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Chapter 78 : Taxonomy and Classification of Viruses

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Abstract:

This chapter describes the rules and processes utilized for the taxonomic classification of viruses. Taxonomy at its most basic level involves the classification and naming of objects. Living objects have been grouped for hundreds of years according to the Linnaean system, a classification scheme that places living things hierarchically into groups of species followed by groupings into higher-level taxa dependent on common shared characteristics. Taxonomy functions beyond mere categorization. By having information about, and an understanding of, a few of the organisms in a group of closely related taxa, it is often possible to extend that knowledge to other organisms in related taxa for which much less biological information may be available. Virus classification and taxonomic assignment are the responsibility of the International Committee on Taxonomy of Viruses (ICTV), which has been charged with the task of developing, refining, and maintaining a universal viral taxonomy. The ICTV currently recognizes five hierarchical ranks that are used to define the universal viral taxonomy: the order, family, subfamily, genus, and species. The 2012 ICTV viral taxonomy comprises 7 orders, 96 families, 22 subfamilies, 420 genera, and 2,618 species.

Citation: Lefkowitz E. 2015. Taxonomy and Classification of Viruses, p 1393-1404. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch78
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Figures

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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 with permission of Elsevier from . doi:10.1128/9781555817381.ch78.f1

Citation: Lefkowitz E. 2015. Taxonomy and Classification of Viruses, p 1393-1404. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch78
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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; for small virions, only their size and symmetry are depicted. RT, reverse transcribing; +, positive-sense genome; –, negative-sense genome. Reprinted with modification with permission of Academic Press from . doi:10.1128/9781555817381.ch78.f2

Citation: Lefkowitz E. 2015. Taxonomy and Classification of Viruses, p 1393-1404. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch78
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References

