Skip to main content
Top
Published in: Archives of Virology 4/2008

01-04-2008 | Original Article

Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T = 3 virion architecture

Authors: Olivier Le Gall, Peter Christian, Claude M. Fauquet, Andrew M. Q. King, Nick J. Knowles, Nobuhiko Nakashima, Glyn Stanway, Alexander E. Gorbalenya

Published in: Archives of Virology | Issue 4/2008

Login to get access

Abstract

Despite the apparent natural grouping of “picorna-like” viruses, the taxonomical significance of this putative “supergroup” was never addressed adequately. We recently proposed to the ICTV that an order should be created and named Picornavirales, to include viruses infecting eukaryotes that share similar properties: (i) a positive-sense RNA genome, usually with a 5′-bound VPg and 3′-polyadenylated, (ii) genome translation into autoproteolytically processed polyprotein(s), (iii) capsid proteins organized in a module containing three related jelly-roll domains which form small icosahedral, non-enveloped particles with a pseudo-T = 3 symmetry, and (iv) a three-domain module containing a superfamily III helicase, a (cysteine) proteinase with a chymotrypsin-like fold and an RNA-dependent RNA polymerase. According to the above criteria, the order Picornavirales includes the families Picornaviridae, Comoviridae, Dicistroviridae, Marnaviridae, Sequiviridae and the unassigned genera Cheravirus, Iflavirus and Sadwavirus. Other taxa of “picorna-like” viruses, e.g. Potyviridae, Caliciviridae, Hypoviridae, do not conform to several of the above criteria and are more remotely related: therefore they are not being proposed as members of the new order. Newly described viruses, not yet assigned to an existing taxon by ICTV, may belong to the proposed order.
Literature
1.
go back to reference 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 149:1045–1060PubMed 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 149:1045–1060PubMed
2.
go back to reference Allaire M, Chernaia MM, Malcolm BA, James MN (1994) Picornaviral 3C cysteine proteinases have a fold similar to chymotrypsin-like serine proteinases. Nature 369:72–76PubMedCrossRef Allaire M, Chernaia MM, Malcolm BA, James MN (1994) Picornaviral 3C cysteine proteinases have a fold similar to chymotrypsin-like serine proteinases. Nature 369:72–76PubMedCrossRef
3.
go back to reference Argos P, Kamer G, Nicklin MJ, Wimmer E (1984) Similarity in gene organization and homology between proteins of animal picornaviruses and a plant comovirus suggest common ancestry of these virus families. Nucleic Acids Res 12:7251–7267PubMedCrossRef Argos P, Kamer G, Nicklin MJ, Wimmer E (1984) Similarity in gene organization and homology between proteins of animal picornaviruses and a plant comovirus suggest common ancestry of these virus families. Nucleic Acids Res 12:7251–7267PubMedCrossRef
4.
go back to reference Arnold E, Luo M, Vriend G, Rossmann MG, Palmenberg AC, Parks GD, Nicklin MJ, Wimmer E (1987) Implications of the picornavirus capsid structure for polyprotein processing. Proc Natl Acad Sci USA 84:21–25PubMedCrossRef Arnold E, Luo M, Vriend G, Rossmann MG, Palmenberg AC, Parks GD, Nicklin MJ, Wimmer E (1987) Implications of the picornavirus capsid structure for polyprotein processing. Proc Natl Acad Sci USA 84:21–25PubMedCrossRef
5.
go back to reference Atkins JF, Wills NM, Loughran G, Wu CY, Parsawar K, Ryan MD, Wang CH, Nelson CC (2007) A case for “StopGo”: reprogramming translation to augment codon meaning of GGN by promoting unconventional termination (Stop) after addition of glycine and then allowing continued translation (Go). RNA 13:803–810PubMedCrossRef Atkins JF, Wills NM, Loughran G, Wu CY, Parsawar K, Ryan MD, Wang CH, Nelson CC (2007) A case for “StopGo”: reprogramming translation to augment codon meaning of GGN by promoting unconventional termination (Stop) after addition of glycine and then allowing continued translation (Go). RNA 13:803–810PubMedCrossRef
6.
go back to reference Bazan JF, Fletterick RJ (1988) Viral cysteine proteases are homologous to the trypsin-like family of serine proteases: structural and functional implications. Proc Natl Acad Sci USA 85:7872–7876PubMedCrossRef Bazan JF, Fletterick RJ (1988) Viral cysteine proteases are homologous to the trypsin-like family of serine proteases: structural and functional implications. Proc Natl Acad Sci USA 85:7872–7876PubMedCrossRef
7.
go back to reference Berger PH, Adams MJ, Barnett OW, Brunt AA, Hammond J, Hill JH, Jordan CV, Kashiwazaki S, Rybicki E, Spence N, Stenger DC, Ohki ST, Uyeda I, van Zaayen A, Valkonen JP, Vetten HJ (2005) Potyviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth report of the ICTV. Elsevier/Academic Press, London, pp 819–841 Berger PH, Adams MJ, Barnett OW, Brunt AA, Hammond J, Hill JH, Jordan CV, Kashiwazaki S, Rybicki E, Spence N, Stenger DC, Ohki ST, Uyeda I, van Zaayen A, Valkonen JP, Vetten HJ (2005) Potyviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth report of the ICTV. Elsevier/Academic Press, London, pp 819–841
8.
go back to reference Bishop NE, Anderson DA (1993) RNA-dependent cleavage of VP0 capsid protein in provirions of hepatitis A virus. Virology 197:616–623PubMedCrossRef Bishop NE, Anderson DA (1993) RNA-dependent cleavage of VP0 capsid protein in provirions of hepatitis A virus. Virology 197:616–623PubMedCrossRef
