Molecular and Biological Basis of Picornavirus Taxonomy

Glyn Stanway; Tapani Hovi; Nick J. Knowles; Timo Hyypiä

doi:10.1128/9781555817916.ch2

Chapter 2 : Molecular and Biological Basis of Picornavirus Taxonomy

Authors: Glyn Stanway¹, Tapani Hovi², Nick J. Knowles³, Timo Hyypiä⁴

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Affiliations: 1: Department of Biological Sciences, University of Essex, Colchester, C04 3SQ, United Kingdom; 2: Enterovirus Laboratory, KTL, Mannerheimintie 166, 00300 Helsinki, Finland; 3: Institute for Animal Health (IAH), Pirbright Laboratory, Ash Road, Pirbright, Woking, Surrey, GU24 ONE. United Kingdom; 4: Department of Virology, Haartman Institute, University of Helsinki, P.O. Box 21, 00014 Helsinki, Finland

Content Type: Monograph

Publication Year: 2002

Category: Viruses and Viral Pathogenesis

Book DOI: 10.1128/9781555817916

Chapter DOI: 10.1128/9781555817916.ch2

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Abstract:

Picornaviruses have traditionally been defined in terms of serotypes, grouped into genera. Recently, a radical change has been introduced with the advent of the concept of a picornavirus species, generally consisting of several serotypes. This classification has evolved in response to developments in one’s understanding of the biological and genetic properties of picornaviruses, which has accelerated greatly over the past few years. This chapter examines some of the properties that can be used to group, or differentiate between, picornaviruses and some of the complications that arise from attempting to classify viruses, which are potentially highly plastic in terms of sequence and even genome organization. Enteroviruses were originally classified as poliovirus (PV), coxsackievirus A (CVA), coxsackievirus B (CVB), and echovirus on the basis of their pathogenicity in experimental animals. The current number of established picornavirus serotypes is very high, especially among the two closely related genera, enteroviruses and rhinoviruses. The three types of PV are classical examples of easily distinguishable enterovirus serotypes, whereas definite cross-reactivity is readily demonstrable between, for example, several established CVA serotypes. As the sequences of numerous picornaviruses have become available, they have shown that there is essentially one common genome organization. To provide biologically important insights, taxonomy should ultimately be based on genetic relationships, which in turn reflect the evolutionary history of the viruses.

Citation: Stanway G, Hovi T, Knowles N, Hyypiä T. 2002. Molecular and Biological Basis of Picornavirus Taxonomy, p 17-24. In Semler B, Wimmer E (ed), Molecular Biology of Picornavirus. ASM Press, Washington, DC. doi: 10.1128/9781555817916.ch2

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Molecular and Biological Basis of Picornavirus Taxonomy

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FIGURE 1

Genome structure of a typical picornavirus, together with a schematic representation of the polyproteins encoded by each genus. Most picornaviruses encode four structural proteins (1A–1D), also called VP4, VP2, VP3, and VP1). However, it appears that members of the genera Parechovirus and Kobuvirus do not undergo the cleavage of VP0 to VP4 and VP2 and so there are only three structural proteins. The main differences in terms of genome organization are the L protein and 2A. At least four (the Aphthovirus and Erbovirus L proteins are distantly related) different types of L protein are found in the five genera that have a protein at this locus. There are also four structurally diverse protein types at the 2A locus. In the figure, for both L and 2A, similar structural types of proteins are shaded in the same way. *Note that one of the two Aphthovirus species, FMDV, encodes three tandem copies of VPg.

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FIGURE 1

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FIGURE 2

Phylogenetic trees expressing the relationship between a representative of each picornavirus species, based on amino acid identities of the P1 or 2C plus 3CD proteins. Sequences were compared using the program ClustalW and the trees were drawn using the program Treedraw ( 41 ). Abbreviations are as given in Table 1 . Species names within each genus are enclosed by dotted lines.