/content/book/10.1128/9781555817381.mcm11.ch78
1. Linné CV,, Engel-Ledeboer MSJ,, Engel H. 1964. Carolus Linnaeus Systema Naturae, 1735. B. de Graff, Nieuwkoop, The Netherlands.
2. Koonin EV,, Senkevich TG,, Dolja VV. 2009. Compelling reasons why viruses are relevant for the origin of cells. Nat Rev Microbiol 7:615. (Author’s reply, 7:615.)
3. Mushegian A. 2008. Gene content of LUCA, the last universal common ancestor. Front Biosci 13:46574666.
4. Villarreal LP. 2005. Viruses and the Evolution of Life. ASM Press, Washington, DC.
5. Domingo E,, Parrish CR,, Holland JJ. 2008. Origin and Evolution of Viruses, 2nd ed. Academic Press, San Diego, CA.
6. Koonin EV,, Senkevich TG,, Dolja VV. 2006. The ancient Virus World and evolution of cells. Biol Direct 1:29. doi:10.1186/1745-6150-1-29.
7. Gibbs AJ,, Calisher CH,, Garcia-Arenal F. 1995. Molecular Basis of Virus Evolution. Cambridge University Press, Cambridge, United Kingdom.
8. Koonin EV,, Wolf YI,, Nagasaki K,, Dolja VV. 2008. The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Nat Rev Microbiol 6:925939.
9. Baltimore D. 1971. Expression of animal virus genomes. Bacteriol Rev 35:235241.
10. Fields BN,, Knipe DM,, Howley PM (ed). 2007. Fields Virology, 5th ed. Wolters Kluwer Health/Lippincott Williams & Wilkins, Philadelphia, PA.
11. 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.
12. Lapage SP,, Sneath PHA,, Lessel EF, Skerman VBD, Seeliger HPR, Clark WA (ed). 1992. International Code of Nomenclature of Bacteria. American Society for Microbiology, Washington, DC.
13. Polaszek A. 2005. A universal register for animal names. Nature 437:477.
14. King AMQ,, Adams MJ,, Carstens EB,, Lefkowitz EJ (ed). 2012. Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. Academic Press, London, United Kingdom.
15. Schleifer KH. 2008. The International Union of Microbiological Societies, IUMS. Res Microbiol 159:4548.
16. Adams MJ,, Lefkowitz EJ,, King AM,, Carstens EB. 2014. Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2014). Arch Virol 159:28312841.
17. Carstens EB. 2010. Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2009). Arch Virol 155:133146.
18. Wildy P (ed). 1971. Classification and Nomenclature of Viruses: First Report of the International Committee on Nomenclature of Viruses. S. Karger, Basel, Switzerland.
19. Van Regenmortel MHV,, Fauquet CM,, Bishop DHL (ed). 2000. Virus Taxonomy: Classification and Nomenclature of Viruses: Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press, San Diego, CA.
20. Adams MJ,, Lefkowitz EJ,, King AM,, Carstens EB. 2013. Recently agreed changes to the International Code of Virus Classification and Nomenclature. Arch Virol 158:26332639.
21. Adams MJ,, Lefkowitz EJ,, King AM,, Carstens EB. 2014. Recently agreed changes to the statutes of the International Committee on Taxonomy of Viruses. Arch Virol 159:175180.
22. Simmonds P,, Bukh J,, Combet C,, Deléage G,, Enomoto N,, Feinstone S,, Halfon P,, Inchauspé G,, Kuiken C,, Maertens G,, Mizokami M,, Murphy DG,, Okamoto H,, Pawlotsky JM,, Penin F,, Sablon E,, Shin IT,, Stuyver LJ,, Thiel HJ,, Viazov S,, Weiner AJ,, Widell A. 2005. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 42:962973.
23. Henchal EA,, Putnak JR. 1990. The dengue viruses. Clin Microbiol Rev 3:376396.
24. Robertson DL,, Anderson JP,, Bradac JA,, Carr JK,, Foley B,, Funkhouser RK,, Gao F,, Hahn BH,, Kalish ML,, Kuiken C,, Learn GH,, Leitner T,, McCutchan F,, Osmanov S,, Peeters M,, Pieniazek D,, Salminen M,, Sharp PM,, Wolinsky S,, Korber B. 2000. HIV-1 nomenclature proposal. Science 288:5556.
25. Büchen-Osmond C. 1997. Further progress in ICTVdB, a universal virus database. Arch Virol 142:17341739.
26. Buechen-Osmond C,, Dallwitz M. 1996. Towards a universal virus database—progress in the ICTVdB. Arch Virol 141:392399.
27. Davison AJ,, Eberle R,, Ehlers B,, Hayward GS,, McGeoch DJ,, Minson AC,, Pellett PE,, Roizman B,, Studdert MJ,, Thiry E. 2009. The order Herpesvirales. Arch Virol 154: 171177.
28. Le Gall O,, Christian P,, Fauquet CM,, King AM,, Knowles NJ,, Nakashima N,, Stanway G,, Gorbalenya AE. 2008. Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T = 3 virion architecture. Arch Virol 153:715727.