9.
go back to reference Blair WS, Semler BL (1991) Role for the P4 amino acid residue in substrate utilization by the poliovirus 3CD proteinase. J Virol 65:6111–6123PubMed Blair WS, Semler BL (1991) Role for the P4 amino acid residue in substrate utilization by the poliovirus 3CD proteinase. J Virol 65:6111–6123PubMed
10.
go back to reference Buck KW, Esteban R, Hillman BI (2005) Narnaviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth report of the ICTV. Elsevier/Academic Press, London, pp 751–756 Buck KW, Esteban R, Hillman BI (2005) Narnaviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth report of the ICTV. Elsevier/Academic Press, London, pp 751–756
11.
go back to reference Candresse T, Svanella-Dumas L, Le Gall O (2006) Characterization and partial genome sequence of stocky prune virus, a new member of the genus Cheravirus. Arch Virol 151:1179–1188PubMedCrossRef Candresse T, Svanella-Dumas L, Le Gall O (2006) Characterization and partial genome sequence of stocky prune virus, a new member of the genus Cheravirus. Arch Virol 151:1179–1188PubMedCrossRef
12.
go back to reference Carrington JC, Cary SM, Dougherty WG (1988) Mutational analysis of tobacco etch virus polyprotein processing: cis and trans proteolytic activities of polyproteins containing the 49-kilodalton proteinase. J Virol 62:2313–2320PubMed Carrington JC, Cary SM, Dougherty WG (1988) Mutational analysis of tobacco etch virus polyprotein processing: cis and trans proteolytic activities of polyproteins containing the 49-kilodalton proteinase. J Virol 62:2313–2320PubMed
13.
go back to reference Chandrasekar V, Johnson JE (1998) The structure of tobacco ringspot virus: a link in the evolution of icosahedral capsids in the picornavirus superfamily. Structure 6:157–171PubMedCrossRef Chandrasekar V, Johnson JE (1998) The structure of tobacco ringspot virus: a link in the evolution of icosahedral capsids in the picornavirus superfamily. Structure 6:157–171PubMedCrossRef
14.
go back to reference Cheah KC, Leong LE, Porter AG (1990) Site-directed mutagenesis suggests close functional relationship between a human rhinovirus 3C cysteine protease and cellular trypsin-like serine proteases. J Biol Chem 265:7180–7187PubMed Cheah KC, Leong LE, Porter AG (1990) Site-directed mutagenesis suggests close functional relationship between a human rhinovirus 3C cysteine protease and cellular trypsin-like serine proteases. J Biol Chem 265:7180–7187PubMed
15.
go back to reference Chen ZG, Stauffacher C, Li Y, Schmidt T, Bomu W, Kamer G, Shanks M, Lomonossoff G, Johnson JE (1989) Protein-RNA interactions in an icosahedral virus at 3.0 Å resolution. Science 245:154–159PubMedCrossRef Chen ZG, Stauffacher C, Li Y, Schmidt T, Bomu W, Kamer G, Shanks M, Lomonossoff G, Johnson JE (1989) Protein-RNA interactions in an icosahedral virus at 3.0 Å resolution. Science 245:154–159PubMedCrossRef
16.
go back to reference Christian P, Carstens E, Domier L, Johnson J, Johnson K, Nakashima N, Scotti P, van der Wilk F (2005) Dicistroviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 783–788 Christian P, Carstens E, Domier L, Johnson J, Johnson K, Nakashima N, Scotti P, van der Wilk F (2005) Dicistroviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 783–788
17.
go back to reference Christian P, Carstens E, Domier L, Johnson J, Johnson K, Nakashima N, Scotti P, van der Wilk F (2005) Iflavirus. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 779–782 Christian P, Carstens E, Domier L, Johnson J, Johnson K, Nakashima N, Scotti P, van der Wilk F (2005) Iflavirus. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 779–782
18.
go back to reference Culley AI, Lang AS, Suttle CA (2003) High diversity of unknown picorna-like viruses in the sea. Nature 424:1054–1057PubMedCrossRef Culley AI, Lang AS, Suttle CA (2003) High diversity of unknown picorna-like viruses in the sea. Nature 424:1054–1057PubMedCrossRef
19.
go back to reference Culley AI, Lang AS, Suttle CA (2005) Marnaviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth report of the ICTV. Elsevier/Academic Press, London, pp 789–792 Culley AI, Lang AS, Suttle CA (2005) Marnaviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth report of the ICTV. Elsevier/Academic Press, London, pp 789–792
20.
go back to reference Culley AI, Lang AS, Suttle CA (2007) The complete genomes of three viruses assembled from shotgun libraries of marine RNA virus communities. Virol J (electronic resource) 4:69 Culley AI, Lang AS, Suttle CA (2007) The complete genomes of three viruses assembled from shotgun libraries of marine RNA virus communities. Virol J (electronic resource) 4:69
21.
go back to reference Dolja VV, Boyko VP, Agranovsky AA, Koonin EV (1991) Phylogeny of capsid proteins of rod-shaped and filamentous RNA plant viruses: two families with distinct patterns of sequence and probably structure conservation. Virology 184:79–86PubMedCrossRef Dolja VV, Boyko VP, Agranovsky AA, Koonin EV (1991) Phylogeny of capsid proteins of rod-shaped and filamentous RNA plant viruses: two families with distinct patterns of sequence and probably structure conservation. Virology 184:79–86PubMedCrossRef
22.
