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

Abstract

Background: 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.

Methods: 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.

Results: 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.

Conclusions: 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.

Keywords: Genome organization; Porcine sapovirus; Recombination.

Fig. 1

Schematic of strain p2 genome organization. The full genome of strain p2 is a linear, positive-sense,single-stranded RNA of 7387 bp with a poly (A) tail at the 3’ end. The nucleotides coordinate of 5’ UTR, ORF 1 and ORF 2, and 3’ UTR are indicated on the map. ORF1 encoded a single polyprotein which was subsequently cleaved into seven nonstructural proteins containing the RdRp region and the major capsid protein VP1. ORF2 encoded the minor capsid protein VP2 (171 aa)

Fig. 2

Phylogenetic tree based on the complete VP1 nucleotide sequences of 42 SaV strains using MEGA 7. These strains represented all reported 8 genogroups (GIII, GV-GXI) of porcine SaV. GIII strains were grouped into 5 genotypes (GIII-1 – GIII-5). Among those strains, the p2 strain determined in this study was marked with box. Each SaV strain is presented as the following format: strain ID- GenBank accession number

Fig. 3

Phylogenetic tree of the 3’ end of RdRp nucleotide sequences (780 bp) of SaV strains. Only 25 of 42 strains had the available sequences of 3’ end of the RdRp region covering the RdRp-capsid junction and GIII strains were grouped into 5 genotypes (GIII-1-GIII-5). The strain p2 reported in this study was indicated in box

Fig. 4

Identification of recombinant p2 strain based on RDP 4. BOOTSCAN evidence for the recombination origin on the basis of pairwise distance, modeled with a window size 200, step size 25, and 100 Bootstrap replicates