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. 2002 Nov 12;21(3):181–198. doi: 10.1016/0168-1702(91)90032-Q

The cloning and sequencing of the virion protein genes from a British isolate of porcine respiratory coronavirus: comparison with transmissible gastroenteritis virus genes

Paul Britton 1,∗, Karen L Mawditt 1, Kevin W Page 1,∗
PMCID: PMC7133898  PMID: 1662846

Abstract

Previous analysis of porcine respiratory coronavirus (PRCV) mRNA species showed that mRNAs 2 and 3 were smaller than the corresponding transmissible gastroenteritis virus (TGEV) mRNA species (Page et al. (1991) J. Gen. Virol. 72, 579–587). Sequence analysis showed that mRNA 3 was smaller due to the presence of a new putative RNA-leader binding site upstream of the PRCV ORF-3 gene. However, this observation did not explain the deletion observed in PRCV mRNA 2. Polymerase chain reaction (PCR) was used to generate cDNA from the 3' coding region of the putative polymerase gene to the poly (A) tail of PRCV for comparison to the equivalent region from TGEV. The PRCV S protein was found to consist of 1225 amino acids, which had 98% similarity to the TGEV S protein. However, the PRCV S gene contained a 672 nucleotide deletion, corresponding to 224 amino acids (residues 21 to 245 in TGEV S protein), 59 nucleotides downstream of the S gene initiation codon. The PRCV genome from the ORF-3 gene to the poly (A) tail was sequenced for comparison to TGEV in order to identify other potential differences between the two viruses. Four ORFs were identified that showed 98% similarity to the TGEV ORF-4, M, N and ORF-7 genes. No other deletions or any PRCV specific sequences were identified.

Keywords: Porcine respiratory coronavirus, Transmissible gastroenteritis virus, Coronavirus, Spike, Membrane protein, Nucleoprotein

