Primary structure of the sialodacryoadenitis virus genome: Sequence of thestructural-protein region and its application for differential diagnosis

Sialodacryoadenitis virus (SDAV) is a coronavirus that is commonly found in laboratory rats and that causes sialodacryoadenitis and respiratory illnes s, me cloned and sequenced the 3' terminal 9.8 bb of the genomic RNA and an alyzed the structure of the viral genome. As with mouse hepatitis coronavir uses (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 protei n of 439 amino acids (aa) was identified. The putative functional site for acetylesterase activity was present in the NE protein as Phe-GIS-Asp-Ser (F GDS), suggesting that the SDAV HE protein might have retained the esterase activity, Immediately upstream of the HE gene and downstream of the polymer ase Ib gene, the NS2 nonstructural-protein gene was identified with a codin g capacity of 274 aa, A motif of UCUAAAC was identified as a potential tran scription signal for subgenomic mRNA synthesis. Large insertions of 172, 12 7, and 44 aa were detected in the N-terminal half of the predicted S protei n 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 distinguis h the rat coronavirus from mouse coronaviruses. This is the first report on the comprehensive genetic information of any rat coronavirus.