Full-length genomic analysis of porcine rotavirus strains isolated from pigs with diarrhea in Northern Italy

Abstract

Group A rotaviruses (RVA) cause acute dehydrating diarrhea in young of man and many animal species, including pigs. Swine RVA has an important economic impact on the farming industry, and pigs represent a potential reservoir for zoonotic transmission of RVA to humans. To investigate the genetic diversity of porcine RVA strains in Italy and identify their possible zoonotic characteristics, 25 RVA-positive feces were collected from diarrheic pigs in Northern Italy, in 2009-2010; all viral strains were characterized by G and P genotyping RT-PCR. Three samples were selected for full genome sequencing. Sequencing of the NSP3 genes of all samples was also performed. Rotavirus diagnosis was carried out by ELISA and electron microscopy. RT-PCR and Sanger sequencing were performed in a one-tube format, using primer sets specific for each of the 11 genome segments. Analysis of the G (VP7) and P (VP4) genotypes showed that all strains identified were typical porcine RVAs (G4, G5, G9; P[6], P[13], P[23]). Full-length genome sequencing was performed on selected G9 isolates. Most segments belonged to the genotype constellation 1 (Wa-like), which is shared by most human RVA strains, but gene types such as I5 (VP6) and A8 (NSP1), which are typical of porcine and rare among human RVAs, were also detected. We identified RVA strains showing the T7 genotype, an NSP3 gene type that was previously reported in unusual strains of possible porcine or bovine origin from children with diarrhea. Recent reports suggested that G9 RVA may have been introduced from swine to human populations involving gene reassortment events. The observation that some of the RVA genotypes from swine in Italy were similar to viruses characterized in children underlines the importance of animal RVA surveillance, to clarify and monitor the role of animals as genetic reservoirs of emerging RVA strains pathogenic for humans.

Keywords: Full genome sequencing; Genotype; Group A rotavirus; Swine; Zoonoses.