1887

Abstract

Duck hepatitis virus type 1 (DHV-1) was previously classified as an enterovirus, based primarily on observed morphology and physicochemical properties of the virion. The complete nucleotide sequences of two strains (DRL-62 and R85952) of DHV-1 have been determined. Excluding the poly(A) tail, the genomes are 7691 and 7690 nt, respectively, and contain a single, large open reading frame encoding a polyprotein of 2249 aa. The genome of DHV-1 is organized as are those of members of the family : 5′ untranslated region (UTR)–VP0–VP3–VP1–2A1–2A2–2B–2C–3A–3B–3C–3D–3′ UTR. Analysis of the genomic and predicted polyprotein sequences revealed several unusual features, including the absence of a predicted maturation cleavage of VP0, the presence of two unrelated 2A protein motifs and a 3′ UTR extended markedly compared with that of any other picornavirus. The 2A1 protein motif is related to the 2A protein type of the genus and the adjacent 2A2 protein is related to the 2A protein type present in the genus . Phylogenetic analysis using the 3D protein sequence shows that the two DHV-1 strains are related more closely to members of the genus than to other picornaviruses. However, the two DHV-1 strains form a monophyletic group, clearly distinct from members of the genus .

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.81804-0
2006-11-01
2019-11-16
Loading full text...

Full text loading...

/deliver/fulltext/jgv/87/11/3307.html?itemId=/content/journal/jgv/10.1099/vir.0.81804-0&mimeType=html&fmt=ahah