go back to reference Dolja VV, Carrington JC (1992) Evolution of positive-strand RNA viruses. Semin Virol 3:315–326 Dolja VV, Carrington JC (1992) Evolution of positive-strand RNA viruses. Semin Virol 3:315–326
23.
go back to reference Dunham DM, Jiang X, Berke T, Smith AW, Matson DO (1998) Genomic mapping of a calicivirus VPg. Arch Virol 143:2421–2430PubMedCrossRef Dunham DM, Jiang X, Berke T, Smith AW, Matson DO (1998) Genomic mapping of a calicivirus VPg. Arch Virol 143:2421–2430PubMedCrossRef
24.
go back to reference Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (2005) Virus taxonomy, VIIIth report of the ICTV. Elsevier/Academic Press, London Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (2005) Virus taxonomy, VIIIth report of the ICTV. Elsevier/Academic Press, London
25.
go back to reference Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRef Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRef
26.
go back to reference Fenner F, Gibbs AJ (eds) (1988) Portraits of viruses: a history of virology. Karger, Basel Fenner F, Gibbs AJ (eds) (1988) Portraits of viruses: a history of virology. Karger, Basel
27.
go back to reference Franssen H, Leunissen J, Goldbach R, Lomonossoff GP, Zimmern D (1984) Homologous sequences in nonstructural proteins from cowpea mosaic virus and picornaviruses. EMBO J 3:855–861PubMed Franssen H, Leunissen J, Goldbach R, Lomonossoff GP, Zimmern D (1984) Homologous sequences in nonstructural proteins from cowpea mosaic virus and picornaviruses. EMBO J 3:855–861PubMed
28.
go back to reference Goldbach R (1986) Molecular evolution of plant RNA viruses. Annu Rev Phytopathol 24:289–310CrossRef Goldbach R (1986) Molecular evolution of plant RNA viruses. Annu Rev Phytopathol 24:289–310CrossRef
29.
go back to reference Goldbach R (1987) Genome similarities between plant and animal RNA viruses. Microbiol Sci 4:197–202PubMed Goldbach R (1987) Genome similarities between plant and animal RNA viruses. Microbiol Sci 4:197–202PubMed
30.
go back to reference Goldbach R, Wellink J (1988) Evolution of plus-strand RNA viruses. Intervirology 29:260–267PubMed Goldbach R, Wellink J (1988) Evolution of plus-strand RNA viruses. Intervirology 29:260–267PubMed
31.
go back to reference Gorbalenya AE, Koonin EV (1993) Comparative analysis of amino acid sequences of key enzymes of replication and expression of positive-strand RNA viruses. Validity of approach and functional and evolutionary implications. Sov Sci Rev D Physicochem Biol 11:1–84 Gorbalenya AE, Koonin EV (1993) Comparative analysis of amino acid sequences of key enzymes of replication and expression of positive-strand RNA viruses. Validity of approach and functional and evolutionary implications. Sov Sci Rev D Physicochem Biol 11:1–84
32.
go back to reference Gorbalenya AE, Koonin EV (1993) Helicases: amino acid sequence comparisons and structure-function relationships. Curr Opin Struct Biol 3:419–429CrossRef Gorbalenya AE, Koonin EV (1993) Helicases: amino acid sequence comparisons and structure-function relationships. Curr Opin Struct Biol 3:419–429CrossRef
33.
go back to reference Gorbalenya AE, Blinov VM, Donchenko AP (1986) Poliovirus-encoded proteinase 3C: a possible evolutionary link between cellular serine and cysteine proteinase families. FEBS Lett 194:253–257PubMedCrossRef Gorbalenya AE, Blinov VM, Donchenko AP (1986) Poliovirus-encoded proteinase 3C: a possible evolutionary link between cellular serine and cysteine proteinase families. FEBS Lett 194:253–257PubMedCrossRef
34.
go back to reference Gorbalenya AE, Donchenko AP, Blinov VM, Koonin EV (1989) Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases: a distinct protein superfamily with a common structural fold. FEBS Lett 243:103–114PubMedCrossRef Gorbalenya AE, Donchenko AP, Blinov VM, Koonin EV (1989) Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases: a distinct protein superfamily with a common structural fold. FEBS Lett 243:103–114PubMedCrossRef
35.
go back to reference Gorbalenya AE, Koonin EV, Wolf YI (1990) A new superfamily of putative NTP-binding domains encoded by genomes of small DNA and RNA viruses. FEBS Lett 262:145–148PubMedCrossRef Gorbalenya AE, Koonin EV, Wolf YI (1990) A new superfamily of putative NTP-binding domains encoded by genomes of small DNA and RNA viruses. FEBS Lett 262:145–148PubMedCrossRef
36.
go back to reference Gorbalenya AE, Pringle FM, Zeddam JL, Luke BT, Cameron CE, Kalmakoff J, Hanzlik TN, Gordon KH, Ward VK (2002) The palm subdomain-based active site is internally permuted in viral RNA-dependent RNA polymerases of an ancient lineage. J Mol Biol 324:47–62PubMedCrossRef Gorbalenya AE, Pringle FM, Zeddam JL, Luke BT, Cameron CE, Kalmakoff J, Hanzlik TN, Gordon KH, Ward VK (2002) The palm subdomain-based active site is internally permuted in viral RNA-dependent RNA polymerases of an ancient lineage. J Mol Biol 324:47–62PubMedCrossRef
37.
go back to reference Gromeier M, Wimmer E, Gorbalenya AE (1999) Genetics, pathogenesis and evolution of picornaviruses. In: Domingo E, Webster RG, Holland JJ (eds) Academic Press, pp 287–343 Gromeier M, Wimmer E, Gorbalenya AE (1999) Genetics, pathogenesis and evolution of picornaviruses. In: Domingo E, Webster RG, Holland JJ (eds) Academic Press, pp 287–343
38.