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FIGURE 2

References

/content/book/10.1128/9781555817916.chap2

1. Acharya, R.,, E. Fry,, D. Stuart,, G. Fox,, D. Rowlands,, and F. Brown. 1989. The three-dimensional structure of foot-and-mouth disease virus at 2.9 Å resolution. Nature 337: 709– 716.

2. Andino, R.,, N. Böddeker,, D. Silvera,, and A. V. Gamarnik. 1999. Intracellular determinants of picornavirus replication. Trends Microbiol. 7: 76– 82.

3. Cammack, N.,, A. Phillips,, G. Dunn,, V. Patel,, and P. D. Minor. 1988. Intertypic genomic rearrangements of poliovirus strains in vaccines. Virology 167: 507– 514.

4. Chow, M.,, J. F. E. Newman,, D. Filman,, J. M. Hogle,, D. J. Rowlands,, and F. Brown. 1987. Myristoylation of picornavirus capsid protein VP4 and its structural significance. Nature 327: 482– 486.

5. Committee on the ECHO Viruses. 1955. Enteric cytopathogenic human orphan (ECHO) viruses. Science 122: 1187– 1188.

6. Cooper, P. D.,, V. I. Agol,, H. L. Bachrach,, F. Brown,, Y. Ghendon,, A. J. Gibbs,, H. H. Gillespie,, K. Lonberg-Holm,, B. Mandel,, J. L. Melnick,, S. B. Mohanty,, R. C. Povey,, R. R. Rueckert,, F. L. Schaffet,, and D. A. J. Tyrrell. 1978. Picornaviridae: second report. Intervirology 10: 165– 180.

7. Ehrenfeld, E.,, and B. L. Semler. 1995. Anatomy of the poliovirus internal ribosome entry site. Curr. Top. Microbiol. Immunol. 203: 65– 83.

8. Evans, D. J.,, and J. W. Almond. 1998. Cell receptors for picornaviruses as determinants of cell tropism and pathogenesis. Trends Microbiol. 6: 198– 202.

9. Furione, M.,, S. Guillot,, D. Otelea,, J. Balanant,, A. Candrea,, and R. Crainic. 1993. Polioviruses with natural recombinant genomes isolated from vaccine-associated paralytic poliomyelitis. Virology 196: 199– 208.

10. Grist, N. R.,, E. J. Bell,, and F. Assaad. 1978. Enteroviruses in human disease. Prog. Med. Virol. 24: 114– 157.

11. Hogle, J. M.,, M. Chow,, and D. J. Filman. 1985. Three-dimensional structure of poliovirus at 2.9 Å resolution. Science 229: 1358– 1365.

12. Hogle, J. M.,, and D. J. Filman. 1989. 3-dimensional structure of a viral antigen. Adv. Vet. Sci. Comp. Med. 33: 65– 91.

13. Holland, J.,, and E. Domingo. 1998. Origin and evolution of viruses. Virus Genes 16: 13– 21.

14. Hughes, P. J.,, and G. Stanway. 2000. The 2A proteins of three picornaviruses are related to each other and to the H-rev 107 family of proteins involved in the control of cell proliferation. J. Gen. Virol. 81: 201– 207.

15. Huttunen, P.,, J. Santti,, T. Pulli,, and T. Hyypiä. 1996. The major echovirus subgroup is genetically coherent and related to Coxsackie B viruses. J. Gen. Virol. 77: 715– 725.

16. Hyypiä, T.,, T. Hovi,, N. J. Knowles,, and G. Stanway. 1997. Classification of enteroviruses based on molecular and biological properties. J. Gen. Virol. 78: 1– 11.

17. Hyypiä, T.,, M. Kallajoki,, M. Maaronen,, G. Stanway,, R. Kandolf,, P. Auvinen,, and H. Kalimo. 1993. Pathogenic differences between Coxsackie A and B virus infections in newborn mice. Virus Res. 27: 71– 78.

