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. 2006 Jan 30;167(2):370–376. doi: 10.1016/0042-6822(88)90097-9

Sequence analysis of the 3′ end of the feline coronavirus FIPV 79-1146 genome: Comparison with the genome of porcine coronavirus TGEV reveals large insertions

Raoul J De Groot 1,1, Arno C Andeweg 1, Marian C Horzinek 1, Willy JM Spaan 1
PMCID: PMC7130511  PMID: 3201747

Abstract

The genetic information, carried on mRNA 6 of feline infectious peritonitis virus (FIPV) strain 79–1146, was determined by sequence analysis of cDNA clones derived from the 3′ end of the FIPV genome. Two ORFs were found, encoding polypeptides of 11 K (ORF-1) and 22K (ORF-2). The FIPV sequence was compared to the 3′ end sequence of transmissible gastroenteritis virus (TGEV). ORF-1 has a homologous counterpart (ORF-X3) in the TGEV genome; both ORFs are located at the same position relative to the nucleocapsid gene. However, as a result of an in-frame insertion or deletion, ORF-1 is 69 nucleotides larger than ORF-X3. A similar event has occurred immediately downstream of ORF1: a 624-nucleotide segment, containing the complete ORF-2, is absent in the TGEV sequence. Most sequence similarity (98.5%) was found in the 3′ noncoding sequences. ORF-X3 and ORF-1 are preceded by the sequence AAC-TAAAC, which is assumed to be the transcription-initiation signal in FIPV and TGEV (P. A. Kapke and D. A. Brian (1986)Virology 151, 41–49). By S1 nuclease analysis, the 5′ end of FIPV RNA 6 was mapped immediately upstream of this sequence. A 700-nucleotide TGEV-specific RNA was found by cross-hybridization with an FIPV 3′ end probe, suggesting that TGEV ORF-X3 is also carried on a separate mRNA. The differences at the 3′ ends of the FIPV and TGEV genomes maybe the result of RNA recombination events.