References

  1. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. ( 1997; ). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef]
    [Google Scholar]
  2. Auvinen, P. & Hyypiä, T. ( 1990; ). Echoviruses include genetically distinct serotypes. J Gen Virol 71, 2133–2139.[CrossRef]
    [Google Scholar]
  3. Bateman, A. & Haft, D. H. ( 2002; ). HMM-based databases in InterPro. Brief Bioinform 3, 236–245.[CrossRef]
    [Google Scholar]
  4. Beales, L. P., Holzenburg, A. & Rowlands, D. J. ( 2003; ). Viral internal ribosome entry site structures segregate into two distinct morphologies. J Virol 77, 6574–6579.[CrossRef]
    [Google Scholar]
  5. Beard, C. W. & Mason, P. W. ( 2000; ). Genetic determinants of altered virulence of Taiwanese foot-and-mouth disease virus. J Virol 74, 987–991.[CrossRef]
    [Google Scholar]
  6. Chow, M., Newman, J. F. E., Filman, D., Hogle, J. M., Rowlands, D. J. & Brown, F. ( 1987; ). Myristylation of picornavirus capsid protein VP4 and its structural significance. Nature 327, 482–486.[CrossRef]
    [Google Scholar]
  7. Cohen, S. H., Naviaux, R. K., vanden Brink, K. M. & Jordan, G. W. ( 1988; ). Comparison of the nucleotide sequences of diabetogenic and nondiabetogenic encephalomyocarditis virus. Virology 166, 603–607.[CrossRef]
    [Google Scholar]
  8. Cui, T. & Porter, A. G. ( 1995; ). Localization of binding site for encephalomyocarditis virus RNA polymerase in the 3′-noncoding region of the viral RNA. Nucleic Acids Res 23, 377–382.[CrossRef]
    [Google Scholar]
  9. Davis, D. ( 1987; ). Temperature and pH stability of duck hepatitis virus. Avian Pathol 16, 21–30.[CrossRef]
    [Google Scholar]
  10. Doherty, M., Todd, D., McFerran, N. & Hoey, E. M. ( 1999; ). Sequence analysis of a porcine enterovirus serotype 1 isolate: relationships with other picornaviruses. J Gen Virol 80, 1929–1941.
    [Google Scholar]
  11. Domingo, E., Mateu, M. G., Escarmis, C., Martinez-Salas, E., Andreu, D., Giralt, E., Verdaguer, N. & Fita, I. ( 1995; ). Molecular evolution of aphthoviruses. Virus Genes 11, 197–207.[CrossRef]
    [Google Scholar]
  12. Donnelly, M. L. L., Gani, D., Flint, M., Monaghan, S. & Ryan, M. D. ( 1997; ). The cleavage activities of aphthovirus and cardiovirus 2A proteins. J Gen Virol 78, 13–21.
    [Google Scholar]
  13. Donnelly, M. L., Hughes, L. E., Luke, G., Mendoza, H., ten Dam, E., Gani, D. & Ryan, M. D. ( 2001; ). The ‘cleavage’ activities of foot-and-mouth disease virus 2A site-directed mutants and naturally occurring ‘2A-like’ sequences. J Gen Virol 82, 1027–1041.
    [Google Scholar]
  14. Dougherty, W. G. & Semler, B. L. ( 1993; ). Expression of virus-encoded proteinases: functional and structural similarities with cellular enzymes. Microbiol Rev 57, 781–822.
    [Google Scholar]
  15. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  16. Forss, S., Strebel, K., Beck, E. & Schaller, H. ( 1984; ). Nucleotide sequence and genome organization of foot-and-mouth disease virus. Nucleic Acids Res 12, 6587–6601.[CrossRef]
    [Google Scholar]
  17. Gorbalenya, A. E. & Koonin, E. V. ( 1993; ). Comparative analysis of the amino acid sequences of the key enzymes of the replication and expression of positive-strand RNA viruses. Sov Sci Rev Sect D Physicochem Biol Rev 11, 1–84.
    [Google Scholar]
  18. Gorbalenya, A. E., Koonin, E. V. & Lai, M. M.-C. ( 1991; ). Putative papain-related thiol proteases of positive-strand RNA viruses. FEBS Lett 288, 201–205.[CrossRef]
    [Google Scholar]
  19. Gough, R. E., Collins, M. S., Borland, E. & Keymer, I. F. ( 1984; ). Astrovirus-like particles associated with hepatitis in ducklings. Vet Rec 114, 279.
    [Google Scholar]
  20. Gromeier, M., Wimmer, E. & Gorbalenya, A. E. ( 1999; ). Genetics, pathogenesis and evolution of picornaviruses. In Origin and Evolution of Viruses, pp. 287–343. Edited by E. Domingo, R. Webster & J. Holland. San Diego: Academic Press.