go back to reference Habayeb MS, Ekengren SK, Hultmark D (2006) Nora virus, a persistent virus in Drosophila, defines a new picorna-like virus family. J Gen Virol 87:3045–3051PubMedCrossRef Habayeb MS, Ekengren SK, Hultmark D (2006) Nora virus, a persistent virus in Drosophila, defines a new picorna-like virus family. J Gen Virol 87:3045–3051PubMedCrossRef
39.
go back to reference Hansen JL, Long AM, Schultz SC (1997) Structure of the RNA-dependent RNA polymerase of poliovirus. Structure 5:1109–1122PubMedCrossRef Hansen JL, Long AM, Schultz SC (1997) Structure of the RNA-dependent RNA polymerase of poliovirus. Structure 5:1109–1122PubMedCrossRef
40.
go back to reference Harber JJ, Bradley J, Anderson CW, Wimmer E (1991) Catalysis of poliovirus VP0 maturation cleavage is not mediated by serine 10 of VP2. J Virol 65:326–334PubMed Harber JJ, Bradley J, Anderson CW, Wimmer E (1991) Catalysis of poliovirus VP0 maturation cleavage is not mediated by serine 10 of VP2. J Virol 65:326–334PubMed
41.
go back to reference Hemmer O, Greif C, Dufourcq P, Reinbolt J, Fritsch C (1995) Functional characterization of the proteolytic activity of the tomato black ring nepovirus RNA-1-encoded polyprotein. Virology 206:362–371PubMedCrossRef Hemmer O, Greif C, Dufourcq P, Reinbolt J, Fritsch C (1995) Functional characterization of the proteolytic activity of the tomato black ring nepovirus RNA-1-encoded polyprotein. Virology 206:362–371PubMedCrossRef
42.
go back to reference Higaki JN, Evnin LB, Craik CS (1989) Introduction of a cysteine protease active site into trypsin. Biochemistry (Mosc) 28:9256–9263CrossRef Higaki JN, Evnin LB, Craik CS (1989) Introduction of a cysteine protease active site into trypsin. Biochemistry (Mosc) 28:9256–9263CrossRef
43.
go back to reference Hogle JM, Chow M, Filman DJ (1985) Three-dimensional structure of poliovirus at 2.9 Å resolution. Science 229:1358–1365PubMedCrossRef Hogle JM, Chow M, Filman DJ (1985) Three-dimensional structure of poliovirus at 2.9 Å resolution. Science 229:1358–1365PubMedCrossRef
44.
go back to reference Ikegami M, Iwanami T, Jones AT, Karasev AV, Le Gall O, Lehto K, Sanfacon H, Wellink J, Wetzel T (2002) Taxonomy of recognized and putative species in the family Comoviridae. In: XIIth IUMS Virology meeting, Paris, France, 27th July–12th August 2002 Ikegami M, Iwanami T, Jones AT, Karasev AV, Le Gall O, Lehto K, Sanfacon H, Wellink J, Wetzel T (2002) Taxonomy of recognized and putative species in the family Comoviridae. In: XIIth IUMS Virology meeting, Paris, France, 27th July–12th August 2002
45.
go back to reference Iwanami T, Kondo Y, Karasev AV (1999) Nucleotide sequences and taxonomy of Satsuma dwarf virus. J Gen Virol 80:793–797PubMed Iwanami T, Kondo Y, Karasev AV (1999) Nucleotide sequences and taxonomy of Satsuma dwarf virus. J Gen Virol 80:793–797PubMed
46.
go back to reference Kamer G, Argos P (1984) Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res 12:7269–7282PubMedCrossRef Kamer G, Argos P (1984) Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res 12:7269–7282PubMedCrossRef
47.
go back to reference King AF, Sangar DV, Harris TJ, Brown F (1980) Heterogeneity of the genome-linked protein of foot-and-mouth disease virus. J Virol 34:627–634PubMed King AF, Sangar DV, Harris TJ, Brown F (1980) Heterogeneity of the genome-linked protein of foot-and-mouth disease virus. J Virol 34:627–634PubMed
48.
go back to reference Koonin EV (1991) The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J Gen Virol 72:2197–2206PubMed Koonin EV (1991) The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J Gen Virol 72:2197–2206PubMed
49.
go back to reference Koonin EV, Dolja VV (1993) Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit Rev Biochem Mol Biol 28:375–430PubMedCrossRef Koonin EV, Dolja VV (1993) Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit Rev Biochem Mol Biol 28:375–430PubMedCrossRef
50.
go back to reference Koonin EV, Choi GH, Nuss DL, Shapira R, Carrington JC (1991) Evidence for common ancestry of a chestnut blight hypovirulence-associated double-stranded RNA and a group of positive-strand RNA plant viruses. Proc Natl Acad Sci USA 88:10647–10651PubMedCrossRef Koonin EV, Choi GH, Nuss DL, Shapira R, Carrington JC (1991) Evidence for common ancestry of a chestnut blight hypovirulence-associated double-stranded RNA and a group of positive-strand RNA plant viruses. Proc Natl Acad Sci USA 88:10647–10651PubMedCrossRef
51.
go back to reference Koopmans MK, Green KY, Ando T, Clarke IN, Estes MK, Matson DO, Nakata S, Neill JD, Smith AW, Studdert MJ, Thiel HJ (2005) Caliciviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth report of the ICTV. Elsevier/Academic Press, London, pp 843–851 Koopmans MK, Green KY, Ando T, Clarke IN, Estes MK, Matson DO, Nakata S, Neill JD, Smith AW, Studdert MJ, Thiel HJ (2005) Caliciviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth report of the ICTV. Elsevier/Academic Press, London, pp 843–851
52.
go back to reference Lain S, Riechmann JL, Garcia JA (1990) RNA helicase: a novel activity associated with a protein encoded by a positive strand RNA virus. Nucleic Acids Res 18:7003–7006PubMedCrossRef Lain S, Riechmann JL, Garcia JA (1990) RNA helicase: a novel activity associated with a protein encoded by a positive strand RNA virus. Nucleic Acids Res 18:7003–7006PubMedCrossRef
