Porcine Rotavirus A G3P[6] with a Putative Novel G3-XII Lineage and P[6]-Ig Sublineage Associated with Neonatal Diarrhea in Southern Brazil

Neonatal diarrhea remains a significant threat to piglet health, resulting in substantial economic losses worldwide. Among the viral pathogens associated with this condition, rotavirus (RV) has been extensively reported in Brazil; however, lineage-level classification of circulating strains remains limited. This study aimed to characterize G and P genotypes of porcine RV field strains associated with diarrhea in piglets in Southern Brazil. A total of 10 fecal samples were collected by field veterinarian from diarrheic suckling piglets aged 1 to 14 days and analyzed by RT-PCR for the detection of RV species A, B, C, and H. RV species A (RVA) was detected in 90% (9/10) of the samples, while no other RV species were identified. Genotyping based on the VP7 and VP4 genes revealed a single G3P[6] genotype combination in all RVA-positive samples. Nucleotide (nt) and deduced amino acid (aa) sequence analysis revealed high genetic similarity among strains, with values of up to 99.3% for nt and 98.0% for aa of the VP7 gene and 100% for the VP4 gene (nt and aa). Phylogenetic analysis indicated that the VP7 sequences clustered with Brazilian G3 strains, forming a distinct group consistent with a novel lineage (putative G3-XII), whereas VP4 sequences supported a new sublineage (putative P[6]-Ig). These findings demonstrate low genetic variability of RVA field strains in this neonatal diarrhea outbreak, suggesting the circulation of a single viral population. They also emphasize the importance of continuous molecular surveillance to gain a deeper understanding of viral evolution and transmission dynamics in swine populations.