  21. Hahn, H. & Palmenberg, A. C. ( 1996; ). Mutational analysis of the encephalomyocarditis virus primary cleavage. J Virol 70, 6870–6875.
    [Google Scholar]
  22. Haider, S. A. & Calnek, B. W. ( 1979; ). In vitro isolation, propagation, and characterization of duck hepatitis virus type III. Avian Dis 23, 715–729.[CrossRef]
    [Google Scholar]
  23. Hall, T. A. ( 1999; ). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95–98.
    [Google Scholar]
  24. Higgins, D. G. & Sharp, P. M. ( 1988; ). clustal: a package for performing multiple sequence alignment on a microcomputer. Gene 73, 237–244.[CrossRef]
    [Google Scholar]
  25. Hollinger, F. B. & Emerson, S. U. ( 2001; ). Hepatitis A virus. In Fields Virology, 4th edn, vol. 1, pp. 799–840. Edited by D. M. Knipe, P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Martin, B. Roizman & S. E. Straus. Philadelphia, PA: Lippincott Williams & Wilkins.
  26. Hughes, P. J. & Stanway, G. ( 2000; ). The 2A proteins of three diverse picornaviruses are related to each other and to the H-rev107 family of proteins involved in the control of cell proliferation. J Gen Virol 81, 201–207.
    [Google Scholar]
  27. Ito, M., Yamashita, T., Tsuzuki, H., Takeda, N. & Sakae, K. ( 2004; ). Isolation and identification of a novel human parechovirus. J Gen Virol 85, 391–398.[CrossRef]
    [Google Scholar]
  28. Johansson, S., Niklasson, B., Maizel, J., Gorbalenya, A. E. & Lindberg, A. M. ( 2002; ). Molecular analysis of three Ljungan virus isolates reveals a new, close-to-root lineage of the Picornaviridae with a cluster of two unrelated 2A proteins. J Virol 76, 8920–8930.[CrossRef]
    [Google Scholar]
  29. Johansson, E. S., Niklasson, B., Tesh, R. B., Shafren, D. R., Travassos da Rosa, A. P. A. & Lindberg, A. M. ( 2003; ). Molecular characterization of M1146, an American isolate of Ljungan virus (LV) reveals the presence of a new LV genotype. J Gen Virol 84, 837–844.[CrossRef]
    [Google Scholar]
  30. Joki-Korpela, P., Roivainen, M., Lankinen, H., Pöyry, T. & Hyypiä, T. ( 2000; ). Antigenic properties of human parechovirus 1. J Gen Virol 81, 1709–1718.
    [Google Scholar]
  31. King, A. M. Q., Brown, F., Christian, P. & 8 other authors ( 2000; ). Family Picornaviridae. In Virus Taxonomy: Seventh Report of the International Committee on Taxonomy of Viruses, pp. 657–678. Edited by M. H. V. van Regenmortel, C. M. Fauquet, D. H. L. Bishop, C. H. Calisher, E. B. Carstens, M. K. Estes, S. M. Lemon, J. Maniloff, M. A. Mayo, D. J. McGeoch, C. R. Pringle & R. B. Wickner. New York: Academic Press.
  32. Koonin, E. V. ( 1991; ). The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J Gen Virol 72, 2197–2206.[CrossRef]
    [Google Scholar]
  33. Koonin, E. V. & Dolja, V. V. ( 1993; ). Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit Rev Biochem Mol Biol 28, 375–430.[CrossRef]
    [Google Scholar]
  34. Kozak, M. ( 1986; ). Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44, 283–292.[CrossRef]
    [Google Scholar]
  35. Kräusslich, H. G. & Wimmer, E. ( 1988; ). Viral proteinases. Annu Rev Biochem 57, 701–754.[CrossRef]
    [Google Scholar]
  36. Levine, P. P. & Fabricant, J. ( 1950; ). A hitherto-undescribed virus disease of ducks in North America. Cornell Vet 40, 71–86.
    [Google Scholar]
  37. Li, F., Browning, G. F., Studdert, M. J. & Crabb, B. S. ( 1996; ). Equine rhinovirus 1 is more closely related to foot-and-mouth disease virus than to other picornaviruses. Proc Natl Acad Sci U S A 93, 990–995.[CrossRef]
    [Google Scholar]
  38. Marvil, P., Knowles, N. J., Mockett, A. P. A., Britton, P., Brown, T. D. K. & Cavanagh, D. ( 1999; ). Avian encephalomyelitis virus is a picornavirus and is most closely related to hepatitis A virus. J Gen Virol 80, 653–662.
