P. 2005. Viruses and the Evolution of Life. ASM Press, Washington, DC.
44. Walsh, D. A.,, and A. K. Sharma. 2009. Molecular phylogenetics: testing evolutionary hypotheses. Methods Mol. Biol. 502:131168.

Tables

Generic image for table
TABLE 1

ICTVdb character list

Citation: Lefkowitz E. 2011. Taxonomy and Classification of Viruses, p 1265-1275. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch75
Generic image for table
TABLE 2

Criteria for taxonomic classification

Citation: Lefkowitz E. 2011. Taxonomy and Classification of Viruses, p 1265-1275. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch75
Generic image for table
TABLE 3

Taxonomic classification of viruses infecting humans

Citation: Lefkowitz E. 2011. Taxonomy and Classification of Viruses, p 1265-1275. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch75
Generic image for table
TABLE 4

Summary of important characteristics used to differentiate families of viruses infecting humans

+: positive sense; −: negative sense.

Genus (unassigned family).

Not classified by the ICTV.

NA, not applicable.

Citation: Lefkowitz E. 2011. Taxonomy and Classification of Viruses, p 1265-1275. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch75

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error