Complete genome sequences for nine simian enteroviruses Free

Abstract

Analysis of the VP1 capsid-coding sequences of the simian picornaviruses has suggested that baboon enterovirus (BaEV), SV19, SV43 and SV46 belong to the species (HEV-A) and SA5 belongs to HEV-B, whereas SV4/A2 plaque virus (two isolates of a single serotype), SV6 and N125/N203 (two isolates of a single serotype) appear to represent new species in the genus. We have further characterized by complete genomic sequencing the genetic relationships among the simian enteroviruses serotypes (BaEV, N125/N203, SA5, SV4/A2 plaque virus, SV6, SV19, SV43 and SV46) and to other enteroviruses. Phylogenetic and pairwise sequence relationships for the P1 region paralleled those of VP1 alone, and confirmed that SV4/A-2 plaque virus, SV6 and N125/N203 represent unique genetic clusters that probably correspond to three new species. However, sequence relationships in the P2 and P3 regions were quite different. In 2C, SV19, SV43 and SV46 remain clustered with the human viruses of HEV-A, but BaEV, SV6 and N125/N203 cluster together; in 3CD, SA5 (HEV-B) also joined this cluster. The 3′-non-translated region (NTR) sequences are highly conserved within each of the four human enterovirus species, but the 3′-NTRs of the simian enteroviruses are distinct from those of all human enteroviruses and generally distinct from one another. These results suggest that host species may have a significant influence on the evolution of enterovirus non-capsid sequences.

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2007-12-01
2024-03-29
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References

  1. Barton D. J., O'Donnell B. J., Flanegan J. B. 2001; 5′ cloverleaf in poliovirus RNA is a cis -acting replication element required for negative-strand synthesis. EMBO J 20:1439–1448 [CrossRef]
    [Google Scholar]
  2. Belov G. A., Altan-Bonnet N., Kovtunovych G., Jackson C. L., Lippincott-Schwartz J., Ehrenfeld E. 2007; Hijacking components of the cellular secretory pathway for replication of poliovirus RNA. J Virol 81:558–567 [CrossRef]
    [Google Scholar]
  3. Blom N., Hansen J., Blaas D., Brunak S. 1996; Cleavage site analysis in picornaviral polyproteins: discovering cellular targets by neural networks. Protein Sci 5:2203–2216 [CrossRef]
    [Google Scholar]
  4. Brown B. A., Oberste M. S., Maher K., Pallansch M. A. 2003; Complete genomic sequencing shows that polioviruses and members of human enterovirus species C are closely related in the non-capsid coding region. J Virol 77:8973–8984 [CrossRef]
    [Google Scholar]
  5. Brown D. M., Kauder S. E., Cornell C. T., Jang G. M., Racaniello V. R., Semler B. L. 2004; Cell-dependent role for the poliovirus 3′ noncoding region in positive-strand RNA synthesis. J Virol 78:1344–1351 [CrossRef]
    [Google Scholar]
  6. Das S., Dasgupta A. 1993; Identification of the cleavage site and determinants required for poliovirus 3Cpro-catalyzed cleavage of human TBP. J Virol 67:3326–3331
    [Google Scholar]
  7. Earle J. A. P., Skuce R. A., Fleming C. S., Hoey E. M., Martin S. J. 1988; The complete nucleotide sequence of a bovine enterovirus. J Gen Virol 69:253–263 [CrossRef]
    [Google Scholar]
  8. Fuentes-Marins R., Rodriguez A. R., Kalter S. S., Hellman A., Crandell R. A. 1963; Isolation of enteroviruses from the “normal” baboon ( Papio doguera . J Bacteriol 85:1045–1050
    [Google Scholar]
