The complete sequence of the bovine torovirus genome

Virus Research

Volumn 115, Issue 1, 2006, Pages 56-68

  Draker, Ryan ^a   Roper, Rachel L ^b   Petric, Martin ^c   Tellier, Raymond ^a,d  

^a UNIVERSITY OF TORONTO   (Canada)

^b EAST CAROLINA UNIVERSITY   (United States)

^c BRITISH COLUMBIA CENTRE FOR DISEASE CONTROL   (Canada)

^d HOSPITAL FOR SICK CHILDREN   (Canada)

Author keywords

Bovine torovirus; Complete sequence; Long PCR; Nidovirales; Proteases

Indexed keywords

POLYPROTEIN; RNA DIRECTED RNA POLYMERASE; VIRUS ENZYME;

AMPLICON; ARTICLE; CONTROLLED STUDY; COW; GENE AMPLIFICATION; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; RIBOSOMAL FRAMESHIFTING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; TOROVIRUS; VIRUS GENOME; VIRUS ISOLATION;

AMINO ACID SEQUENCE; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OPEN READING FRAMES; RNA REPLICASE; SEQUENCE ALIGNMENT; SERINE ENDOPEPTIDASES; TOROVIRUS;

ARTERIVIRUS; BERNE VIRUS; BOVINE TOROVIRUS; CORONAVIRIDAE; NIDOVIRALES; PICORNAVIRIDAE; TOROVIRUS;

EID: 28844441279     PISSN: 01681702     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virusres.2005.07.005     Document Type: Article

References (60)

1. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 17 1997 3389 3402
2. G.M. Beards, C. Hall, J. Green, T.H. Flewett, F. Lamouliatte, and P. Du Pasquier An enveloped virus in stools of children and adults with gastroenteritis that resembles the Breda virus of calves Lancet 1 8385 1984 1050 1052
3. I. Brierley Ribosomal frameshifting viral RNAs J. Gen. Virol. 76 Pt 8 1995 1885 1892
4. D.W. Brown, G.M. Beards, and T.H. Flewett Detection of Breda virus antigen and antibody in humans and animals by enzyme immunoassay J. Clin. Microbiol. 25 4 1987 637 640
5. D. Cavanagh Nidovirales: a new order comprising Coronaviridae and Arteriviridae Arch. Virol. 142 3 1997 629 633
6. Cavanagh, D., Brian, D.A., Brinton, M., Enjuanes, L., Holmes, K.V., Horzinek, M.C., Lai, M.M.C., Laude, H., Plagemann, P.G.W., Siddell, S., Spaan, W.J.M., Taguchi, F., Talbot, P.J. (1994) Revision of the taxonomy of the Coronavirus, Torovirus and Arterivirus genera. Archives of Virology 135, 227-237.
7. D. Cavanagh, and M.C. Horzinek Genus Torovirus assigned to the Coronaviridae Arch. Virol. 128 3-4 1993 395 396
8. K.H. Chu, J. Qi, Z.G. Yu, and V. Anh Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes Mol. Biol. Evol. 21 1 2004 200 206
9. R. Condit Principles of virology D. Knipe P. Howley D. Griffin R. Lamb M. Martin B. Roizman S. Straus Fields' Virology fourth ed. 2001 Lippincott Williams Wilkins Philadelphia 19 52
10. L.A. Cornelissen, C.M. Wierda, F.J. van der Meer, A.A. Herrewegh, M.C. Horzinek, H.F. Egberink, and R.J. de Groot Hemagglutinin-esterase, a novel structural protein of torovirus J. Virol. 71 7 1997 5277 5286
11. J.A. Cowley, C.M. Dimmock, K.M. Spann, and P.J. Walker Gill-associated virus of Penaeus monodon prawns: an invertebrate virus with ORF1a and ORF1b genes related to arteri- and coronaviruses J. Gen. Virol. 81 Pt 6 2000 1473 1484
12. C. Drosten, S. Gunther, W. Preiser, S. van der Werf, H.R. Brodt, S. Becker, H. Rabenau, M. Panning, L. Kolesnikova, R.A. Fouchier, A. Berger, A.M. Burguiere, J. Cinatl, M. Eickmann, N. Escriou, K. Grywna, S. Kramme, J.C. Manuguerra, S. Muller, V. Rickerts, M. Sturmer, S. Vieth, H.D. Klenk, A.D. Osterhaus, H. Schmitz, and H.W. Doerr Identification of a novel coronavirus in patients with severe acute respiratory syndrome N. Engl. J. Med. 348 20 2003 1967 1976
13. L. Duckmanton, S. Carman, E. Nagy, and M. Petric Detection of bovine torovirus in fecal specimens of calves with diarrhea from Ontario farms J. Clin. Microbiol. 36 5 1998 1266 1270
14. L.M. Duckmanton, R. Tellier, P. Liu, and M. Petric Bovine torovirus: sequencing of the structural genes and expression of the nucleocapsid protein of Breda virus Virus Res. 58 1-2 1998 83 96
15. L. Duckmanton, B. Luan, J. Devenish, R. Tellier, and M. Petric Characterization of torovirus from human fecal specimens Virology 239 1 1997 158 168
16. D. Fischer, C. Barret, K. Bryson, A. Elofsson, A. Godzik, D. Jones, K.J. Karplus, L.A. Kelley, R.M. MacCallum, K. Pawowski, B. Rost, L. Rychlewski, and M. Sternberg CAFASP-1: critical assessment of fully automated structure prediction methods Proteins Suppl. 3 1999 209 217
17. J.M. González, P. Gomez-Puertas, D. Cavanagh, A.E. Gorbalenya, and L. Enjuanes A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae Arch. Virol. 148 11 2003 2207 2235
18. A. Guarne, J. Tormo, R. Kirchweger, D. Pfistermueller, I. Fita, and T. Skern Structure of the foot-and-mouth disease virus leader protease: a papain-like fold adapted for self-processing and eIF4G recognition Embo. J. 17 24 1998 7469 7479
19. 2+-binding finger connecting the two domains of a papain-like fold J. Biol. Chem. 274 21 1999 14918 14925
20. A.E. Hoet, K.O. Cho, K.O. Chang, S.C. Loerch, T.E. Wittum, and L.J. Saif Enteric and nasal shedding of bovine torovirus (Breda virus) in feedlot cattle Am. J. Vet. Res. 63 3 2002 342 348
21. A.E. Hoet, P.R. Nielsen, M. Hasoksuz, C. Thomas, T.E. Wittum, and L.J. Saif Detection of bovine torovirus and other enteric pathogens in feces from diarrhea cases in cattle J. Vet. Diagn. Invest. 15 3 2003 205 212