53.
go back to reference Laine P, Savolainen C, Blomqvist S, Hovi T (2005) Phylogenetic analysis of human rhinovirus capsid protein VP1 and 2A protease coding sequences confirms shared genus-like relationships with human enteroviruses. J Gen Virol 86:697–706PubMedCrossRef Laine P, Savolainen C, Blomqvist S, Hovi T (2005) Phylogenetic analysis of human rhinovirus capsid protein VP1 and 2A protease coding sequences confirms shared genus-like relationships with human enteroviruses. J Gen Virol 86:697–706PubMedCrossRef
54.
go back to reference Lang AS, Culley AI, Suttle CA (2004) Genome sequence and characterization of a virus (HaRNAV) related to picorna-like viruses that infects the marine toxic bloom-forming alga Heterosigma akashiwo. Virology 320:206–217PubMedCrossRef Lang AS, Culley AI, Suttle CA (2004) Genome sequence and characterization of a virus (HaRNAV) related to picorna-like viruses that infects the marine toxic bloom-forming alga Heterosigma akashiwo. Virology 320:206–217PubMedCrossRef
55.
go back to reference Lawson MA, Semler BL (1991) Poliovirus thiol proteinase 3C can utilize a serine nucleophile within the putative catalytic triad. Proc Natl Acad Sci USA 88:9919–9923PubMedCrossRef Lawson MA, Semler BL (1991) Poliovirus thiol proteinase 3C can utilize a serine nucleophile within the putative catalytic triad. Proc Natl Acad Sci USA 88:9919–9923PubMedCrossRef
56.
go back to reference Le Gall O, Iwanami T, Jones AT, Lehto K, Sanfacon H, Wellink J, Wetzel T, Yoshikawa N (2005) Cheravirus. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 803–805 Le Gall O, Iwanami T, Jones AT, Lehto K, Sanfacon H, Wellink J, Wetzel T, Yoshikawa N (2005) Cheravirus. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 803–805
57.
go back to reference Le Gall O, Iwanami T, Jones AT, Lehto K, Sanfacon H, Wellink J, Wetzel T, Yoshikawa N (2005) Sequiviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 793–798 Le Gall O, Iwanami T, Jones AT, Lehto K, Sanfacon H, Wellink J, Wetzel T, Yoshikawa N (2005) Sequiviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 793–798
58.
go back to reference Le Gall O, Iwanami T, Jones AT, Lehto K, Sanfacon H, Wellink J, Wetzel T, Yoshikawa N (2005) Comoviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 807–818 Le Gall O, Iwanami T, Jones AT, Lehto K, Sanfacon H, Wellink J, Wetzel T, Yoshikawa N (2005) Comoviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 807–818
59.
go back to reference Le Gall O, Iwanami T, Jones AT, Lehto K, Sanfacon H, Wellink J, Wetzel T, Yoshikawa N (2005) Sadwavirus. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 799–802 Le Gall O, Iwanami T, Jones AT, Lehto K, Sanfacon H, Wellink J, Wetzel T, Yoshikawa N (2005) Sadwavirus. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 799–802
60.
go back to reference Le Gall O, Sanfaçon H, Ikegami M, Iwanami T, Jones T, Karasev A, Lehto K, Wellink J, Wetzel T, Yoshikawa N (2007) Cheravirus and Sadwavirus : two unassigned genera of plant positive-sense single-stranded RNA viruses formerly considered atypical members of the genus Nepovirus (family Comoviridae). Arch Virol 152:1767–1774PubMedCrossRef Le Gall O, Sanfaçon H, Ikegami M, Iwanami T, Jones T, Karasev A, Lehto K, Wellink J, Wetzel T, Yoshikawa N (2007) Cheravirus and Sadwavirus : two unassigned genera of plant positive-sense single-stranded RNA viruses formerly considered atypical members of the genus Nepovirus (family Comoviridae). Arch Virol 152:1767–1774PubMedCrossRef
61.
go back to reference Liljas L, Tate J, Lin T, Christian P, Johnson JE (2002) Evolutionary and taxonomic implications of conserved structural motifs between picornaviruses and insect picorna-like viruses. Arch Virol 147:59–84PubMedCrossRef Liljas L, Tate J, Lin T, Christian P, Johnson JE (2002) Evolutionary and taxonomic implications of conserved structural motifs between picornaviruses and insect picorna-like viruses. Arch Virol 147:59–84PubMedCrossRef
62.
go back to reference Margis R, Pinck L (1992) Effects of site-directed mutagenesis on the presumed catalytic triad and substrate-binding pocket of grapevine fanleaf nepovirus 24-kDa proteinase. Virology 190:884–888PubMedCrossRef Margis R, Pinck L (1992) Effects of site-directed mutagenesis on the presumed catalytic triad and substrate-binding pocket of grapevine fanleaf nepovirus 24-kDa proteinase. Virology 190:884–888PubMedCrossRef
63.
go back to reference Martin A, Benichou D, Chao SF, Cohen LM, Lemon SM (1999) Maturation of the hepatitis A virus capsid protein VP1 is not dependent on processing by the 3Cpro proteinase. J Virol 73:6220–6227PubMed Martin A, Benichou D, Chao SF, Cohen LM, Lemon SM (1999) Maturation of the hepatitis A virus capsid protein VP1 is not dependent on processing by the 3Cpro proteinase. J Virol 73:6220–6227PubMed
64.
go back to reference Matthews DA, Smith WW, Ferre RA, Condon B, Budahazi G, Sisson W, Villafranca JE, Janson CA, McElroy HE, Gribskov CL, et al (1994) Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein. Cell 77:761–771PubMedCrossRef Matthews DA, Smith WW, Ferre RA, Condon B, Budahazi G, Sisson W, Villafranca JE, Janson CA, McElroy HE, Gribskov CL, et al (1994) Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein. Cell 77:761–771PubMedCrossRef
