title: Reverse transcriptase polymerase chain reaction-based diagnosis and molecular characterization of a new rat coronavirus strain.
abstract: OBJECTIVE
  Rat coronaviruses (RCV) are highly infectious and spread rapidly through laboratory rat colonies, causing sneezing, nasal and ocular discharges, photophobia, and cervical swelling. Current diagnostic methods include serologic testing and histologic examination. During a recent rat coronavirus outbreak, we tested a rapid, noninvasive method of RCV diagnosis that involved use of reverse transcriptase-polymerase chain reaction (RT-PCR) analysis to detect RCV RNA on cages housing infected rats.
  
  
  METHODS
  The RT-PCR was used to detect RCV RNA in tissues from infected rats and on cages housing infected rats and to amplify portions of the RCV N, M, and S genes for molecular characterization.
  
  
  RESULTS
  The RT-PCR detected RCV RNA on cages and in tissues from infected rats. The RCV-NJ N gene is most closely related to the MHV-Y N gene. The M proteins of RCV-NJ and RCV-SDA are 99% homologous, and the six RCV S protein fragments are 97 to 100% homologous.
  
  
  CONCLUSIONS
  Use of RT-PCR with cage-swab specimens was capable of diagnosing RCV infection in and viral excretion from rats. Additionally, molecular characterization of the N, M, and S genes of RCV-NJ provided baseline information that can be used in performing further epidemiologic studies.
authors.affiliation: Section of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut 06520-8016, USA.
authors.forename: S R
authors.initials: SR
authors.lastname: Compton
authors.forename: B E
authors.initials: BE
authors.lastname: Vivas-Gonzalez
authors.forename: J D
authors.initials: JD
authors.lastname: Macy
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D018352:Coronavirus Infections / Q000175:diagnosis / Q000662:veterinary* / Q000821:virology; D000086862:Coronavirus M Proteins; D000086462:Coronavirus Nucleocapsid Proteins; D017941:Coronavirus, Rat / Q000235:genetics*; D004262:DNA Restriction Enzymes; D004355:Drug Stability; D008297:Male; D008969:Molecular Sequence Data; D019251:Nucleocapsid / Q000737:chemistry / Q000235:genetics; D019590:Nucleocapsid Proteins; D010969:Plastics; D012367:RNA, Viral / Q000737:chemistry / Q000302:isolation & purification; D051381:Rats; D017207:Rats, Sprague-Dawley; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012376:Rodent Diseases / Q000821:virology*; D014763:Viral Matrix Proteins / Q000737:chemistry / Q000235:genetics; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D000086862:Coronavirus M Proteins; D000086462:Coronavirus Nucleocapsid Proteins; D019590:Nucleocapsid Proteins; D010969:Plastics; D012367:RNA, Viral; D014763:Viral Matrix Proteins; D014764:Viral Proteins; D004262:DNA Restriction Enzymes