References

  1. Bae I., Jackwood D.J., Benfield D.A., Saif L.J., Wesley R.D., Hill H. Differentiation of transmissible gastroenteritis virus from porcine respiratory coronavirus and other antigenically related coronaviruses by using cDNA probes specific for the 5' region of the S glycoprotein gene. J. Clin. Microbiol. 1991;29:215–218. doi: 10.1128/jcm.29.1.215-218.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Boursnell M.E., Brown T.D., Foulds I.J., Green P.F., Tomley F.M., Binns M.M. Completion of the sequence of the genome of the coronavirus avian infectious bronchitis virus. J. Gen. Virol. 1987;68:57–77. doi: 10.1099/0022-1317-68-1-57. [DOI] [PubMed] [Google Scholar]
  3. Bredenbeek P.J., Pachuk C.J., Noten A.F.H., Charite J., Luytjes W., Weiss S.R., Spaan W.J.M. 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. Nucl. Acids Res. 1990;18:1825–1832. doi: 10.1093/nar/18.7.1825. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Britton P., Page K.W. Sequence of the S gene from a virulent British field isolate of transmissible gastroenteritis virus. Virus Res. 1990;18:71–80. doi: 10.1016/0168-1702(90)90090-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Britton P., Garwes D.J., Millson G.C., Page K., Bountiff L., Stewart F., Walmsley J. Towards a genetically-engineered vaccine against porcine transmissible gastroenteritis virus. In: Magnien E., editor. Nijhoff; The Netherlands: 1986. pp. 301–313. (Biomolecular Engineering in the European Community (Final Report)). [Google Scholar]
  6. Britton P., Garwes D.J., Page K., Walmsley J. Expression of porcine transmissible gastroenteritis virus genes in E. coli as β-galactosidase chimaeric proteins. In: Lai M.M.C., Stohlman S.A., editors. Vol. 218. Plenum; New York, NY: 1987. pp. 55–64. (Coronaviruses, Advances in Experimental Medicine and Biology). [DOI] [PubMed] [Google Scholar]
  7. Britton P., Carmenes R.S., Page K.W., Garwes D.J., Parra F. Sequence of the nucleoprotein from a virulent British field isolate of transmissible gastroenteritis virus and its expression in Saccharomyces cerevisiae. Mol. Microbiol. 1988;2:89–99. [PubMed] [Google Scholar]
  8. Britton P., Carmenes R.S., Page K.W., Garwes D.J. The integral membrane protein from a virulent isolate of transmissible gastroenteritis virus: molecular characterization, sequence and expression in Escherichia coli. Mol. Microbiol. 1988;2:497–505. doi: 10.1111/j.1365-2958.1988.tb00056.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Britton P., Lopez Otin C., Martin Alonso J., Parra F. Sequence of the coding regions from the 3.0 kb and 3.9 kb mRNA subgenomic species from a virulent isolate of transmissible gastroenteritis virus. Arch. Virol. 1989;105:165–178. doi: 10.1007/BF01311354. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Britton P., Garwes D.J., Page K., Stewart F. Molecular aspects of the relationship of transmissible gastroenteritis virus (TGEV) with porcine respiratory coronavirus (PRCV) In: Cavanagh D., Brown T.D.K., editors. Vol. 276. Plenum; New York, NY: 1990. pp. 441–446. (Coronaviruses and Their Diseases, Advances in Experimental Medicine and Biology). [DOI] [PubMed] [Google Scholar]
  11. Brown I., Cartwright S. New porcine coronavirus? Vet. Rec. 1986;119:282–283. doi: 10.1136/vr.119.11.282. [DOI] [PubMed] [Google Scholar]
  12. Callebaut P., Correa I., Pensaert M., Jimenez G., Enjuanes L. Antigenic differentiation between transmissible gastroenteritis virus of swine and a related porcine respiratory coronavirus. J. Gen. Virol. 1988;69:1725–1730. doi: 10.1099/0022-1317-69-7-1725. [DOI] [PubMed] [Google Scholar]
  13. Correa I., Jimenez G., Sune C., Bullido M.J., Enjuanes L. Antigenic structure of the E2 glycoprotein from transmissible gastroenteritis coronavirus. Virus Res. 1988;10:77–93. doi: 10.1016/0168-1702(88)90059-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Correa I., Gebauer F., Bullido M.J., Sune C., Baay M.F.D., Zwaagstra K.A., Posthumus W.P.A., Lenstra J.A., Enjuanes L. Localisation of antigenic sites of the E2 glycoprotein of transmissible gastroenteritis coronavirus. J. Gen. Virol. 1990;71:271–279. doi: 10.1099/0022-1317-71-2-271. [DOI] [PubMed] [Google Scholar]
  15. Cox E., Pensaert M.B., Callebaut P., Van Deun K. Intestinal replication of a porcine respiratory coronavirus closely related antigenically to the enteric transmissible gastroenteritis virus. Vet. Microbiol. 1990;23:237–243. doi: 10.1016/0378-1135(90)90154-N. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. De Groot R.J., Maduro J., Lenstra J.A., Horzinek M.C., Van der Zeijst B.A.M., Spaan W.J.M. cDNA cloning and sequence analysis of the gene encoding the peplomer protein of feline infectious peritonitis virus. J. Gen. Virol. 1987;68:2639–2646. doi: 10.1099/0022-1317-68-10-2639. [DOI] [PubMed] [Google Scholar]