22. A.E. Hoet, J. Smiley, C. Thomas, P.R. Nielsen, T.E. Wittum, and L.J. Saif Association of enteric shedding of bovine torovirus (Breda virus) and other enteropathogens with diarrhea in veal calves Am. J. Vet. Res. 64 4 2003 485 490
23. F.B. Jamieson, E.E. Wang, C. Bain, J. Good, L. Duckmanton, and M. Petric Human torovirus: a new nosocomial gastrointestinal pathogen J. Infect. Dis. 178 5 1998 1263 1269
24. L.A. Kelley, R.M. MacCallum, and M. Sternberg Recognition of remote protein homologies using three dimensional information to generate a position specific scoring matrix in the program 3D-PSSM S. Istrail P. Pevzner M. Waterman RECOMB 99, Proceedings of the Third Annual Conference on Computational Molecular Biology 1999 The Association for Computing Machinery New York 218 225
25. L.A. Kelley, R.M. MacCallum, and M.J. Sternberg Enhanced genome annotation using structural profiles in the program 3D-PSSM J. Mol. Biol. 299 2 2000 499 520
26. M. Koopmans, H. Cremers, G. Woode, and M.C. Horzinek Breda virus (Toroviridae) infection and systemic antibody response in sentinel calves Am. J. Vet. Res. 51 9 1990 1443 1448
27. M. Koopmans, and M.C. Horzinek Toroviruses of animals and humans: a review Adv. Virus Res. 43 1994 233 273
28. M. Koopmans, L. van Wuijckhuise-Sjouke, Y.H. Schukken, H. Cremers, and M.C. Horzinek Association of diarrhea in cattle with torovirus infections on farms Am. J. Vet. Res. 52 11 1991 1769 1773
29. E. Kostouros, K. Siu, E.L. Ford-Jones, M. Petric, and R. Tellier Molecular characterization of rotavirus strains from children in Toronto, Canada J. Clin. Virol. 28 1 2003 77 84
30. A. Kroneman, L.A. Cornelissen, M.C. Horzinek, R.J. de Groot, and H.F. Egberink Identification and characterization of a porcine torovirus J. Virol. 72 5 1998 3507 3511
31. T.G. Ksiazek, D. Erdman, C.S. Goldsmith, S.R. Zaki, T. Peret, S. Emery, S. Tong, C. Urbani, J.A. Comer, W. Lim, P.E. Rollin, S.F. Dowell, A.E. Ling, C.D. Humphrey, W.J. Shieh, J. Guarner, C.D. Paddock, P. Rota, B. Fields, J. DeRisi, J.Y. Yang, N. Cox, J.M. Hughes, J.W. LeDuc, W.J. Bellini, and L.J. Anderson A novel coronavirus associated with severe acute respiratory syndrome N. Engl. J. Med. 348 20 2003 1953 1966
32. M.M. Lai, and D. Cavanagh The molecular biology of coronaviruses Adv. Virus. Res. 48 1997 1 100
33. M.M. Lai, and K.V. Holmes Coronaviridae: the viruses and their replication fourth ed. D. Knipe P.M. Howley D.E. Griffin M.A. Martin R.A. Lamb B. Roizman Fields Virology vol. 1 (2 vols.) 2001 Lippincott Williams & Wilkins Philadelphia 1163 1186
34. N. Lee, D. Hui, A. Wu, P. Chan, P. Cameron, G.M. Joynt, A. Ahuja, M.Y. Yung, C.B. Leung, K.F. To, S.F. Lui, C.C. Szeto, S. Chung, and J.J. Sung A major outbreak of severe acute respiratory syndrome in Hong Kong N. Engl. J. Med. 348 20 2003 1986 1994
35. W.K. Leung, K.F. To, P.K. Chan, H.L. Chan, A.K. Wu, N. Lee, K.Y. Yuen, and J.J. Sung Enteric involvement of severe acute respiratory syndrome-associated coronavirus infection Gastroenterology 125 4 2003 1011 1017
36. T.A. Martino, R. Tellier, M. Petric, D.M. Irwin, A. Afshar, and P.P. Liu The complete consensus sequence of coxsackievirus B6 and generation of infectious clones by long RT-PCR Virus Res. 64 1 1999 77 86
37. M.R. Martzen, S.M. McCraith, S.L. Spinelli, F.M. Torres, S. Fields, E.J. Grayhack, and E.M. Phizicky A biochemical genomics approach for identifying genes by the activity of their products Science 286 5442 1999 1153 1155
38. K.W. Pedersen, Y. van der Meer, N. Roos, and E.J. Snijder Open reading frame 1a-encoded subunits of the arterivirus replicase induce endoplasmic reticulum-derived double-membrane vesicles which carry the viral replication complex J. Virol. 73 3 1999 2016 2026
39. S.M. Poutanen, D.E. Low, B. Henry, S. Finkelstein, D. Rose, K. Green, R. Tellier, R. Draker, D. Adachi, M. Ayers, A.K. Chan, D.M. Skowronski, I. Salit, A.E. Simor, A.S. Slutsky, P.W. Doyle, M. Krajden, M. Petric, R.C. Brunham, and A.J. McGeer Identification of severe acute respiratory syndrome in Canada N. Engl. J. Med. 348 20 2003 1995 2005