Reference

  1. Armstrong J., Nieman H., Smeekens S., Rottier P., Warren G. Sequence and topology of a model intracellular membrane protein El glycoprotein, from a coronavirus. Nature (London) 1984;308:751–752. doi: 10.1038/308751a0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Armstrong J., Smeedkens S., Spaan W., Rottier P., Van Der Zeijst B.A.M. Cloning and sequencing the nucleocapsid and E1 genes of coronavirus. Adv. Exp. Med. Biol. 1984;173:155–161. doi: 10.1007/978-1-4615-9373-7_16. [DOI] [PubMed] [Google Scholar]
  3. Boursnell M.E.G., Binns M.M., Brown T.D.K. Sequencing of coronavirus IBV genomic RNA: Three open reading frames in the 5′“unique” region of RNA D. J. Gen. Virol. 1985;66:2235–2258. doi: 10.1099/0022-1317-66-10-2253. [DOI] [PubMed] [Google Scholar]
  4. Boursnell M.E.G., Brown T.D.K., 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]
  5. Britton P., Carmenes R.S., Page K.W., Garwes D.J., Parra F. Sequence of the nucleoprotein gene 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]
  6. Brown T.D.K., Boursnell M.E.G., Binns M.M. A leader sequence is present on mRNA A of avian infectious bronchitis virus. J. Gen. Virol. 1984;65:1437–1442. doi: 10.1099/0022-1317-65-8-1437. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. de Groot R.J., Ter Haar R.J., Horzinek M.C., Van Der Zeijst B.A.M. Intracellular RNAs of the feline infectious peritonitis coronavirus strain 79-1146. J. Gen. Virol. 1987;68:995–1002. doi: 10.1099/0022-1317-68-4-995. [DOI] [PubMed] [Google Scholar]
  9. Horzinek M.C., Lutz H., Pedersen N.C. Antigenic relationships among homologous structural polypeptides of porcine, feline and canine coronaviruses. Infect. Immun. 1982;37:1148–1155. doi: 10.1128/iai.37.3.1148-1155.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Jacobs L., de Groot R.J., Horzinek M.C., Van Der Zeijst B.A.M., Spaan W.J.M. 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]
  11. Jacobs L., Van Der Zeijst B.A.M., Horzinek M.C. Characterization and translation of transmissible gastroenteritis virus m RNAs. J. Virol. 1986;57:1–6. doi: 10.1128/jvi.57.3.1010-1015.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. 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]
  13. Kozak M. Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell. 1986;44:283–292. doi: 10.1016/0092-8674(86)90762-2. [DOI] [PubMed] [Google Scholar]
  14. Kozak M. Bifunctional messenger RNAs in eukaryotes. Cell. 1986;47:481–483. doi: 10.1016/0092-8674(86)90609-4. [DOI] [PubMed] [Google Scholar]
  15. Lai M.M.C., Baric R.S., Brayton P.R., Stohlman S.A. Vol. 81. 1984. Characterization of leader RNA sequences on the virion and mRNAs of mouse hepatitis virus, a cytoplasmic RNA virus; pp. 3626–3630. (Proc. Natl. Acad. Sci. USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Luytjes W., Bredenbeek P.J., Noten A.F.H., Horzinek M.C., Spaan W.J.M. Sequence of mouse hepatitis virus A59 mRNA 2: Indications for RNA recombination between coronaviruses and influenza C virus. Virology. 1988;166:415–422. doi: 10.1016/0042-6822(88)90512-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Luytjes W., Sturman L.S., Bredenbeek P.J., Charite J., van Der Zeijst B.A.M., Horzinek M.C., Spaan W.J.M. 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]
  18. Making S., Keck J.G., Stohlman S.A., Lai M.M.C. High-frequency RNA recombination of murine coronaviruses. J. Virol. 1986;57:729–737. doi: 10.1128/jvi.57.3.729-737.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Maniatis T., Fritsch E.F., Sambrook J. Cold Spring Harbor Laboratory; Cold Spring Harbor, NY: 1982. (Molecular Cloning: A Laboratory Manual). [Google Scholar]
  20. Peabody D.S., Berg P. Termination-reinitiation occurs in the translation of mammalian cell mRNAs. Mol. Cell. Biol. 1986;6:2695–2703. doi: 10.1128/mcb.6.7.2695. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Peabody D.S., Subramani, Berg P. Effect of upstream reading frames on translational efficiency in simian virus 40 recombinants. Mol. Cell. Biol. 1986;6:2704–2711. doi: 10.1128/mcb.6.7.2704. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Pedersen N.C., Ward J., Mengeling W.L. Antigenic relationship of the feline infectious peritonitis virus to coronaviruses of other species. Arch. Virol. 1978;58:45–53. doi: 10.1007/BF01315534. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. 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]
  24. Rottier P.J.M., Spaan W.J.M., Horzinek M.C., Van Der Zeijst B.A.M. Translation of three mouse hepatitis virus stain A59 subgenomic RNAs inXenopus laevis oocytes. J. Virol. 1981;39:20–26. doi: 10.1128/jvi.38.1.20-26.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Sanger F., Nicklen S., Coulson A.R. Vol. 74. 1977. DNA sequencing with chain-terminating inhibitors; pp. 5463–5467. (Proc. Natl. Acad. Sci. USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. 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]
  27. Siddell S. Coronavirus JHM: Coding assignment of subgenomic mRNAs. J. Gen. Virol. 1983;64:113–125. doi: 10.1099/0022-1317-64-1-113. [DOI] [PubMed] [Google Scholar]
  28. Siddell S., Wege H., Ter Mellen V. The biology of coronaviruses. J. Gen. Virol. 1983;64:761–776. doi: 10.1099/0022-1317-64-4-761. [DOI] [PubMed] [Google Scholar]
  29. Skinner M.A., Ebner D., Siddel S.G. Coronavirus MHV-JHM mRNA 5 allows translation of a second, downstream open reading frame. J. Gen. Virol. 1985;66:581–592. doi: 10.1099/0022-1317-66-3-581. [DOI] [PubMed] [Google Scholar]
  30. Skinner M.A., Siddel S.G. Coding sequence of coronavirus MHV-JHM mRNA 4. J. Gen Virol. 1985;66:593–596. doi: 10.1099/0022-1317-66-3-593. [DOI] [PubMed] [Google Scholar]
  31. Smith A.R., Boursnell M.E.G., Binns M.M., Brown T.D.K., Inglis S.C. Identification of a new gene product encoded by mRNA D of infectious bronchitis virus. Adv. Exp. Med. Biol. 1987;218 doi: 10.1007/978-1-4684-1280-2_6. [DOI] [PubMed] [Google Scholar]
  32. Spaan W., Delius E., Skinner M., Armstrong J., Rottier P., Smeekens S., Van Der Zeijst B.A.M., Siddell S.G. Coronavirus mRNA synthesis involves fusion of non-contiguous sequences. EMBO J. 1983;2:1839–1844. doi: 10.1002/j.1460-2075.1983.tb01667.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Staden R. Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. Nucleic Acids Res. 1982;10:4731–4751. doi: 10.1093/nar/10.15.4731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Stern D.F., Sefton B.M. Coronavirus multiplication: Location of genes for virion proteins on the avian infectious bronchitis virus genome. J. Virol. 1984;50:22–29. doi: 10.1128/jvi.50.1.22-29.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]

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