18. Jackson, T.,, D. Sheppard,, M. Denyer,, W. Blakemore,, and A. M. Q. King. 2000. The epithelial integrin alpha v beta 6 is a receptor for foot-and-mouth disease virus. J. Virol. 74: 4949– 4956.

19. Joki-Korpela, P.,, and T. Hyypiä. 1998. Diagnosis and epidemiology of echovirus 22 infections. Clin. Infect. Dis. 27: 129– 136.

20. King, A. M. Q.,, F. Brown,, P. Christian,, T. Hovi,, T. Hyypiä,, N. J. Knowles,, S. M. Lemon,, P. D. Minor,, A. C. Palmenberg,, T. Skern,, and G. Stanway,. 2000. Picornaviridae, p. 657– 673. In M. H. V. Van Regenmortel,, C. M. Fauquet,, D. H. L. Bishop,, C. H. Calisher,, E. B. Carsten,, M. K. Estes,, S. M. Lemon,, J. Maniloff,, M. A. Mayo,, D. J. McGeoch,, C. R. Pringle,, and R. B. Wickner (ed.), Virus Taxonomy. Seventh Report of the International Committee on the Taxonomy of Viruses. Academic Press, New York, N.Y.

21. Lemon, S. M.,, and B. H. Robertson. 1993. Current perspectives in the virology and molecular biology of hepatitis A virus. Semin. Virol. 4: 285– 296.

22. Marvil, P.,, N. J. Knowles,, A. P. A. Mockett,, P. Britton,, T. D. K. Brown,, and D. Cavanagh. 1999. Avian encephalomyelitis virus is a picornavirus and is most closely related to hepatitis A virus. J. Gen. Virol. 80: 653– 662.

23. Mateu, M. G. 1995. Antibody recognition of picornaviruses and escape from neutralization—a structural view. Virus Res. 38: 1– 24.

24. Melnick, J. L., 1996. Enteroviruses: polioviruses, coxsackieviruses, echoviruses, and newer enteroviruses, p. 655– 712. In B. N. Fields,, D. M. Knipe,, P. M. Howley, et al. (ed.), Fields Virology. Lippincott-Raven Publishers, Philadelphia, Pa.

25. Niklasson, B.,, L. Kinnunen,, B. Hornfeldt,, C. Benemar,, J. Horling,, O. Hedlund,, L. Matskova,, T. Hyypiä,, and G. Winberg. 1999. A new Picornavirus isolated from bank voles ( Clethrionomys glareolus). Virology 255: 86– 93.

26. Oberste, M. S.,, K. Maher,, D. R. Kilpatrick,, and M. A. Pallansch. 1999. Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification. J. Virol. 73: 1941– 1948.

27. Palmenberg, A. C. 1990. Proteolytic processing of the picornaviral polyprotein. Ann. Rev. Microbiol. 44: 603– 623.

28. Pöyry, T.,, L. Kinnunen,, T. Hovi,, and T. Hyypiä. 1999. Relationships between simian and human enteroviruses. J. Gen. Virol. 80: 635– 638.

29. Pöyry, T.,, L. Kinnunen,, T. Hyypiä,, B. Brown,, C. Horsnell,, T. Hovi,, and G. Stanway. 1996. Genetic and phylogenetic clustering of enteroviruses. J. Gen. Virol. 77: 1699– 1717.

30. Pulli, T.,, E. Koivunen,, and T. Hyypiä. 1997. Cell-surface interactions of echovirus 22. J. Biol. Chem. 272: 21176– 21180.

31. Pulli, T.,, H. Lankinen,, M. Roivainen,, and T. Hyypiä. 1998. Antigenic sites of coxsackievirus A9. Virology 240: 202– 212.

32. Rico-Hesse, R.,, M. A. Pallansch,, B. K. Nottay,, and O. M. Kew. 1987. Geographic distribution of wild poliovirus type 1 genotypes. Virology 160: 311– 322.

