title: Complete genomic sequences, a key residue in the spike protein and deletions in nonstructural protein 3b of US strains of the virulent and attenuated coronaviruses, transmissible gastroenteritis virus and porcine respiratory coronavirus.
abstract: Transmissible gastroenteritis virus (TGEV) isolates that have been adapted to passage in cell culture maintain their infectivity in vitro but may lose their pathogenicity in vivo. To better understand the genomic mechanisms for viral attenuation, we sequenced the complete genomes of two virulent TGEV strains and their attenuated counterparts: virulent TGEV Miller M6 and attenuated TGEV Miller M60 and virulent TGEV Purdue and attenuated TGEV Purdue P115, together with the ISU-1 strain of porcine respiratory coronavirus (PRCV-ISU-1), a naturally occurring TGEV deletion mutant with an altered respiratory tropism and reduced virulence. Pairwise comparison at both the nucleotide (nt) and amino acid (aa) levels between virulent and attenuated TGEV strains identified a common change in nt 1753 of the spike gene, resulting in a serine to alanine mutation at aa position 585 of the spike proteins of the attenuated TGEV strains. Alanine was also present in this protein in PRCV-ISU-1. Particularly noteworthy, the serine to alanine mutation resides in the region of the major antigenic site A/B (aa 506-706) that elicits neutralizing antibodies and within the domain mediating the cell surface receptor aminopeptidase N binding (aa 522-744). Comparison of the predicted polypeptide products of ORF3b showed significant deletions in the naturally attenuated PRCV-ISU-1 and TGEV Miller M60; these deletions occurred at a common break point, suggesting a related mechanism of recombination that may affect viral virulence or tropism. Sequence comparisons at both genomic and protein levels indicated that PRCV-ISU-1 had a closer relationship with TGEV Miller strains than Purdue strains. Phylogenetic analyses showed that virulence is an evolutionarily labile trait in TGEV and that TGEV strains as a group share a common ancestor with PRCV.
authors.affiliation: Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691, USA.
authors.forename: Xinsheng
authors.initials: X
authors.lastname: Zhang
authors.forename: Mustafa
authors.initials: M
authors.lastname: Hasoksuz
authors.forename: David
authors.initials: D
authors.lastname: Spiro
authors.forename: Rebecca
authors.initials: R
authors.lastname: Halpin
authors.forename: Shiliang
authors.initials: S
authors.lastname: Wang
authors.forename: Sarah
authors.initials: S
authors.lastname: Stollar
authors.forename: Daniel
authors.initials: D
authors.lastname: Janies
authors.forename: Nagesh
authors.initials: N
authors.lastname: Hadya
authors.forename: Yuxin
authors.initials: Y
authors.lastname: Tang
authors.forename: Elodie
authors.initials: E
authors.lastname: Ghedin
authors.forename: Linda
authors.initials: L
authors.lastname: Saif
mesh_terms: D000595:Amino Acid Sequence; D016679:Genome, Viral; D008562:Membrane Glycoproteins / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D045722:Porcine Respiratory Coronavirus / Q000235:genetics* / Q000472:pathogenicity; D016415:Sequence Alignment; D064370:Spike Glycoprotein, Coronavirus; D005760:Transmissible gastroenteritis virus / Q000235:genetics* / Q000472:pathogenicity; D014759:Viral Envelope Proteins / Q000235:genetics*; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D014774:Virulence
chemical_list: D008562:Membrane Glycoproteins; D064370:Spike Glycoprotein, Coronavirus; D014759:Viral Envelope Proteins; D017361:Viral Nonstructural Proteins