65.
go back to reference Mayo MA, Fritsch C (1994) A possible consensus sequence for VPg of viruses in the family Comoviridae. FEBS Lett 354:129–130PubMedCrossRef Mayo MA, Fritsch C (1994) A possible consensus sequence for VPg of viruses in the family Comoviridae. FEBS Lett 354:129–130PubMedCrossRef
66.
go back to reference Mayo MA, Ball LA (2006) ICTV in San Francisco: a report from the Plenary Session. Arch Virol 151:413–422 PubMedCrossRef Mayo MA, Ball LA (2006) ICTV in San Francisco: a report from the Plenary Session. Arch Virol 151:413–422 PubMedCrossRef
67.
go back to reference Meyers G, Wirblich C, Thiel HJ (1991) Genomic and subgenomic RNAs of rabbit hemorrhagic disease virus are both protein-linked and packaged into particles. Virology 184:677–686PubMedCrossRef Meyers G, Wirblich C, Thiel HJ (1991) Genomic and subgenomic RNAs of rabbit hemorrhagic disease virus are both protein-linked and packaged into particles. Virology 184:677–686PubMedCrossRef
68.
go back to reference Mirzayan C, Wimmer E (1994) Biochemical studies on poliovirus polypeptide 2C: evidence for ATPase activity. Virology 199:176–187PubMedCrossRef Mirzayan C, Wimmer E (1994) Biochemical studies on poliovirus polypeptide 2C: evidence for ATPase activity. Virology 199:176–187PubMedCrossRef
69.
go back to reference Miyashita K, Utsumi R, Utsumi T, Komano T, Satoh N (1995) Mutational analysis of the putative substrate-binding site of 3C proteinase of coxsackievirus B3. Biosci Biotechnol Biochem 59:121–122PubMedCrossRef Miyashita K, Utsumi R, Utsumi T, Komano T, Satoh N (1995) Mutational analysis of the putative substrate-binding site of 3C proteinase of coxsackievirus B3. Biosci Biotechnol Biochem 59:121–122PubMedCrossRef
70.
go back to reference Murphy JF, Rhoads RE, Hunt AG, Shaw JG (1990) The VPg of tobacco etch virus RNA is the 49-kDa proteinase or the N-terminal 24-kDa part of the proteinase. Virology 178:285–288PubMedCrossRef Murphy JF, Rhoads RE, Hunt AG, Shaw JG (1990) The VPg of tobacco etch virus RNA is the 49-kDa proteinase or the N-terminal 24-kDa part of the proteinase. Virology 178:285–288PubMedCrossRef
71.
go back to reference Nakashima N, Shibuya N (2006) Multiple coding sequences for the genome-linked virus protein (VPg) in dicistroviruses. J Invertebr Pathol 92:100–104PubMedCrossRef Nakashima N, Shibuya N (2006) Multiple coding sequences for the genome-linked virus protein (VPg) in dicistroviruses. J Invertebr Pathol 92:100–104PubMedCrossRef
72.
go back to reference Nuss DL, Hillman BI, Rigling D, Suzuki N (2005) Hypoviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 597–601 Nuss DL, Hillman BI, Rigling D, Suzuki N (2005) Hypoviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 597–601
73.
go back to reference Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358 Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358
74.
go back to reference Palmenberg AC, Kirby EM, Janda MR, Drake NL, Duke GM, Potratz KF, Collett MS (1984) The nucleotide and deduced amino acid sequences of the encephalomyocarditis viral polyprotein coding region. Nucl Acids Res 12:2969–2985PubMedCrossRef Palmenberg AC, Kirby EM, Janda MR, Drake NL, Duke GM, Potratz KF, Collett MS (1984) The nucleotide and deduced amino acid sequences of the encephalomyocarditis viral polyprotein coding region. Nucl Acids Res 12:2969–2985PubMedCrossRef
75.
go back to reference Pfister T, Wimmer E (2001) Polypeptide p41 of a Norwalk-Like Virus Is a Nucleic Acid-Independent Nucleoside Triphosphatase. J Virol 75:1611–1619PubMedCrossRef Pfister T, Wimmer E (2001) Polypeptide p41 of a Norwalk-Like Virus Is a Nucleic Acid-Independent Nucleoside Triphosphatase. J Virol 75:1611–1619PubMedCrossRef
76.
go back to reference Prasad BV, Hardy ME, Dokland T, Bella J, Rossmann MG, Estes MK (1999) X-ray crystallographic structure of the Norwalk virus capsid. Science 286:287–290PubMedCrossRef Prasad BV, Hardy ME, Dokland T, Bella J, Rossmann MG, Estes MK (1999) X-ray crystallographic structure of the Norwalk virus capsid. Science 286:287–290PubMedCrossRef
77.
go back to reference Rossmann MG, Johnson JE (1987) Icosahedral RNA virus structure. Annu Rev Biochem 58:533–573CrossRef Rossmann MG, Johnson JE (1987) Icosahedral RNA virus structure. Annu Rev Biochem 58:533–573CrossRef
78.
go back to reference Rossmann MG, Arnold E, Erickson JW, Frankenberger EA, Griffith JP, Hecht HJ, Johnson JE, Kamer G, Luo M, Mosser AG et al (1985) Structure of a human common cold virus and functional relationship to other picornaviruses. Nature 317:145–153PubMedCrossRef Rossmann MG, Arnold E, Erickson JW, Frankenberger EA, Griffith JP, Hecht HJ, Johnson JE, Kamer G, Luo M, Mosser AG et al (1985) Structure of a human common cold virus and functional relationship to other picornaviruses. Nature 317:145–153PubMedCrossRef
79.
go back to reference Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMed Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMed
80.
go back to reference Shukla DD, Ward CW, Brunt AA (1994) The Potyviridae. CAB International, Wallingford Shukla DD, Ward CW, Brunt AA (1994) The Potyviridae. CAB International, Wallingford
81.
