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Chapter 2 : Molecular and Biological Basis of Picornavirus Taxonomy

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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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Figures

Image of FIGURE 1
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 and 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 and 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 species, FMDV, encodes three tandem copies of VPg.

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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Image of FIGURE 2
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 ( ). Abbreviations are as given in Table 1 . Species names within each genus are enclosed by dotted lines.

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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Tables

Generic image for table
TABLE 1

Current classification of

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.

Tentative species of genus.

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
Generic image for table
TABLE 2

Main distinguishing features of the genomes of picornavirus genera

VP0 cleavage does not occur in these viruses.

VP4 does not appear to be myristoylated in these 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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