40. J. Qi, H. Luo, and B. Hao CVTree: a phylogenetic tree reconstruction tool based on whole genomes Nucleic Acids Res. 32 Web Server issue 2004 W45 W47
41. J. Qi, B. Wang, and B.I. Hao Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach J. Mol. Evol. 58 1 2004 1 11
42. C.L. Rowe, S.C. Baker, M.J. Nathan, and J.O. Fleming Evolution of mouse hepatitis virus: detection and characterization of spike deletion variants during persistent infection J. Virol. 71 4 1997 2959 2969
43. S.L. Smits, A. Lavazza, K. Matiz, M.C. Horzinek, M.P. Koopmans, and R.J. de Groot Phylogenetic and evolutionary relationships among torovirus field variants: evidence for multiple intertypic recombination events J. Virol. 77 17 2003 9567 9577
44. E.J. Snijder, P.J. Bredenbeek, J.C. Dobbe, V. Thiel, J. Ziebuhr, L.L. Poon, Y. Guan, M. Rozanov, W.J. Spaan, and A.E. Gorbalenya Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage J. Mol. Biol. 331 5 2003 991 1004
45. E.J. Snijder, J.A. den Boon, P.J. Bredenbeek, M.C. Horzinek, R. Rijnbrand, and W.J. Spaan The carboxyl-terminal part of the putative Berne virus polymerase is expressed by ribosomal frameshifting and contains sequence motifs which indicate that toro- and coronaviruses are evolutionarily related Nucleic Acids Res. 18 15 1990 4535 4542
46. E.J. Snijder, J.A. den Boon, M.C. Horzinek, and W.J. Spaan Comparison of the genome organization of toro- and coronaviruses: evidence for two nonhomologous RNA recombination events during Berne virus evolution Virology 180 1 1991 448 452
47. E.J. Snijder, and M.C. Horzinek Toroviruses: replication, evolution and comparison with other members of the coronavirus-like superfamily J. Gen. Virol. 74 Pt 11 1993 2305 2316
48. E.J. Snijder, and J.J. Meulenberg The molecular biology of arteriviruses J. Gen. Virol. 79 Pt 5 1998 961 979
49. E.J. Snijder, A.L. Wassenaar, L.C. van Dinten, W.J. Spaan, and A.E. Gorbalenya The arterivirus nsp4 protease is the prototype of a novel group of chymotrypsin-like enzymes, the 3C-like serine proteases J. Biol. Chem. 271 9 1996 4864 4871
50. R. Tellier, J. Bukh, S.U. Emerson, R.H. Miller, and R.H. Purcell Long PCR and its application to hepatitis viruses: amplification of hepatitis A, hepatitis B, and hepatitis C virus genomes J. Clin. Microbiol. 34 12 1996 3085 3091
51. R. Tellier, J. Bukh, S.U. Emerson, and R.H. Purcell Amplification of the full-length hepatitis A virus genome by long reverse transcription-PCR and transcription of infectious RNA directly from the amplicon Proc. Natl. Acad. Sci. U.S.A. 93 9 1996 4370 4373
52. R. Tellier, J. Bukh, S.U. Emerson, and R.H. Purcell Long PCR amplification of large fragments of viral genomes: a technical overview Methods Mol. Biol. 226 2003 167 172
53. J.D. Thompson, T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res. 25 24 1997 4876 4882
54. C. Upton, S. Slack, A.L. Hunter, A. Ehlers, and R.L. Roper Poxvirus orthologous clusters: toward defining the minimum essential poxvirus genome J. Virol. 77 13 2003 7590 7600
55. Y. van der Meer, H. van Tol, J.K. Locker, and E.J. Snijder ORF1a-encoded replicase subunits are involved in the membrane association of the arterivirus replication complex J. Virol. 72 8 1998 6689 6698
56. M. Weiss, F. Steck, R. Kaderli, and M.C. Horzinek Antibodies to Berne virus in horses and other animals Vet. Microbiol. 9 6 1984 523 531
57. G.N. Woode, D.E. Reed, P.L. Runnels, M.A. Herrig, and H.T. Hill Studies with an unclassified virus isolated from diarrheic calves Vet. Microbiol. 7 3 1982 221 240
58. J. Ziebuhr, S. Bayer, J.A. Cowley, and A.E. Gorbalenya The 3C-like proteinase of an invertebrate nidovirus links coronavirus and potyvirus homologs J. Virol. 77 2 2003 1415 1426
59. J. Ziebuhr, E.J. Snijder, and A.E. Gorbalenya Virus-encoded proteinases and proteolytic processing in the Nidovirales J. Gen. Virol. 81 Pt 4 2000 853 879
60. M. Zuker Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res. 31 13 2003 3406 3415