  9. Harris K. S., Xiang W., Alexander L., Lane W. S., Paul A. V., Wimmer E. 1994; Interaction of poliovirus polypeptide 3CDpro with the 5′ and 3′ termini of the poliovirus genome. Identification of viral and cellular factors needed for efficient binding. J Biol Chem 269:27004–27014
    [Google Scholar]
  10. Hoffert W. R., Bates M. E., Cheever F. S. 1958; Study of enteric viruses of simian origin. Am J Hyg 68:15–30
    [Google Scholar]
  11. Jackson R. J. 2002; Proteins involved in the function of picornavirus internal ribosome entry sites. In Molecular Biology of Picornaviruses pp 171–183 Edited by Semler B. L., Wimmer E. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  12. Jones D. T., Taylor W. R., Thornton J. M. 1992; The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275–282
    [Google Scholar]
  13. Jones-Engel L., Engel G. A., Heidrich J., Chalise M., Poudel N., Viscidi R., Barry P. A., Allan J. S., Grant R., Kyes R. 2006; Temple monkeys and health implications of commensalism, Kathmandu, Nepal. Emerg Infect Dis 12:900–906 [CrossRef]
    [Google Scholar]
  14. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism pp 21–132 Edited by Munro H. N. New York: Academic Press;
    [Google Scholar]
  15. Kalter S. S. 1960; Animal “orphan” enteroviruses. Bull World Health Organ 22:319–337
    [Google Scholar]
  16. Kalter S. S. 1982; Enteric viruses of nonhuman primates. Vet Pathol Suppl 19:33–43 [CrossRef]
    [Google Scholar]
  17. Kalter S. S., Kim C. S., Sueltenfuss E. A. 1967; Further characterization of agents isolated from normal baboon ( Papio sp.). J Infect Dis 117:301–306 [CrossRef]
    [Google Scholar]
  18. Kimura M. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [CrossRef]
    [Google Scholar]
  19. Knowles N. J. 2006 The picornavirus home page http://www.picornaviridae.com/ Pirbright, Woking, UK: Institute for Animal Health, Pirbright Laboratory;
    [Google Scholar]
  20. Kräusslich H.-G., Nicklin M. J., Toyoda H., Etchison D., Wimmer E. 1987; Poliovirus protease 2A induces cleavage of eucaryotic initiation factor 4F polypeptide p220. J Virol 61:2711–2718
    [Google Scholar]
  21. Krumbholz A., Dauber M., Henke A., Birch-Hirschfeld E., Knowles N. J., Stelzner A., Zell R. 2002; Sequencing of porcine enterovirus groups II and III reveals unique features of both virus groups. J Virol 76:5813–5821 [CrossRef]
    [Google Scholar]
  22. Kumar S., Tamura K., Jakobsen I. B., Nei M. 2001; mega2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244–1245 [CrossRef]
    [Google Scholar]
  23. Lloyd R. E., Grubman M. J., Ehrenfeld E. 1988; Relationship of p220 cleavage during picornavirus infection to 2A proteinase sequencing. J Virol 62:4216–4223
    [Google Scholar]
  24. Lole K. S., Bollinger R. C., Paranjape R. S., Gadkari D., Kulkarni S. S., Novak N. G., Ingersoll R., Sheppard H. W., Ray S. C. 1999; Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73:152–160
    [Google Scholar]
  25. Lyons T., Murray K. E., Roberts A. W., Barton D. J. 2001; Poliovirus 5′-terminal cloverleaf RNA is required in cis for VPg uridylylation and the initiation of negative-strand RNA synthesis. J Virol 75:10696–10708 [CrossRef]
    [Google Scholar]
  26. Mellits K. H., Meredith J. M., Rohll J. B., Evans D. J., Almond J. W. 1998; Binding of a cellular factor to the 3′ untranslated region of the RNA genomes of entero- and rhinoviruses plays a role in virus replication. J Gen Virol 79:1715–1723
    [Google Scholar]
