Comparison of genomic and predicted amino acid sequences of respiratory and enteric bovine coronaviruses isolated from the same animal with fatal shipping pneumonia

References

1. Almazán F., González J. M., Pénzes Z., Izeta A., Calvo E., Plana-Durán J., Enjuanes L. 2000; Engineering the largest RNA virus genome as an infectious bacterial artificial chromosome. Proceedings of the National Academy of Sciences, USA 97:5516–5521
   [Google Scholar]
2. Ballesteros M. L., Sanchez C. M., Martin-Caballero J., Enjuanes L. 1995; Molecular bases of tropism in the PUR46 cluster of transmissible gastroenteritis coronaviruses. Advances in Experimental Medicine and Biology 380:557–562
   [Google Scholar]
3. Ballesteros M. L., Sanchez C. M., Enjuanes L. 1997; Two amino acid changes at the N-terminus of transmissible gastroenteritis coronavirus spike protein result in the loss of enteric tropism. Virology 227:378–388
   [Google Scholar]
4. Bonilla P. J., Gorbalenya A. E., Weiss S. R. 1994; Mouse hepatitis virus strain A59 RNA polymerase gene ORF 1a: heterogeneity among MHV strains. Virology 198:736–740
   [Google Scholar]
5. Boursnell M. E. G., Brown T. D. K., Foulds I. J., Green P. F., Tomley F. M., Binns M. M. 1987; Completion of the sequence of the genome of the coronavirus avian infectious bronchitis virus. Journal of General Virology 68:57–77
   [Google Scholar]
6. Bredenbeek P. J., Pachuk C. J., Noten A. F., Charite J., Luytjes W., Weiss S. R., Spaan W. J. 1990; The primary structure and expression of the second open reading frame of the polymerase gene of the coronavirus MHV-A59; a highly conserved polymerase is expressed by an efficient ribosomal frameshifting mechanism. Nucleic Acids Research 18:1825–1832
   [Google Scholar]
7. Brierley I. 1995; Ribosomal frameshifting on viral RNAs. Journal of General Virology 76:1885–1892
   [Google Scholar]
8. Chambers P., Pringle C. R., Easton A. J. 1990; Heptad repeat sequences are located adjacent to hydrophobic regions in several types of virus fusion glycoproteins. Journal of General Virology 71:3075–3080
   [Google Scholar]
9. Chouljenko V. N., Kousoulas K. G., Lin X., Storz J. 1998; Nucleotide and predicted amino acid sequences of all genes encoded by the 3′ genomic portion (9·5 kb) of respiratory bovine coronaviruses and comparisons among respiratory and enteric coronaviruses. Virus Genes 17:33–42
   [Google Scholar]
10. Denison M., Perlman S. 1987; Identification of putative polymerase gene product in cells infected with murine coronavirus A59. Virology 157:565–568
    [Google Scholar]
11. Eleouet J. F., Rasschaert D., Lambert P., Levy L., Vende P., Laude H. 1995; Complete sequence (20 kilobases) of the polyprotein-encoding gene 1 of transmissible gastroenteritis virus. Virology 206:817–822
    [Google Scholar]
12. Gallagher T. M., Escarmis C., Buchmeier M. J. 1991; Alteration of the pH dependence of coronavirus-induced cell fusion: effect of mutations in the spike glycoprotein. Journal of Virology 65:1916–1928
    [Google Scholar]
13. Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. 1989; Coronavirus genome: prediction of putative functional domains in the non-structural polyprotein by comparative amino acid sequence analysis. Nucleic Acids Research 17:4847–4861
    [Google Scholar]
14. Herold J., Raabe T., Schelle-Prinz B., Siddell S. G. 1993; Nucleotide sequence of the human coronavirus 229E RNA polymerase locus. Virology 195:680–691
    [Google Scholar]
15. Herold J., Siddell S. G., Gorbalenya A. E. 1999; A human RNA viral cysteine proteinase that depends upon a unique Zn²⁺-binding finger connecting the two domains of a papain-like fold. Journal of Biological Chemistry 274:14918–14925
    [Google Scholar]
16. Hofmann M. A., Chang R. Y., Ku S., Brian D. A. 1993; Leader–mRNA junction sequences are unique for each subgenomic mRNA species in the bovine coronavirus and remain so throughout persistent infection. Virology 196:163–171
    [Google Scholar]
17. Kanjanahaluethai A., Baker S. C. 2000; Identification of mouse hepatitis virus papain-like proteinase 2 activity. Journal of Virology 74:7911–7921
    [Google Scholar]
18. Krempl C., Schultze B., Laude H., Herrler G. 1997; Point mutations in the S protein connect the sialic acid binding activity with the enteropathogenicity of transmissible gastroenteritis coronavirus. Journal of Virology 71:3285–3287
    [Google Scholar]
19. Kubo H., Takase-Yoden S., Taguchi F. 1993; Neutralization and fusion inhibition activities of monoclonal antibodies specific for the S1 subunit of the spike protein of neurovirulent murine coronavirus JHMV c1-2 variant. Journal of General Virology 74:1421–1425
    [Google Scholar]
20. Lee H. J., Shieh C. K., Gorbalenya A. E., Koonin E. V., La Monica N., Tuler J., Bagdzhadzhyan A., Lai M. M. C. 1991; The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase. Virology 180:567–582
    [Google Scholar]
21. Lim K. P., Ng L. F., Liu D. X. 2000; Identification of a novel cleavage activity of the first papain-like proteinase domain encoded by open reading frame 1a of the coronavirus avian infectious bronchitis virus and characterization of the cleavage products. Journal of Virology 74:1674–1685
    [Google Scholar]
22. Morgenstern B. 1999; DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15:211–218