go back to reference Spaan WJM, Cavanagh D, de Groot RJ, Enjuanes L, Gorbalenya AE, Snijder EJ, Walker PJ (2005) Nidovirales. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 937–945 Spaan WJM, Cavanagh D, de Groot RJ, Enjuanes L, Gorbalenya AE, Snijder EJ, Walker PJ (2005) Nidovirales. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 937–945
82.
go back to reference Stanway G, Brown F, Christian P, Hovi T, Hyypiä T, King AMQ, Knowles NJ, Lemon SM, Minor PD, Pallansch MA, Palmenberg AC, Skern T (2005) Picornaviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 757–778 Stanway G, Brown F, Christian P, Hovi T, Hyypiä T, King AMQ, Knowles NJ, Lemon SM, Minor PD, Pallansch MA, Palmenberg AC, Skern T (2005) Picornaviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp 757–778
83.
go back to reference Takao Y, Mise K, Nagasaki K, Okuno T, Honda D (2006) Complete nucleotide sequence and genome organization of a single-stranded RNA virus infecting the marine fungoid protist Schizochytrium sp. J Gen Virol 87:723–733PubMedCrossRef Takao Y, Mise K, Nagasaki K, Okuno T, Honda D (2006) Complete nucleotide sequence and genome organization of a single-stranded RNA virus infecting the marine fungoid protist Schizochytrium sp. J Gen Virol 87:723–733PubMedCrossRef
84.
go back to reference Tanner NK, Linder P (2001) DExD/H box helicases: from generic motors to specific dissociation functions. Mol Cell 8:251–262PubMedCrossRef Tanner NK, Linder P (2001) DExD/H box helicases: from generic motors to specific dissociation functions. Mol Cell 8:251–262PubMedCrossRef
85.
go back to reference Tate J, Liljas L, Scotti P, Christian P, Lin T, Johnson JE (1999) The crystal structure of cricket paralysis virus: the first view of a new virus family. Nat Struct Biol 6:765–774PubMedCrossRef Tate J, Liljas L, Scotti P, Christian P, Lin T, Johnson JE (1999) The crystal structure of cricket paralysis virus: the first view of a new virus family. Nat Struct Biol 6:765–774PubMedCrossRef
86.
go back to reference Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876–4882PubMedCrossRef Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876–4882PubMedCrossRef
87.
go back to reference Turnbull-Ross AD, Mayo MA, Reavy B, Murant AF (1993) Sequence analysis of the parsnip yellow fleck virus polyprotein: evidence of affinities with picornaviruses. J Gen Virol 74:555–561PubMedCrossRef Turnbull-Ross AD, Mayo MA, Reavy B, Murant AF (1993) Sequence analysis of the parsnip yellow fleck virus polyprotein: evidence of affinities with picornaviruses. J Gen Virol 74:555–561PubMedCrossRef
88.
go back to reference Tzanetakis IE, Postman JD, Gergerich RC, Martin RR (2006) A virus between families: nucleotide sequence and evolution of Strawberry latent ringspot virus. Virus Res 121:199–204PubMedCrossRef Tzanetakis IE, Postman JD, Gergerich RC, Martin RR (2006) A virus between families: nucleotide sequence and evolution of Strawberry latent ringspot virus. Virus Res 121:199–204PubMedCrossRef
89.
go back to reference Verbeek M, Dullemans AM, van den Heuvel JF, Maris PC, van der Vlugt RA (2007) Identification and characterisation of tomato torrado virus, a new plant picorna-like virus from tomato. Arch Virol 152: 881–890PubMedCrossRef Verbeek M, Dullemans AM, van den Heuvel JF, Maris PC, van der Vlugt RA (2007) Identification and characterisation of tomato torrado virus, a new plant picorna-like virus from tomato. Arch Virol 152: 881–890PubMedCrossRef
90.
go back to reference Wetzel T, Ebel R, Moury B, Le Gall O, Endisch S, Reustle GM, Krczal G (2006) Sequence analysis of grapevine isolates of Raspberry ringspot nepovirus. Arch Virol 151:599–606PubMedCrossRef Wetzel T, Ebel R, Moury B, Le Gall O, Endisch S, Reustle GM, Krczal G (2006) Sequence analysis of grapevine isolates of Raspberry ringspot nepovirus. Arch Virol 151:599–606PubMedCrossRef
91.
go back to reference Wildy P (1971) Classification and nomenclature of viruses. First report of the International Committee on Nomenclature of Viruses. Monogr Virol 5:1–65 Wildy P (1971) Classification and nomenclature of viruses. First report of the International Committee on Nomenclature of Viruses. Monogr Virol 5:1–65
92.
go back to reference Wilson JE, Powell MJ, Hoover SE, Sarnow P (2000) Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites. Mol Cell Biol 20:4990–4999PubMedCrossRef Wilson JE, Powell MJ, Hoover SE, Sarnow P (2000) Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites. Mol Cell Biol 20:4990–4999PubMedCrossRef
93.
go back to reference Ypma-Wong MF, Filman DJ, Hogle JM, Semler BL (1988) Structural domains of the poliovirus polyprotein are major determinants for proteolytic cleavage at Gln-Gly pairs. J Biol Chem 263:17846–17856PubMed Ypma-Wong MF, Filman DJ, Hogle JM, Semler BL (1988) Structural domains of the poliovirus polyprotein are major determinants for proteolytic cleavage at Gln-Gly pairs. J Biol Chem 263:17846–17856PubMed
Metadata
Title
Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T = 3 virion architecture
Authors
Olivier Le Gall
Peter Christian
Claude M. Fauquet
Andrew M. Q. King
Nick J. Knowles
Nobuhiko Nakashima
Glyn Stanway
Alexander E. Gorbalenya
Publication date
01-04-2008
Publisher
Springer Vienna
Published in
Archives of Virology / Issue 4/2008
Print ISSN: 0304-8608
Electronic ISSN: 1432-8798
DOI
https://doi.org/10.1007/s00705-008-0041-x