  27. Mirmomeni M. H., Hughes P. J., Stanway G. 1997; An RNA tertiary structure in the 3′ untranslated region of enteroviruses is necessary for efficient replication. J Virol 71:2363–2370
    [Google Scholar]
  28. O'Neill R. E., Racaniello V. R. 1989; Inhibition of translation in cells infected with poliovirus 2Apro mutant correlates with phosphorylation of the alpha subunit of eucaryotic initiation factor 2. J Virol 63:5069–5075
    [Google Scholar]
  29. Oberste M. S., Schnurr D., Maher K., al-Busaidy S., Pallansch M. A. 2001; Molecular identification of new picornaviruses and characterization of a proposed enterovirus 73 serotype. J Gen Virol 82:409–416
    [Google Scholar]
  30. Oberste M. S., Maher K., Pallansch M. A. 2002; Molecular phylogeny and classification of the simian picornaviruses. J Virol 76:1244–1251 [CrossRef]
    [Google Scholar]
  31. Oberste M. S., Maher K., Pallansch M. A. 2003; Genetic evidence that SV2 and six other simian picornaviruses represent a new genus in Picornaviridae . Virology 314:283–293 [CrossRef]
    [Google Scholar]
  32. Oberste M. S., Maher K., Pallansch M. 2004a; Evidence for frequent recombination within Human enterovirus B based on complete genomic sequences of all 37 serotypes. J Virol 78:855–867 [CrossRef]
    [Google Scholar]
  33. Oberste M. S., Maher K., Schnurr D., Peters H., Sessions W., Kirk C., Chatterjee N., Fuller S., Hanauer J. M., Pallansch M. A. 2004b; Enterovirus 68 is associated with respiratory illness and shares features with both the enteroviruses and the rhinoviruses. J Gen Virol 85:2577–2584 [CrossRef]
    [Google Scholar]
  34. Oberste M. S., Michele S. M., Maher K., Schnurr D., Cisterna D., Junttila N., Uddin M., Chomel J.-J., Lau C.-S. & other authors (2004c). Molecular identification and characterization of two proposed new enterovirus serotypes, EV74 and EV75. J Gen Virol 85:3205–3212 [CrossRef]
    [Google Scholar]
  35. Oberste M. S., Peñaranda S., Maher K., Pallansch M. A. 2004d; Complete genome sequences of members of the species Human enterovirus A . J Gen Virol 85:1597–1607 [CrossRef]
    [Google Scholar]
  36. Oberste M. S., Maher K., Michele S. M., Uddin M., Belliot G., Pallansch M. A. 2005; Enteroviruses 76, 89, 90 and 91 represent a novel group within the species Human enterovirus A . J Gen Virol 86:445–451 [CrossRef]
    [Google Scholar]
  37. Oberste M. S., Maher K., Williams A. J., Dybdahl-Sissoko N., Brown B. A., Gookin M. T., Peñaranda S., Mishrik N. G., Uddin M., Pallansch M. A. 2006; Species-specific RT-PCR amplification of human enteroviruses: a tool for rapid species identification of uncharacterized enteroviruses. J Gen Virol 87:119–128 [CrossRef]
    [Google Scholar]
  38. Pallansch M. A., Roos R. P. 2001; Enteroviruses: polioviruses, coxsackieviruses, echoviruses, and newer enteroviruses. In Fields Virology , 4th edn. pp 723–775 Edited by Knipe D. M., Howley P. M., Griffin D. E., Lamb R. A., Martin M. A., Roizman B., Straus S. E. Philadelphia: Lippincott Williams & Wilkins;
    [Google Scholar]
  39. Paul A. V. 2002; Possible unifying mechanism of picornavirus genome replication. In Molecular Biology of Picornaviruses pp 227–246 Edited by Semler B. L., Wimmer E. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  40. Pilipenko E. V., Maslova S. V., Sinyakov A. N., Agol V. I. 1992; Towards identification of cis -acting elements involved in the replication of enterovirus and rhinovirus RNAs: a proposal for the existence of tRNA-like terminal structures. Nucleic Acids Res 20:1739–1745 [CrossRef]