    [Google Scholar]
  39. Melnick, J. L., Agol, V. I., Bachrach, H. L. & 18 other authors ( 1974; ). Picornaviridae. Intervirology 4, 303–316.[CrossRef]
    [Google Scholar]
  40. Mulders, M. N., Salminen, M., Kalkkinen, N. & Hovi, T. ( 2000; ). Molecular epidemiology of coxsackievirus B4 and disclosure of the correct VP1/2Apro cleavage site: evidence for high genomic diversity and long-term endemicity of distinct genotypes. J Gen Virol 81, 803–812.
    [Google Scholar]
  41. Nicholas, K. B., Nicholas, H. B., Jr & Deerfield, D. W., II ( 1997; ). GeneDoc: analysis and visualization of genetic variation. EMBNEW News 4, 14.
    [Google Scholar]
  42. Oberste, M. S., Maher, K., Kennett, M. L., Campbell, J. J., Carpenter, M. S., Schnurr, D. & Pallansch, M. A. ( 1999a; ). Molecular epidemiology and genetic diversity of echovirus type 30 (E30): genotypes correlate with temporal dynamics of E30 isolation. J Clin Microbiol 37, 3928–3933.
    [Google Scholar]
  43. Oberste, M. S., Maher, K., Kilpatrick, D. R. & Pallansch, M. A. ( 1999b; ). Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification. J Virol 73, 1941–1948.
    [Google Scholar]
  44. Page, R. D. M. ( 1996; ). TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12, 357–358.
    [Google Scholar]
  45. Pallansch, M. A. & Roos, R. P. ( 2001; ). Enteroviruses: polioviruses, coxsackieviruses, echoviruses and newer enteroviruses. In Fields Virology, 4th edn, vol. 1, pp. 723–775. Edited by D. M. Knipe, P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Martin, B. Roizman & S. E. Straus. Philadelphia, PA: Lippincott Williams & Wilkins.
  46. Palmenberg, A. C. ( 1989; ). Sequence alignments of picornaviral capsid proteins. In Molecular Aspects of Picornavirus Infection and Detection, pp. 211–241. Edited by B. L. Semler & E. Ehrenfeld. Washington, DC: American Society for Microbiology.
  47. Palmenberg, A. C. ( 1990; ). Proteolytic processing of picornaviral polyprotein. Annu Rev Microbiol 44, 603–623.[CrossRef]
    [Google Scholar]
  48. Palmenberg, A. C., Parks, G. D., Hall, D. J., Ingraham, R. H., Seng, T. W. & Pallai, P. V. ( 1992; ). Proteolytic processing of the cardioviral P2 region: primary 2A/2B cleavage in clone-derived precursors. Virology 190, 754–762.[CrossRef]
    [Google Scholar]
  49. Paul, A. V., Tada, H., von der Helm, K., Wissel, T., Kiehn, R., Wimmer, E. & Deinhardt, F. ( 1987; ). The entire nucleotide sequence of the genome of human hepatitis A virus (isolate MBB). Virus Res 8, 153–171.[CrossRef]
    [Google Scholar]
  50. Pevear, D. C., Borkowski, J., Calenoff, M., Oh, C. K., Ostrowski, B. & Lipton, H. L. ( 1988; ). Insights into Theiler's virus neurovirulence based on a genomic comparison of the neurovirulent GDVII and less virulent BeAn strains. Virology 165, 1–12.[CrossRef]
    [Google Scholar]
  51. Pöyry, T., Kinnunen, L., Hyypiä, T., Brown, B., Horsnell, C., Hovi, T. & Stanway, G. ( 1996; ). Genetic and phylogenetic clustering of enteroviruses. J Gen Virol 77, 1699–1717.[CrossRef]
    [Google Scholar]
  52. Pringle, C. R. ( 1999; ). Virus taxonomy at the XIth International Congress of Virology, Sydney, Australia, 1999. Arch Virol 144, 2065–2070.[CrossRef]
    [Google Scholar]
  53. Pulli, T., Koivunen, E. & Hyypiä, T. ( 1997; ). Cell-surface interactions of echovirus 22. J Biol Chem 272, 21176–21180.[CrossRef]
    [Google Scholar]
  54. Racaniello, V. R. ( 2001; ). Picornaviridae: the viruses and their replication. In Fields Virology, 4th edn, pp. 685–722. Edited by D. M. Knipe, P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Martin, B. Riozman & S. E. Straus. Philadelphia, PA: Lippincott Williams & Wilkins.
  55. Reuber, T. L. & Ausubel, F. M. ( 1996; ). Isolation of Arabidopsis genes that differentiate between resistance responses mediated by the RPS2 and RPM1 disease resistance genes. Plant Cell 8, 241–249.[CrossRef]
