Sequence comparison of porcine respiratory coronavirus isolates reveals heterogeneity in the S, 3, and 3-1 genes (original) (raw)

Abstract

Four new porcine respiratory coronavirus (PRCV) isolates were genetically characterized. Subgenomic mRNA patterns and the nucleotide sequences of the 5' ends of the S genes, the open reading frame (ORF) 3/3a genes, and the ORF 3-1/3b genes of these PRCV isolates were determined and compared with those of other PRCV and transmissible gastroenteritis virus (TGEV) isolates. The S, ORF 3/3a, and ORF 3-1/3b genes are under intense study because of their possible roles in determining tissue tropism and virulence. Northern (RNA) blot analysis of subgenomic mRNAs revealed that mRNA 2, which encodes for the S gene, of the PRCV isolates migrated faster than the mRNA 2 of TGEV. The PRCV isolates AR310 and LEPP produced eight subgenomic mRNA species, the same number as produced by the virulent Miller strain of TGEV. However, the PRCV isolates IA1894 and ISU-1 produced only seven subgenomic mRNA species. All four of the PRCV isolates were found to have a large in-frame deletion in the 5' end of the S gene; however, the size and location of the deletion varied. Analysis of the ORF 3/3a gene nucleotide sequences from the four PRCV isolates also showed a high degree of variability in this area. The ORF 3 gene of the PRCV isolates AR310 and LEPP was preceded by a CTAAAC leader RNA-binding site, and the ORF 3 gene was predicted to yield a protein of 72 amino acids, the same size as that of the virulent Miller strain of TGEV. The PRCV isolates AR310 and LEPP are the first PRCV isolates found to have an intact ORF 3 gene. The ORF 3a gene of the PRCV isolate IA1894 was preceded by a CTAAAC leader RNA-binding site and was predicted to yield a truncated protein of 54 amino acids due to a 23-nucleotide deletion. The CTAAAC leader RNA-binding site and ATG start codon of ORF 3 gene of the PRCV isolate ISU-1 were removed because of a 168-nucleotide deletion. Analysis of the ORF 3-1/3b gene nucleotide sequences from the four PRCV nucleotides isolates also showed variability.