    [Google Scholar]
  41. Pilipenko E. V., Poperechny K. V., Maslova S. V., Melchers W. J., Slot H. J., Agol V. I. 1996; Cis -element, oriR , involved in the initiation of (−) strand poliovirus RNA: a quasi-globular multi-domain RNA structure maintained by tertiary (‘kissing’) interactions. EMBO J 15:5428–5436
    [Google Scholar]
  42. Pöyry T., Kinnunen L., Hyypia 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]
  43. Pöyry T., Kinnunen L., Hovi T., Hyypia T. 1999; Relationships between simian and human enteroviruses. J Gen Virol 80:635–638
    [Google Scholar]
  44. Rodriguez A. R., Kalter S. S., Heberling R. L., Helmke R. J., Guajardo J. E. 1977; Viral infections of the captive Kenya baboon ( Papio cynocephalus ): a five-year epidemiologic study of an outdoor colony. Lab Anim Sci 27:356–371
    [Google Scholar]
  45. Rohll J. B., Moon D. H., Evans D. J., Almond J. W. 1995; The 3′ untranslated region of picornaviruses RNA: features required for efficient genome replication. J Virol 69:7835–7844
    [Google Scholar]
  46. Shen Y., Igo M., Yalamanchili P., Berk A. J., Dasgupta A. 1996; DNA binding domain and subunit interactions of transcription factor IIIC revealed by dissection with poliovirus 3C protease. Mol Cell Biol 16:4163–4171
    [Google Scholar]
  47. Stanway G., Brown F., Christian P., Hovi T., Hyypiä T., King A. M. Q., Knowles N. J., Lemon S. M., Minor P. D. other authors 2005; Picornaviridae . In Virus Taxonomy: Eighth report of the International Committee on the Taxonomy of Viruses pp 757–778 Edited by Fauquet C. M., Mayo M. A., Maniloff J., Desselberger U., Ball L. A. London: Elsevier/Academic Press;
    [Google Scholar]
  48. Teterina N. L., Egger D., Bienz K., Brown D. M., Semler B. L., Ehrenfeld E. 2001; Requirements for assembly of poliovirus replication complexes and negative-strand RNA synthesis. J Virol 75:3841–3850 [CrossRef]
    [Google Scholar]
  49. Todd S., Nguyen J. H. C., Semler B. L. 1995; RNA-protein interactions directed by the 3′ end of human rhinovirus genomic RNA. J Virol 69:3605–3614
    [Google Scholar]
  50. Waggoner S., Sarnow P. 1998; Viral ribonucleoprotein complex formation and nucleolar-cytoplasmic relocalization of nucleolin in poliovirus-infected cells. J Virol 72:6699–6709
    [Google Scholar]
  51. Yalamanchili P., Harris K., Wimmer E., Dasgupta A. 1996; Inhibition of basal transcription by poliovirus: a virus-encoded protease (3Cpro) inhibits formation of TBP-TATA box complex in vitro. J Virol 70:2922–2929
    [Google Scholar]
  52. Yalamanchili P., Banerjee R., Dasgupta A. 1997a; Poliovirus-encoded protease 2Apro cleaves the TATA-binding protein but does not inhibit host cell RNA polymerase II transcription in vitro. J Virol 71:6881–6886
    [Google Scholar]
  53. Yalamanchili P., Datta U., Dasgupta A. 1997b; Inhibition of host cell transcription by poliovirus: cleavage of transcription factor CREB by poliovirus-encoded protease 3Cpro . J Virol 71:1220–1226
    [Google Scholar]
  54. Yalamanchili P., Weidman K., Dasgupta A. 1997c; Cleavage of transcriptional activator Oct-1 by poliovirus encoded protease 3Cpro . Virology 239:176–185 [CrossRef]
    [Google Scholar]
  55. Zell R., Stelzner A. 1997; Application of genome sequence information to the classification of bovine enteroviruses: the importance of 5′- and 3′-nontranslated regions. Virus Res 51:213–229 [CrossRef]
    [Google Scholar]
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