    [Google Scholar]
  56. Richter, W. R., Rdzok, E. J. & Moize, S. M. ( 1964; ). Electron microscopy of viruslike particles associated with duck viral hepatitis. Virology 24, 114–116.[CrossRef]
    [Google Scholar]
  57. Robertson, B. H., Grubman, M. J., Weddell, G. N. & 7 other authors ( 1985; ). Nucleotide and amino acid sequence coding for polypeptides of foot-and-mouth disease virus type A12. J Virol 54, 651–660.
    [Google Scholar]
  58. Rodrigo, M. J. & Dopazo, J. ( 1995; ). Evolutionary analysis of the picornavirus family. J Mol Evol 40, 362–371.[CrossRef]
    [Google Scholar]
  59. Rueckert, R. R. ( 1996; ). Picornaviridae: the viruses and their replication. In Fields Virology, 3rd edn, vol. 1, pp. 609–654. Edited by B. N. Fields, D. M. Knipe & P. M. Howley. Philadelphia, PA: Lippincott–Raven.
  60. Ryan, M. D. & Flint, M. ( 1997; ). Virus-encoded proteinases of the picornavirus super-group. J Gen Virol 78, 699–723.
    [Google Scholar]
  61. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  62. Sambrook, J., Fritsch, E. F. & Maniatis, T. ( 1989; ). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  63. Santti, J., Harvala, H., Kinnunen, L. & Hyypiä, T. ( 2000; ). Molecular epidemiology and evolution of coxsackievirus A9. J Gen Virol 81, 1361–1372.
    [Google Scholar]
  64. Sprang, S. R. ( 1997; ). G protein mechanisms: insights from structural analysis. Annu Rev Biochem 66, 639–678.[CrossRef]
    [Google Scholar]
  65. Stanway, G., Kalkkinen, N., Roivainen, M., Ghazi, F., Khan, M., Smyth, M., Meurman, O. & Hyypiä, T. ( 1994; ). Molecular and biological characteristics of echovirus 22, a representative of a new picornavirus group. J Virol 68, 8232–8238.
    [Google Scholar]
  66. Stanway, G., Brown, F., Christian, P. & 9 other authors ( 2005; ). Family Picornaviridae. In Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses, pp. 757–778. Edited by C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger & L. A. Ball. San Diego: Elsevier Academic Press.
  67. Tauraso, N. M., Coghill, G. E. & Klutch, M. J. ( 1969; ). Properties of the attenuated vaccine strain of duck hepatitis virus. Avian Dis 13, 321–329.[CrossRef]
    [Google Scholar]
  68. Triantafilou, K., Triantafilou, M., Takada, Y. & Fernandez, N. ( 2000; ). Human parechovirus 1 utilizes integrins αvβ3 and αvβ1 as receptors. J Virol 74, 5856–5862.[CrossRef]
    [Google Scholar]
  69. Wildy, P. ( 1971; ). Classification and nomenclature of viruses: first report of the International Committee on Taxonomy of Viruses. Monogr Virol 5, 1–118.
    [Google Scholar]
  70. Woolcock, P. R. ( 2003; ). Duck hepatitis. In Diseases of Poultry, 11th edn, pp. 343–354. Edited by Y. M. Saif, H. J. Barnes, J. R. Glisson, A. M. Fadly, L. R. McDougald & D. E. Swayne. Iowa: Iowa State Press.
  71. Wutz, G., Auer, H., Nowotny, N., Grosse, B., Skern, T. & Kuechler, E. ( 1996; ). Equine rhinovirus serotypes 1 and 2: relationship to each other and to aphthoviruses and cardioviruses. J Gen Virol 77, 1719–1730.[CrossRef]
    [Google Scholar]
  72. Yamashita, T., Sakae, K., Tsuzuki, H., Suzuki, Y., Ishikawa, N., Takeda, N., Miyamura, T. & Yamazaki, S. ( 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.
    [Google Scholar]
  73. Zell, R., Dauber, M., Krumbholz, A., Henke, A., Birch-Hirschfeld, E., Stelzner, A., Prager, D. & Wurm, R. ( 2001; ). Porcine teschoviruses comprise at least eleven distinct serotypes: molecular and evolutionary aspects. J Virol 75, 1620–1631.[CrossRef]
    [Google Scholar]
  74. Zuker, M. ( 2003; ). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406–3415.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.81804-0
Loading
/content/journal/jgv/10.1099/vir.0.81804-0
Loading

Data & Media loading...

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error