  17. De Groot R.J., Andeweg A.C., Horzinek M.C., Spaan W.J.M. Sequence analysis of the 3'-end of the feline coronavirus FIPV79-1146 genome:comparison with the genome of porcine coronavirus TGEV reveals large insertions. Virology. 1988;167:370–376. doi: 10.1016/0042-6822(88)90097-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Delmas B., Rasschaert D., Godet M., Gelfi J., Laude H. Four major antigenic sites of the coronavirus transmissible gastroenteritis virus are located on the amino-terminal half of spike glycoprotein. S.J. Gen. Virol. 1990;71:1313–1323. doi: 10.1099/0022-1317-71-6-1313. [DOI] [PubMed] [Google Scholar]
  19. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucl. Acids Res. 1984;12:387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Fleming J.O., Trousdale M.D., El Zaatari F.A., Stohlman S.A., Weiner L.P. Pathogenicity of antigenic variants of murine coronavirus JHM selected with monoclonal antibodies. J. Virol. 1986;58:869–875. doi: 10.1128/jvi.58.3.869-875.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Garwes D.J., Pocock D.H. The polypeptide structure of transmissible gastroenteritis virus. J. Gen. Virol. 1975;29:25–34. doi: 10.1099/0022-1317-29-1-25. [DOI] [PubMed] [Google Scholar]
  22. Garwes D.J., Stewart F., Cartwright S.F., Brown I. Differentiation of porcine coronavirus from transmissible gastroenteritis virus. Vet. Rec. 1988;122:86–87. doi: 10.1136/vr.122.4.86. [DOI] [PubMed] [Google Scholar]
  23. Garwes D.J., Stewart F., Britton P. The polypeptide of Mr, 14,000 of porcine transmissible gastroenteritis virus: gene assignment and intracellular location. J. Gen. Virol. 1989;70:2495–2499. doi: 10.1099/0022-1317-70-9-2495. [DOI] [PubMed] [Google Scholar]
  24. Güssow D., Clackson T. Direct clone characterization from plaques and colonies by the polymerase chain reaction. Nucl. Acids Res. 1989;17:4000. doi: 10.1093/nar/17.10.4000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Higgins D.G., Sharp P.M. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene. 1988;73:237–244. doi: 10.1016/0378-1119(88)90330-7. [DOI] [PubMed] [Google Scholar]
  26. Jacobs L., Van der Zeijst B.A.M., Horzinek M.C. Characterization and translation of transmissible gastroenteritis virus mRNAs. J. Virol. 1986;57:1010–1015. doi: 10.1128/jvi.57.3.1010-1015.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Jacobs L., De Groot R., Van der Zeijst B.A.M., Horzinek M.C., Spaan W. The nucleotide sequence of the peplomer gene of porcine transmissible gastroenteritis virus (TGEV): comparison with the sequence of the peplomer protein of feline infectious peritonitis virus (FIPV) Virus Res. 1987;8:363–371. doi: 10.1016/0168-1702(87)90008-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Kapke P.A., Brian D.A. Sequence analysis of the porcine transmissible gastroenteritis coronavirus nucleocapsid protein gene. Virology. 1986;151:41–49. doi: 10.1016/0042-6822(86)90102-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Kapke P.A., Tung F.Y.C., Brian D.A., Woods R.D., Wesley R. Nucleotide sequence of the porcine transmissible gastroenteritis coronavirus matrix protein. In: Lai M.M.C., Stohlman S.A., editors. Vol. 218. Plenum; New York, NY: 1987. pp. 117–122. (Coronaviruses, Advances in Experimental Medicine and Biology). [DOI] [PubMed] [Google Scholar]
  30. Laude H., Rasschaert D., Huet J.-C. Sequence and N-terminal processing of the transmembrane protein E1 of the coronavirus transmissible gastroenteritis virus. J. Gen. Virol. 1987;68:1687–1693. doi: 10.1099/0022-1317-68-6-1687. [DOI] [PubMed] [Google Scholar]
  31. Luytjes W., Sturman L.S., Bredenbeek P.J., Charite J., Van der Zeijst B.A., Horzinek M.C., Spaan W.J. Primary structure of the glycoprotein E2 of coronavirus MHV-A59 and identification of the trypsin cleavage site. Virology. 1987;161:479–487. doi: 10.1016/0042-6822(87)90142-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. O'Toole D., Brown I., Bridges A., Cartwright S.F. Pathogenicity of experimental infection with “pneumotropic” porcine coronavirus. Res. Vet. Sci. 1989;47:23–29. doi: 10.1016/S0034-5288(18)31226-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Page K.W., Britton P., Boursnell M.E.G. Sequence analysis of the leader RNA of two porcine coronaviruses: transmissible gastroenteritis virus and porcine respiratory coronavirus. Virus Genes. 1990;4:289–301. doi: 10.1007/BF00570024. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Page K.W., Mawditt K.L., Britton P. Sequence comparison of the 5'-end of mRNA 3 from transmissible gastroenteritis virus and porcine respiratory coronavirus. J. Gen. Virol. 1991;72:579–587. doi: 10.1099/0022-1317-72-3-579. [DOI] [PubMed] [Google Scholar]
