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

SaV causes acute gastroenteritis in humans and animals including pigs, mink, dogs, sea lions, and bats [4, 9, 20]. Porcine SaV and human strains were separated into a different genogroups, however, based on analyses of RdRp or capsid protein genes, porcine SaV that genetically resembled human strains rather than previously recognized porcine strains had been identified [21, 22]. These findings suggested the possibility of a pig reservoir for human strains or vice versa. Meanwhile, recombination as an important survival event for all living creatures, may result in generation of new viruses with unknown pathogenic potential and altered species tropism for both animals and humans [23]. To date, both intra- and inter-genogroup recombinant strains have been reported [11‐13, 22‐24]. So far the recombinant strain was not found in either human beings or animals of China, although the SaV infections in children and pigs were common in this area [25‐27]. Here, we reported a complete genome of a recombinant SaV strain that identified from a piglet with diarrhea in China. Phylogenetic and recombination analysis based on the genomic sequences showed that p2 was an intra-genogroup recombinant within GIII, and the breakpoint located in the RdRp-capsid junction region, which was consistent with most of other SaV recombination events. Previous reports had shown that, in the genome of SaV, recombination mostly occurred at the polymerase-capsid junction region within ORF 1 which was referred as ‘hot spot’ [2, 13]. Chang et al. detected a 2.2 kb RNA in vitro replication assay with the replication complex of SaV Cowden strain extracted from virus-infected cells suggesting that SaV will generate subgenomic RNA during virus replication [8]. Moreover, researchers found that the RdRp-capsid junction region of SaV contained a highly conserved ~20 nucleotide (nt) motif in both genomic and subgenomic RNA molecules which was considered as a transcription start signal [2]. This conserved nucleotide motif may facilitate homologous recombination during co-infection of a cell by different genogroups of virus.

SaV has been detected in a wide range of mammals with potential ability of zoonotic transmission [28‐31]. Recombination was considered as a force of evolution which may produce new virus with potentially different pathogenesis and virulence [32]. Moreover, an infectious NoV chimera comprising the distinct biological properties from the parental viruses has been constructed and is infectious in vivo [32, 33]. Therefore, detection and understanding the recombination of SaV is important. In the current study, p2 strain was identified from a pig with diarrhea, in which bacteria and the common enteric viruses that cause pig gastroenteritis were ruled out. This suggested that this recombinant virus may cause this piglet diarrhea under the nature condition. More researches such as experimental infection should be performed in the future to confirm the pathogenicity of this recombinant strain.