Li Jingjiao, Shen Quan, Zhang Wen, Zhao Tingting, Li Yi, Jiang Jing, Yu Xiangqian, Guo Zhibo, Cui Li, Hua Xiuguo
School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
Virol J. 2017 Mar 16;14(1):57. doi: 10.1186/s12985-017-0729-1.
Sapovirus (SaV), a member of the family Caliciviridae, is an etiologic agent of gastroenteritis in humans and pigs. To date, both intra- and inter-genogroup recombinant strains have been reported in many countries except for China. Here, we report an intra-genogroup recombination of porcine SaV identified from a piglet with diarrhea of China.
A fecal sample from a 15-day-old piglet with diarrhea was collected from Shanghai, China. Common agents of gastroenteritis including porcine circovirus type 2, porcine rotavirus, porcine transmissible gastroenteritis virus, porcine SaV, porcine norovirus, and porcine epidemic diarrhea virus were detected by RT-PCR or PCR method. The complete genome of porcine SaV was then determined by RT-PCR method. Phylogenetic analyses based on the structural region and nonstructural (NS) region were carried out to group this SaV strain, and it was divided into different genotypes based on these two regions. Recombination analysis based on the genomic sequence was further performed to confirm this recombinant event and locate the breakpoint.
All of the agents showed negative results except for SaV. Analysis of the complete genome sequence showed that this strain was 7387 nt long with two ORFs and belonged to SaV GIII. Phylogenetic analyses of the structural region (complete VP1 nucleotide sequences) grouped this strain into GIII-3, whereas of the nonstructural region (RdRp nucleotide sequences) grouped this strain into GIII-2. Recombination analysis based on the genomic sequence confirmed this recombinant event and identified two parental strains that were JJ259 (KT922089, GIII-2) and CH430 (KF204570, GIII-3). The breakpoint located at position 5139 nt of the genome (RdRp-capsid junction region). Etiologic analysis showed the fecal sample was negative with the common agents of gastroenteritis, except for porcine SaV, which suggested that this recombinant strain might lead to this piglet diarrhea.
P2 strain was an intra-genogroup recombinant porcine SaV. To the best of our knowledge, this study would be the first report that intra-genogroup recombination of porcine SaV infection was identified in pig herd in China.
札幌病毒（SaV）是杯状病毒科的成员，是人类和猪肠胃炎的病原体。迄今为止，除中国外，许多国家都报告了基因组内和基因组间的重组毒株。在此，我们报告了从中国一头腹泻仔猪中鉴定出的猪SaV的基因组内重组情况。
从中国上海采集了一头15日龄腹泻仔猪的粪便样本。通过RT-PCR或PCR方法检测了包括猪圆环病毒2型、猪轮状病毒、猪传染性胃肠炎病毒、猪SaV、猪诺如病毒和猪流行性腹泻病毒在内的常见肠胃炎病原体。然后通过RT-PCR方法测定了猪SaV的完整基因组。基于结构区域和非结构（NS）区域进行系统发育分析以对该SaV毒株进行分组，并根据这两个区域将其分为不同的基因型。基于基因组序列进行重组分析以确认这一重组事件并定位断点。
除SaV外，所有病原体检测结果均为阴性。对完整基因组序列的分析表明，该毒株长7387 nt，有两个开放阅读框，属于SaV GIII。基于结构区域（完整的VP1核苷酸序列）的系统发育分析将该毒株归类为GIII-3，而基于非结构区域（RdRp核苷酸序列）的系统发育分析将该毒株归类为GIII-2。基于基因组序列的重组分析证实了这一重组事件，并鉴定出两个亲本毒株，分别是JJ259（KT922089，GIII-2）和CH430（KF204570，GIII-3）。断点位于基因组的5139 nt处（RdRp-衣壳连接区域）。病因分析表明，除猪SaV外，粪便样本中常见的肠胃炎病原体检测结果均为阴性，这表明该重组毒株可能导致了这头仔猪腹泻。
P2毒株是一株基因组内重组的猪SaV。据我们所知，本研究是中国猪群中首次报道猪SaV感染的基因组内重组情况。
