Genomic organization and recombination analysis of a porcine sapovirus identified from a piglet with diarrhea in China

Jingjiao Li,Xiuguo Hua,Li Cui,Zhibo Guo,Jing Jiang,Yi Li,Tingting Zhao,Quan Shen,Xiangqian Yu,Wen Zhang

doi:10.1186/s12985-017-0729-1

Jingjiao Li, Xiuguo Hua + Show 8 more

Open Access

https://doi.org/10.1186/s12985-017-0729-1

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Abstract

BackgroundSapovirus (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.MethodsA 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.ResultsAll 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.ConclusionsP2 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.

Highlights

Sapovirus (SaV), a member of the family Caliciviridae, is an etiologic agent of gastroenteritis in humans and pigs
Genogroup III (GIII) strains have been further clustered into several genotypes based on the partial VP1 or RNA-dependent RNA polymerase (RdRp) sequences reported by different researchers [5, 6]
Result showed that the fecal sample was negative for porcine NoV, PCV 2, porcine rotavirus (PRV), porcine transmissible gastroenteritis virus (PTGV) and porcine epidemic diarrhea virus (PEDV), but was positive for porcine SaV

Summary

Introduction

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. We report an intra-genogroup recombination of porcine SaV identified from a piglet with diarrhea of China. Previous studies suggested that the recombination site was at the polymerasecapsid junction [1, 2] To date, both intra- and intergenogroup recombinant strains have been reported in humans, few porcine recombinant SaV strains have been reported all over the world [10,11,12,13]. No recombinant strain of SaV has been identified either in human or pig in China

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