Primary Structure of the Sialodacryoadenitis Virus Genome: Sequence of the Structural-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 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.

涎泪腺炎病毒（Sialodacryoadenitis virus, SDAV）是一种常见于实验大鼠的冠状病毒，可引发涎泪腺炎与呼吸道疾病。本研究对其基因组RNA的3'端9.8 kb片段进行了克隆与测序，并分析了该病毒的基因组结构。与鼠肝炎冠状病毒（Mouse Hepatitis Viruses, MHVs）类似，SDAV基因组可编码刺突蛋白（spike protein）、小型膜蛋白（small membrane protein）、膜相关蛋白（membrane-associated protein）以及核衣壳蛋白（nucleocapsid protein）。此外，本研究还鉴定出一段可编码439个氨基酸（amino acids, aa）的血凝素酯酶基因（hemagglutinin-esterase gene）。在HE蛋白（hemagglutinin-esterase protein）中存在乙酸酯酶活性（acetylesterase activity）的推定功能位点Phe-Gly-Asp-Ser（FGDS），这表明SDAV的HE蛋白可能保留了酯酶活性（esterase activity）。在HE基因紧上游、聚合酶1b基因（polymerase 1b gene）紧下游的区域，鉴定出一段编码能力为274个氨基酸的NS2非结构蛋白基因（NS2 nonstructural-protein gene）。研究发现一段UCUAAAC基序（motif）可作为亚基因组mRNA合成（subgenomic mRNA synthesis）的潜在转录信号。将SDAV预测刺突蛋白的序列与MHV 2、MHV JHM及MHV A59的对应序列进行比对后，其S蛋白N端半区（N-terminal half）存在长度分别为172、127和44个氨基酸的大片段插入。研究人员将SDAV刺突蛋白基因的序列信息应用于鉴别诊断聚合酶链式反应（differential diagnostic PCR），以实现大鼠冠状病毒（rat coronavirus）与小鼠冠状病毒（mouse coronaviruses）的检测与区分。本研究是首例针对任意大鼠冠状病毒的全面遗传信息报道。