  35. Parker S.E., Gallagher T.M., Buchmeier M.J. Sequence analysis reveals extensive polymorphism and evidence of deletions within the E2 glycoprotein gene of several strains of murine hepatitis virus. Virology. 1989;173:664–673. doi: 10.1016/0042-6822(89)90579-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Pensaert M.B. Transmissible gastroenteritis virus (respiratory variant) In: Horzinek M.C., Pensaert M.B., editors. Vol. 2. Elsevier; Amsterdam: 1989. pp. 154–165. (Virus Infections of Vertebrates). [Google Scholar]
  37. Pensaert M.B., Callebaut P.E., Vergote J. Isolation of a porcine respiratory, non-enteric coronavirus related to transmissible gastroenteritis. Vet. Q. 1986;8:257–260. doi: 10.1080/01652176.1986.9694050. [DOI] [PubMed] [Google Scholar]
  38. Posthumus W.P.A., Lenstra J.A., Schaaper W.M.M., Van Nieuwstadt A.P., Enjuanes L., Meloen R.H. Analysis and simulation of a neutralizing epitope of transmissible gastroenteritis virus. J. Virol. 1990;64:3304–3309. doi: 10.1128/jvi.64.7.3304-3309.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Rasschaert D., Laude H. The predicted primary structure of the peplomer protein E2 of the porcine coronavirus transmissible gastroenteritis virus. J. Gen. Virol. 1987;68:1883–1890. doi: 10.1099/0022-1317-68-7-1883. [DOI] [PubMed] [Google Scholar]
  40. Rasschaert D., Gelfi J., Laude H. Enteric coronavirus TGEV: partial sequence of the genomic RNA, its organization and expression. Biochimie. 1987;69:591–600. doi: 10.1016/0300-9084(87)90178-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Rasschaert D., Duarte M., Laude H. Porcine respiratory coronavirus differs from transmissible gastroenteritis virus by a few genomic deletions. J. Gen. Virol. 1990;71:2599–2607. doi: 10.1099/0022-1317-71-11-2599. [DOI] [PubMed] [Google Scholar]
  42. Sánchez C.M., Jimenez G., Laviada M.D., Correa I., Sune C., Bullido M.J., Gebauer F., Smerdou C., Callebaut P., Escribano J.M., Enjuanes L. Antigenic homology among coronaviruses related to transmissible gastroenteritis virus. Virology. 1990;174:410–417. doi: 10.1016/0042-6822(90)90094-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Schmidt I., Skinner M., Siddell S. Nucleotide sequence of the gene encoding the surface projection glycoprotein of coronavirus MHV-JHM. J. Gen. Virol. 1987;68:47–56. doi: 10.1099/0022-1317-68-1-47. [DOI] [PubMed] [Google Scholar]
  44. Staden R. Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. Nucl. Acids Res. 1982;10:4731–4751. doi: 10.1093/nar/10.15.4731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Van Nieuwstadt A.P., Pol J.M.A. Isolation of a TGE virus-related respiratory coronavirus causing fatal pneumonia in pigs. Vet. Rec. 1989;124:43–44. doi: 10.1136/vr.124.2.43. [DOI] [PubMed] [Google Scholar]
  46. Vennema H., De Groot R.J., Harbour D.A., Horzinek M.C., Spaan W.J.M. Primary structure of the membrane and nucleocapsid protein genes of feline infectious peritonitis virus and immunogenicity of recombinant vaccinia viruses in kittens. Virology. 1991;181:327–335. doi: 10.1016/0042-6822(91)90499-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Von Heijne G. A new method for predicting signal sequence cleavage sites. Nucl. Acids Res. 1986;14:4683–4690. doi: 10.1093/nar/14.11.4683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Wesley R.D. Nucleotide sequence of the E2-peplomer protein gene and partial nucleotide sequence of the upstream polymerase gene of transmissible gastroenteritis virus (Miller strain) In: Cavanagh D., Brown T.D.K., editors. Vol. 276. Plenum; New York, NY: 1990. pp. 301–306. (Coronaviruses and Their Diseases, Advances in Experimental Medicine and Biology). [DOI] [PubMed] [Google Scholar]
  49. Wesley R.D., Cheung A.K., Michael D.D., Woods R.D. Nucleotide sequence of coronavirus TGEV genomic RNA: evidence for 3 mRNA species between the peplomer and matrix protein genes. Virus Res. 1989;13:87–100. doi: 10.1016/0168-1702(89)90008-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Wesley R.D., Woods R.D., Hill H.T., Biwer J.D. Evidence for a porcine respiratory coronavirus, antigenically similar to transmissible gastroenteritis virus, in the United States. J. Vet. Diagn. Invest. 1990;2:312–317. doi: 10.1177/104063879000200411. [DOI] [PubMed] [Google Scholar]
  51. Wesley R.D., Woods R.D., Cheung A.K. Genetic basis for the pathogenesis of transmissible gastroenteritis virus. J. Virol. 1990;64:4761–4766. doi: 10.1128/jvi.64.10.4761-4766.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]

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