Diversity of species and genotypes of rotavirus field strains in a diarrhea outbreak in suckling piglets from an unvaccinated pig herd.

Diarrhea is the primary cause of morbidity and mortality in piglets during the neonatal period. Porcine neonatal diarrhea is a complex disease often caused by porcine rotavirus (PoRV) worldwide. This report describes the diversity of species and genotypes of PoRV field strains currently circulating in the nursery pens of an unvaccinated pig herd in southern Brazil. In a cross-sectional survey, 12 diarrheic fecal samples were obtained from 1 to 3 weeks of suckling piglets during an outbreak of diarrhea. RT-PCR assays were utilized to investigate the RVA, RVB, RVC, and RVH species. The amplified products were sequenced using the Sanger method. All 12 fecal samples were PoRV-positives. Among them, 11 (91.7%) samples were positive for RVA and 8 (66.7%) for RVC. RVA and RVC were co-detected in 7 (58.3%) samples. RNA from only one PoRV species was detected in five (RVA; n = 4 and RVC; n = 1) samples. Further analysis of VP7 (genotype G), VP4 (genotype P), and VP6 (genotype I) genes showed a diversity of four different genotype combinations for RVA (G3-P [6]-I5, G3-P [13]-I5, G4-P [6]-I5, and G5-P [23]-I5) and two (G1-P [4]-I6 and G6-P [4]-I1) for RVC field strains. This genotype diversity is rare in cross-sectional studies involving just one fecal collection on only one pig farm. Despite the small sample size, these reports highlight the intricate nature of PoRV gene reassortment events in pig herds, which can change the epidemiology of PoRV infections. Monitoring the evolution of PoRV field strains and potential heterologous infections is crucial. This will enhance our understanding of the evolution of PoRV wild-type strains and the epidemiology of PoRV infections.