Primary Structure of the Sialodacryoadenitis Virus Genome: Sequence of the Structural-Protein Region and Its Application for Differential Diagnosis

Abstract

Sialodacryoadenitis virus (SDAV) is a coronavirus that is commonly found in laboratory rats and that causes sialodacryoadenitis and respiratory illness. We cloned and sequenced the 3 terminal 9.8 kb of the genomic RNA and analyzed the structure of the viral genome. As with mouse hepatitis coronaviruses (MHVs), the SDAV genome was able to code for a spike protein, a small membrane protein, a membrane-associated protein, and a nucleocapsid protein. In addition, the hemagglutinin-esterase gene capable of encoding a protein of 439 amino acids (aa) was identified. The putative functional site for acetylesterase activity was present in the HE protein as Phe-Gly-Asp-Ser (FGDS), suggesting that the SDAV HE protein might have retained the esterase activity. Immediately upstream of the HE gene and downstream of the polymerase 1b gene, the NS2 nonstructural-protein gene was identified with a coding capacity of 274 aa. A motif of UCUAAAC was identified as a potential transcription signal for subgenomic mRNA synthesis. Large insertions of 172, 127, and 44 aa were detected in the N-terminal half of the predicted S protein of SDAV when its sequence was compared to the sequences of MHV 2, MHV JHM, and MHV A59, respectively. The sequence information on the SDAV S-protein gene was applied to a differential diagnostic PCR to detect and distinguish the rat coronavirus from mouse coronaviruses. This is the first report on the comprehensive genetic information of any rat coronavirus.Sialodacryoadenitis virus (SDAV) is distributed worldwide in laboratory rats. SDAV infects the lacrimal and salivary glands and the upper and lower respiratory tracts of rats, causing the clinical manifestations of enlarged salivary glands, sialoadenitis, dacryoadenitis, rhinitis, tracheitis, and bronchoalveolitis (3, 9, 10). SDAV can also cause reproductive disorders and behavioral changes in the infected animals. Serologic surveys indicate that coronavirus infections are common in laboratory rats housed in research facilities (11,16), and several outbreaks of SDAV in rat colonies have been reported (2,6,12,22,32; J. Storz, personal communication). Therefore, SDAV is an important viral pathogen in comparative laboratory medicine.SDAV is antigenically related to the mouse hepatitis virus (MHV) serogroup of the family Coronaviridae in the order of Nidovirales (20). The MHV serogroup includes Parker's rat coronavirus (PRCV), bovine coronavirus (BCV), and human coronavirus (HCV) strain OC43. Coronavirus is an enveloped virus with a single-stranded positive-sense RNA genome of approximately 31 kb. The 5Ј-most 22 kb of the coronavirus genome encodes the nonstructural RNA-dependent RNA polymerase, while all the structural proteins are encoded in the 3Ј terminal 9 kb of the genome (15). Although a large amount of genetic information has been accumulated for MHV and other coronaviruses, such information is not available for any rat coronavirus, mainly due to the difficulty with propagation of the virus in cell cultures. Percy and coworkers (25) reported that a su...

Common RNA replication signals exist among group 2 coronaviruses: evidence for in vivo recombination between animal and human coronavius molecules

“…Sequence analysis of the leader fusion region of DI RNA progeny from cells infected with HCoV-OC43 helper virus and transfected with reporter-containing BCoV DI RNA. The HCoV-OC43-specific bases G60 and A95 and the BCoV-specific base C133 show that the progeny DI RNA molecule possesses a leader derived from the HCoV-OC43 helper virus and that the recombination site exists somewhere between nts 95 and 133. used to grow SDAV-681 as previously described (Yoo et al, 2000) and mouse L cells were used to grow PV as previously described (Klausegger et al, 1999).…”

Molecular Advances in Severe Acute Respiratory Syndrome-Associated Coronavirus (SARS-CoV)

“…Moreover, there is a tendency of deletions or truncations of these ORFs when crossing the species barriers within the subgroups, e.g . ORF 4a/b in group 2 54., 55., 56., 57., 58.; ORF 3a/b and ORF 7a/b in group 1 41., 42., 47., 48., 50., 70., 71., 72.. The deletions of these redundant accessory ORFs are likely to be the result rather than the cause of crossing the host barriers, as coronavirus host range specificity and tropism have been demonstrated, at least in four studies 7., 73., 74., 75., as determined by the receptorbinding domain of the spike glycoprotein.…”

“…Although the ORF 5a/5b of group 3 CoVs and ORF 5/6 of SARS-CoV are in homologous location, they do not have any significant sequence homology. FECV: feline enteric coronavirus 41., 42., 43., 44., 45.; FIPV: feline infectious peritonitis virus 41., 42., 43., 44., 45.; CCV: canine coronavirus 43., 46.; TGEV: transmissible gastroenteritis virus 41., 47., 48.; PRCV: porcine respiratory coronavirus 41., 47., 48.; PEDV: porcine epidemic diarrhea virus 49., 50.; HCV 229E: human coronavirus 229E 49., 51.; MHV: murine hepatitis virus 52., 53.; RCV: rat coronavirus ( 54 ); BCV: bovine coronavirus ( 55 ); PHEV: porcine hemagglutinating encephalomyelitis virus ( 56 ); HCV OC43: human coronavirus OC43 57., 58.; TCV: turkey coronavirus 59., 60., 61.; IBV: infectious bronchitis virus 62., 63., 64..…”

A Review of Respiratory System Anatomy, Physiology, and Disease in the Mouse, Rat, Hamster, and Gerbil

“…The hypervariable region identified in the SDAV S sequence may be used as a genetic marker to develop a reliable diagnostic PCR. 165 Mouse Mice may develop a transient interstitial pneumonia with seroconversion. Athymic nude mice are particularly susceptible to coronavirus infections, and develop chronic persistent disease and wasting.…”