title: Mouse hepatitis virus strain A59 RNA polymerase gene ORF 1a: heterogeneity among MHV strains.
abstract: Gene 1, the putative RNA replicase gene of coronaviruses, is expressed via two large overlapping open reading frames (ORF 1a and ORF 1b). We have determined the nucleotide sequence of ORF 1a, encoded within the first 13.7 kb of gene 1, for the coronavirus mouse hepatitis virus strain A59 (MHV-A59). Putative papain-like protease domains, a picornavirus 3C-like protease domain, two hydrophobic domains, and a domain "X" of unknown function, previously identified in other coronaviruses (1-3), are also present in ORF 1a of MHV-A59. Comparison between the ORF 1a sequence of MHV-A59 and the published sequence of the JHM strain of MHV (2) showed a high degree of similarity with the exception of several short regions. We sequenced one region of MHV-JHM that contained an 18 amino acid insertion relative to A59 and four other regions in which the sequences of the two strains differed. The MHV-2 and MHV-3 strains were also sequenced in some of these regions. Our analysis confirmed the presence of only one heterogeneous region in ORF 1a of MHV-A59 and MHV-JHM which is also present in MHV-2. Our findings indicate the need to modify the published sequence of MHV-JHM.
authors.affiliation: Department of Microbiology, University of Pennsylvania, Philadelphia 19104-6076.
authors.forename: P J
authors.initials: PJ
authors.lastname: Bonilla
authors.forename: A E
authors.initials: AE
authors.lastname: Gorbalenya
authors.forename: S R
authors.initials: SR
authors.lastname: Weiss
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D003001:Cloning, Molecular; D018076:DNA, Complementary / Q000235:genetics; D005814:Genes, Viral / Q000235:genetics*; D014644:Genetic Variation; D016679:Genome, Viral; D008969:Molecular Sequence Data; D006517:Murine hepatitis virus / Q000201:enzymology / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics*; D015183:Restriction Mapping; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D015678:Viral Structural Proteins / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D015678:Viral Structural Proteins; D012324:RNA-Dependent RNA Polymerase