    [Google Scholar]
23. Rasschaert D., Duarte M., Laude H. 1990; Porcine respiratory coronavirus differs from transmissible gastroenteritis virus by a few genomic deletions. Journal of General Virology 71:2599–2607
    [Google Scholar]
24. Rost B., Casadio R., Fariselli P., Sander C. 1995; Transmembrane helices predicted at 95% accuracy. Protein Science 4:521–533
    [Google Scholar]
25. Routledge E., Stauber R., Pfleiderer M., Siddell S. G. 1991; Analysis of murine coronavirus surface glycoprotein functions by using monoclonal antibodies. Journal of Virology 65:254–262
    [Google Scholar]
26. Sanchez C. M., Izeta A., Sanchez-Morgado J. M., Alonso S., Sola I., Balasch M., Plana-Duran J., Enjuanes L. 1999; Targeted recombination demonstrates that the spike gene of transmissible gastroenteritis coronavirus is a determinant of its enteric tropism and virulence. Journal of Virology 73:7607–7618
    [Google Scholar]
27. Schiller J. J., Kanjanahaluethai A., Baker S. C. 1998; Processing of the coronavirus MHV-JHM polymerase polyprotein: identification of precursors and proteolytic products spanning 400 kilodaltons of ORF1a. Virology 242:288–302
    [Google Scholar]
28. Schuler G. D., Altschul S. F., Lipman D. J. 1991; A workbench for multiple alignment construction and analysis. Proteins 9:180–190
    [Google Scholar]
29. Shi S. T., Schiller J. J., Kanjanahaluethai A., Baker S. C., Oh J. W., Lai M. M. 1999; Colocalization and membrane association of murine hepatitis virus gene 1 products and de novo-synthesized viral RNA in infected cells. Journal of Virology 73:5957–5969
    [Google Scholar]
30. Siddell S. 1995; The Coronaviridae : an introduction. In The Coronaviridae pp 1–10 Edited by Siddell S. G. New York: Plenum Press;
    [Google Scholar]
31. Snijder E. J., den Boon J. A., Horzinek M. C., Spaan W. J. 1991; Comparison of the genome organization of toro- and coronaviruses: evidence for two nonhomologous RNA recombination events during Berne virus evolution. Virology 180:448–452
    [Google Scholar]
32. Spaan W., Cavanagh D., Horzinek M. C. 1988; Coronaviruses: structure and genome expression. Journal of General Virology 69:2939–2952
    [Google Scholar]
33. Stephensen C. B., Casebolt D. B., Gangopadhyay N. N. 1999; Phylogenetic analysis of a highly conserved region of the polymerase gene from 11 coronaviruses and development of a consensus polymerase chain reaction assay. Virus Research 60:181–189
    [Google Scholar]
34. Storz J., Stine L., Liem A., Anderson G. A. 1996; Coronavirus isolation from nasal swab samples in cattle with signs of respiratory tract disease after shipping. Journal of the American Veterinary Medical Association 208:1452–1455
    [Google Scholar]
35. Storz J., Lin X., Purdy C. W., Chouljenko V. N., Kousoulas K. G., Enright F. M., Gilmore W. C., Briggs R. E., Loan R. W. 2000a; Coronavirus and Pasteurella infections in bovine shipping fever pneumonia and Evans’ criteria for causation. Journal of Clinical Microbiology 38:3291–3298
    [Google Scholar]
36. Storz J., Purdy C. W., Lin X., Burrell M., Truax R. E., Briggs R. E., Frank G. H., Loan R. W. 2000b; Isolation of respiratory bovine coronavirus, other cytocidal viruses, and Pasteurella spp. from cattle involved in two natural outbreaks of shipping fever. Journal of the American Veterinary Medical Association 216:1599–1604
    [Google Scholar]
37. Sturman L. S., Ricard C. S., Holmes K. V. 1990; Conformational change of the coronavirus peplomer glycoprotein at pH 8·0 and 37 °C correlates with virus aggregation and virus-induced cell fusion. Journal of Virology 64:3042–3050
    [Google Scholar]
38. Swofford D. L. 2000 PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4 Sunderland, MA: Sinauer Associates;
    [Google Scholar]
39. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25:4876–4882
    [Google Scholar]
40. Tijms M. A., van Dinten L. C., Gorbalenya A. E., Snijder E. J. 2001; A zinc finger-containing papain-like protease couples subgenomic mRNA synthesis to genome translation in a positive-stranded RNA virus. Proceedings of the National Academy of Sciences, USA 98:1889–1894
    [Google Scholar]
41. van der Meer Y., Snijder E. J., Dobbe J. C., Schleich S., Denison M. R., Spaan W. J., Locker J. K. 1999; Localization of mouse hepatitis virus nonstructural proteins and RNA synthesis indicates a role for late endosomes in viral replication. Journal of Virology 73:7641–7657
    [Google Scholar]
42. Wege H., Siddell S., ter Meulen V. 1982; The biology and pathogenesis of coronaviruses. Current Topics in Microbiology and Immunology 99:165–200
    [Google Scholar]
43. Yoo D. W., Parker M. D., Babiuk L. A. 1991; The S2 subunit of the spike glycoprotein of bovine coronavirus mediates membrane fusion in insect cells. Virology 180:395–399
    [Google Scholar]
44. Ziebuhr J., Snijder E. J., Gorbalenya A. E. 2000; Virus-encoded proteinases and proteolytic processing in the Nidovirales . Journal of General Virology 81:853–879
    [Google Scholar]
45. Ziebuhr J., Thiel V., Gorbalenya A. E. 2001; The autocatalytic release of a putative RNA virus transcription factor from its polyprotein precursor involves two paralogous papain-like proteases that cleave the same peptide bond. Journal of Biological Chemistry 276:33220–33232
    [Google Scholar]