29. Bao Y,, Kapustin Y,, Tatusova T,. 2008. Virus classification by pairwise sequence comparison (PASC), p 342348. In Mahy BWJ,, Van Regenmortel MHV (ed), Encyclopedia of Virology. Elsevier, Boston, MA.
30. Lefkowitz EJ,, Wang C,, Upton C. 2006. Poxviruses: past, present and future. Virus Res 117:105118.
31. Adams MJ,, Antoniw JF,, Bar-Joseph M,, Brunt AA,, Candresse T,, Foster GD,, Martelli GP,, Milne RG,, Zavriev SK,, Fauquet CM. 2004. The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Arch Virol 149:10451060.
32. Adams MJ,, Antoniw JF,, Fauquet CM. 2005. Molecular criteria for genus and species discrimination within the family Potyviridae. Arch Virol 150:459479.
33. Gorbalenya AE,, Enjuanes L,, Ziebuhr J,, Snijder EJ. 2006. Nidovirales: evolving the largest RNA virus genome. Virus Res 117:1737.
34. Carstens EB. 2009. Report from the 40th meeting of the Executive Committee of the International Committee of Taxonomy of Viruses. Arch Virol 154:15711574.
35. NCBI Resource Coordinators. 2013. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 41:D8D20.
36. Benson DA,, Cavanaugh M,, Clark K,, Karsch-Mizrachi I,, Lipman DJ,, Ostell J,, Sayers EW. 2013. GenBank. Nucleic Acids Res 41:D36D42.
37. Pruitt KD,, Tatusova T,, Brown GR,, Maglott DR. 2012. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 40:D130D135.
38. Assiri A,, McGeer A,, Perl TM,, Price CS,, Al Rabeeah AA,, Cummings DA,, Alabdullatif ZN,, Assad M,, Almulhim A,, Makhdoom H,, Madani H,, Alhakeem R,, Al-Tawfiq JA,, Cotten M,, Watson SJ,, Kellam P,, Zumla AI,, Memish ZA, KSA MERS-CoV Investigation Team. 2013. Hospital outbreak of Middle East respiratory syndrome coronavirus. N Engl J Med 369:407416.
39. Briese T,, Paweska JT,, McMullan LK,, Hutchison SK,, Street C,, Palacios G,, Khristova ML,, Weyer J,, Swanepoel R,, Egholm M,, Nichol ST,, Lipkin WI. 2009. Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog 5:e1000455. doi:10.1371/journal.ppat.1000455.
40. Lavigne R,, Seto D,, Mahadevan P,, Ackermann HW,, Kropinski AM. 2008. Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Res Microbiol 159:406414.
41. Lima-Mendez G,, Van Helden J,, Toussaint A,, Leplae R. 2008. Reticulate representation of evolutionary and functional relationships between phage genomes. Mol Biol Evol 25:762777.
42. Odom MR,, Hendrickson RC,, Lefkowitz EJ. 2009. Poxvirus protein evolution: family wide assessment of possible horizontal gene transfer events. Virus Res 144:233249.
43. Walsh DA,, Sharma AK. 2009. Molecular phylogenetics: testing evolutionary hypotheses. Methods Mol Biol 502:131168.
44. Delwart EL. 2007. Viral metagenomics. Rev Med Virol 17:115131.
45. Edwards RA,, Rohwer F. 2005. Viral metagenomics. Nat Rev Microbiol 3:504510.
46. Monier A,, Claverie JM,, Ogata H. 2008. Taxonomic distribution of large DNA viruses in the sea. Genome Biol 9:R106. doi:10.1186/gb-2008-9-7-r106.
47. Labonté JM,, Reid KE,, Suttle CA. 2009. Phylogenetic analysis indicates evolutionary diversity and environmental segregation of marine podovirus DNA polymerase gene sequences. Appl Environ Microbiol 75:36343640.
48. Schoenfeld T,, Patterson M,, Richardson PM,, Wommack KE,, Young M,, Mead D. 2008. Assembly of viral metagenomes from Yellowstone hot springs. Appl Environ Microbiol 74:41644174.

Tables

Generic image for table
TABLE 1

ICTVdb character list

Citation: Lefkowitz E. 2015. Taxonomy and Classification of Viruses, p 1393-1404. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch78
Generic image for table
TABLE 2

Criteria for taxonomic classification

Citation: Lefkowitz E. 2015. Taxonomy and Classification of Viruses, p 1393-1404. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch78
Generic image for table
TABLE 3

Taxonomic classification of viruses infecting humans

Citation: Lefkowitz E. 2015. Taxonomy and Classification of Viruses, p 1393-1404. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch78
Generic image for table
TABLE 4

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

Citation: Lefkowitz E. 2015. Taxonomy and Classification of Viruses, p 1393-1404. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch78

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