Full Text

The Full Text of this article is available as a PDF (373.6 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Abraham S., Kienzle T. E., Lapps W. E., Brian D. A. Sequence and expression analysis of potential nonstructural proteins of 4.9, 4.8, 12.7, and 9.5 kDa encoded between the spike and membrane protein genes of the bovine coronavirus. Virology. 1990 Aug;177(2):488–495. doi: 10.1016/0042-6822(90)90513-Q. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. 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(3-4):165–178. doi: 10.1007/BF01311354. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Britton P., Mawditt K. L., Page K. W. The cloning and sequencing of the virion protein genes from a British isolate of porcine respiratory coronavirus: comparison with transmissible gastroenteritis virus genes. Virus Res. 1991 Nov;21(3):181–198. doi: 10.1016/0168-1702(91)90032-Q. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Britton P., Page K. W., Pulford D. J., Garwes D. J., Mawditt K., Stewart F., Parra F., Lopez Otin C., Martin Alonso J., Carmenes R. S. Genomic organisation of a virulent isolate of porcine transmissible gastroenteritis virus. Adv Exp Med Biol. 1990;276:357–364. doi: 10.1007/978-1-4684-5823-7_48. [DOI] [PubMed] [Google Scholar]
  5. Cavanagh D., Brian D. A., Enjuanes L., Holmes K. V., Lai M. M., Laude H., Siddell S. G., Spaan W., Taguchi F., Talbot P. J. Recommendations of the Coronavirus Study Group for the nomenclature of the structural proteins, mRNAs, and genes of coronaviruses. Virology. 1990 May;176(1):306–307. doi: 10.1016/0042-6822(90)90259-T. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Duarte M., Tobler K., Bridgen A., Rasschaert D., Ackermann M., Laude H. Sequence analysis of the porcine epidemic diarrhea virus genome between the nucleocapsid and spike protein genes reveals a polymorphic ORF. Virology. 1994 Feb;198(2):466–476. doi: 10.1006/viro.1994.1058. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. 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 Sep;70(Pt 9):2495–2499. doi: 10.1099/0022-1317-70-9-2495. [DOI] [PubMed] [Google Scholar]
  8. Godet M., L'Haridon R., Vautherot J. F., Laude H. TGEV corona virus ORF4 encodes a membrane protein that is incorporated into virions. Virology. 1992 Jun;188(2):666–675. doi: 10.1016/0042-6822(92)90521-P. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Halbur P. G., Paul P. S., Vaughn E. M., Andrews J. J. Experimental reproduction of pneumonia in gnotobiotic pigs with porcine respiratory coronavirus isolate AR310. J Vet Diagn Invest. 1993 Apr;5(2):184–188. doi: 10.1177/104063879300500207. [DOI] [PubMed] [Google Scholar]
  10. Jouvenne P., Mounir S., Stewart J. N., Richardson C. D., Talbot P. J. Sequence analysis of human coronavirus 229E mRNAs 4 and 5: evidence for polymorphism and homology with myelin basic protein. Virus Res. 1992 Feb;22(2):125–141. doi: 10.1016/0168-1702(92)90039-C. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kapke P. A., Tung F. Y., Brian D. A. Nucleotide sequence between the peplomer and matrix protein genes of the porcine transmissible gastroenteritis coronavirus identifies three large open reading frames. Virus Genes. 1989 May;2(3):293–294. doi: 10.1007/BF00125345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. La Bonnardière C., Laude H. Interferon induction in rotavirus and coronavirus infections: a review of recent results. Ann Rech Vet. 1983;14(4):507–511. [PubMed] [Google Scholar]
  13. Laude H., Van Reeth K., Pensaert M. Porcine respiratory coronavirus: molecular features and virus-host interactions. Vet Res. 1993;24(2):125–150. [PubMed] [Google Scholar]
  14. Page K. W., Britton P., Boursnell M. E. Sequence analysis of the leader RNA of two porcine coronaviruses: transmissible gastroenteritis virus and porcine respiratory coronavirus. Virus Genes. 1990 Dec;4(4):289–301. doi: 10.1007/BF00570024. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. 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 Mar;72(Pt 3):579–587. doi: 10.1099/0022-1317-72-3-579. [DOI] [PubMed] [Google Scholar]
  16. 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 Dec;173(2):664–673. doi: 10.1016/0042-6822(89)90579-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Pensaert M., Callebaut P., Vergote J. Isolation of a porcine respiratory, non-enteric coronavirus related to transmissible gastroenteritis. Vet Q. 1986 Jul;8(3):257–261. doi: 10.1080/01652176.1986.9694050. [DOI] [PubMed] [Google Scholar]
  18. Rasschaert D., Duarte M., Laude H. Porcine respiratory coronavirus differs from transmissible gastroenteritis virus by a few genomic deletions. J Gen Virol. 1990 Nov;71(Pt 11):2599–2607. doi: 10.1099/0022-1317-71-11-2599. [DOI] [PubMed] [Google Scholar]
  19. Rasschaert D., Laude H. The predicted primary structure of the peplomer protein E2 of the porcine coronavirus transmissible gastroenteritis virus. J Gen Virol. 1987 Jul;68(Pt 7):1883–1890. doi: 10.1099/0022-1317-68-7-1883. [DOI] [PubMed] [Google Scholar]
  20. Spaan W., Cavanagh D., Horzinek M. C. Coronaviruses: structure and genome expression. J Gen Virol. 1988 Dec;69(Pt 12):2939–2952. doi: 10.1099/0022-1317-69-12-2939. [DOI] [PubMed] [Google Scholar]
  21. Sánchez C. M., Gebauer F., Suñ C., Mendez A., Dopazo J., Enjuanes L. Genetic evolution and tropism of transmissible gastroenteritis coronaviruses. Virology. 1992 Sep;190(1):92–105. doi: 10.1016/0042-6822(92)91195-Z. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Vaughn E. M., Halbur P. G., Paul P. S. Three new isolates of porcine respiratory coronavirus with various pathogenicities and spike (S) gene deletions. J Clin Microbiol. 1994 Jul;32(7):1809–1812. doi: 10.1128/jcm.32.7.1809-1812.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Vaughn E. M., Paul P. S. Antigenic and biological diversity among transmissible gastroenteritis virus isolates of swine. Vet Microbiol. 1993 Sep;36(3-4):333–347. doi: 10.1016/0378-1135(93)90099-S. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Weiss S. R., Zoltick P. W., Leibowitz J. L. The ns 4 gene of mouse hepatitis virus (MHV), strain A 59 contains two ORFs and thus differs from ns 4 of the JHM and S strains. Arch Virol. 1993;129(1-4):301–309. doi: 10.1007/BF01316905. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. 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 Jun;13(2):87–100. doi: 10.1016/0168-1702(89)90008-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Wesley R. D., Woods R. D., Cheung A. K. Genetic analysis of porcine respiratory coronavirus, an attenuated variant of transmissible gastroenteritis virus. J Virol. 1991 Jun;65(6):3369–3373. doi: 10.1128/jvi.65.6.3369-3373.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Wesley R. D., Woods R. D., Cheung A. K. Genetic basis for the pathogenesis of transmissible gastroenteritis virus. J Virol. 1990 Oct;64(10):4761–4766. doi: 10.1128/jvi.64.10.4761-4766.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. 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 Oct;2(4):312–317. doi: 10.1177/104063879000200411. [DOI] [PubMed] [Google Scholar]
  29. Yokomori K., Lai M. M. Mouse hepatitis virus S RNA sequence reveals that nonstructural proteins ns4 and ns5a are not essential for murine coronavirus replication. J Virol. 1991 Oct;65(10):5605–5608. doi: 10.1128/jvi.65.10.5605-5608.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]