Genetic and antigenic diversity of rotavirus A in feces from Danish pigs

Abstract Rotavirus A (RVA) causes viral gastroenteritis and is frequently detected in young piglets. These viruses are genotyped according to diversity within the outer capsid coding gene segments designated viral protein 4 (VP4) and 7 (VP7). The present study defines a comprehensive baseline for porcine RVA VP4 and VP7 genotypic diversity in Danish swine herds, important for future monitoring efforts. Disparities between amino acid residues in antigenic domains of the Danish RVA field viruses and the vaccine strain named “Ohio State University (OSU) G5P[7]” were also investigated. RVA nucleic acids from positive fecal samples of 63/84 tested Danish swine herds were amplified using conventional reverse transcriptase polymerase chain reaction (RT-PCR) with primers specific for VP7 and VP4 genes and sequenced using Sanger or Illumina technologies. In total, 127 VP7 genes and 110 VP4 genes were sequenced and genotyped. Eight different VP7 genotypes (G2, G3, G4, G5, G9, G10, G11 and G26) and six different VP4 genotypes (P[6], P[7], P[13], P[23], P[26], and P[32]) together with two possibly new VP4 genotypes (P[X1] and P[X2]) were detected, and the most frequent genotype constellations were G9P[23], G9P[13], G5P[13], and G5P[23]. Nine rectal swabs from pigs of nine different herds revealed infections with multiple VP7 genotypes, and four swabs from pigs of four herds presented with various VP4 genotypes. Sampling of several pigs within the same herd revealed co-circulation of different genotypes, which emphasizes that several pigs should be sampled for representative RVA genotyping. Notable differences between the RVA field viruses and the vaccine strain were evident, as on average 11.7/29 and 25.8/37 amino acid residues in immunogenic domains differed in VP7 and VP4 genotypes, respectively. Considering the high RVA field strain diversity and their high divergence from the vaccine strains, future studies are needed to investigate the efficacy of available porcine RVA vaccines.