Other articles of this Issue 4/2008

Archives of Virology 4/2008 Go to the issue
Live Webinar | 27-06-2024 | 18:00 (CEST)

Keynote webinar | Spotlight on medication adherence

Live: Thursday 27th June 2024, 18:00-19:30 (CEST)

WHO estimates that half of all patients worldwide are non-adherent to their prescribed medication. The consequences of poor adherence can be catastrophic, on both the individual and population level.

Join our expert panel to discover why you need to understand the drivers of non-adherence in your patients, and how you can optimize medication adherence in your clinics to drastically improve patient outcomes.

Prof. Kevin Dolgin
Prof. Florian Limbourg
Prof. Anoop Chauhan
Developed by: Springer Medicine
Obesity Clinical Trial Summary

At a glance: The STEP trials

A round-up of the STEP phase 3 clinical trials evaluating semaglutide for weight loss in people with overweight or obesity.

Developed by: Springer Medicine

Highlights from the ACC 2024 Congress

Year in Review: Pediatric cardiology

Watch Dr. Anne Marie Valente present the last year's highlights in pediatric and congenital heart disease in the official ACC.24 Year in Review session.

Year in Review: Pulmonary vascular disease

The last year's highlights in pulmonary vascular disease are presented by Dr. Jane Leopold in this official video from ACC.24.

Year in Review: Valvular heart disease

Watch Prof. William Zoghbi present the last year's highlights in valvular heart disease from the official ACC.24 Year in Review session.

Year in Review: Heart failure and cardiomyopathies

Watch this official video from ACC.24. Dr. Biykem Bozkurt discusses last year's major advances in heart failure and cardiomyopathies.