33. Roivainen, M.,, A. Närvänen,, M. Korkolainen,, M.-L. Huhtala,, and T. Hovi. 1991. Antigenic regions of poliovirus type 3/Sabin capsid proteins recognized by human sera in the peptide scanning technique. Virology 180: 99– 107.

34. Rossmann, M. G.,, E. Arnold,, J. W. Erickson,, E. A. Frankenberger,, J. P. Griffith,, H. J. Hect,, J. E. Johnson,, G. Kamer,, M. Luo,, A. G. Mosser,, R. R. Rueckert,, B. Sherry,, and G. Vriend. 1985. Structure of a human common cold virus and functional relationship to other picornaviruses. Nature 317: 145– 153.

35. Rueckert, R. R., 1996. Picornaviridae: the viruses and their replication, p. 609– 654. In B. N. Fields,, D. M. Knipe,, P. M. Howley, et al. (ed.), Fields Virology. Lippincott-Raven Publishers, Philadelphia, Pa.

36. Ryan, M. D.,, and M. Flint. 1997. Virus encoded proteinases of the picornavirus super-group. J. Gen. Virol. 78: 699– 723.

37. Santti, J.,, T. Hyypiä,, L. Kinnunen,, and M. Salminen. 1999. Evidence of recombination among enteroviruses. J. Virol. 73: 8741– 8749.

38. Stanway, G.,, and T. Hyypiä. 1999. Parechoviruses. J. Virol. 73: 5249– 5254.

39. Stanway, G.,, P. Joki-Korpla,, and T. Hyypiä. 2000. Human parechoviruses—biological and clinical significance. Rev. Med. Virol. 10: 57– 69.

40. Stewart, S. R.,, and B. L. Sender. 1997. RNA determinants of picornavirus cap-independent translation initiation. Semin. Virol. 8: 242– 255.

41. Thompson, J. D.,, D. G. Higgins,, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673– 4680.

42. Wutz, G.,, H. Auer,, N. Nowotny,, B. Grosse,, T. Skern,, and E. Kuechler. 1996. Equine rhinovirus serotype-1 and serotype-2—relationship to each other and to aphthoviruses and cardioviruses. J. Gen. Virol. 77: 1719– 1730.

43. Yamashita, T.,, K. Sakae,, H. Tsuzuki,, Y. Suzuki,, N. Ishikawa,, N. Takeda,, T. Miyamura,, and S. Yamazaki. 1998. Complete nucleotide sequence and genetic organization of Aichi virus, a distinct member of the Picornaviridae associated with acute gastroenteritis in humans. J. Virol. 72: 8408– 8412.

Tables

Molecular and Biological Basis of Picornavirus Taxonomy

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TABLE 1

Current classification of Picornaviridae

a PV, poliovirus; CVA, CVB, coxsackievirus Α, Β; E, echovirus; SVDV, swine vesicular disease virus (a variant of CVB5); EV, enterovirus; BEV, bovine enterovirus; PEV, porcine enterovirus; HRV, human rhinovirus (several HRV serotypes have not yet been assigned to a species); EMCV, encephalomyocarditis virus; TMEV, Theiler's murine encephalomyelitis virus; VHEV, Vilyuisk human encephalomyelitis virus; FMDV, foot-and-mouth disease virus; ERAV, equine rhinitis A virus; HAV, hepatitis A virus; AEV, avian encephalomyelitis-like virus; HPeV, human parechovirus; ERBV, equine rhinitis Β virus; AiV, Aichi virus; PTV, porcine teschovirus.

b Tentative species of Hepatovirus genus.

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TABLE 1

Current classification of Picornaviridae

b Tentative species of Hepatovirus genus.

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TABLE 2

Main distinguishing features of the genomes of picornavirus genera

a VP0 cleavage does not occur in these viruses.

b VP4 does not appear to be myristoylated in these viruses.

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TABLE 2

Main distinguishing features of the genomes of picornavirus genera

a VP0 cleavage does not occur in these viruses.

b VP4 does not appear to be myristoylated in these viruses.