Molecular characterization of porcine group A rotavirus to contain piglet diarrhea for productivity enhancement in North East India

Gastrointestinal tract infections with acute diarrhea are indeed a serious cause of concern that held back the swine industry of North East India and among the various etiological agents causing the disease, group A rotavirus is the most common. In this regard, molecular characterization of the viral strains circulating in the region is of utmost importance for a strategic approach to control the disease. Thus, in the present study, diarrheic fecal samples from piglets of Tripura and Assam were evaluated for genotypic characterization of VP7 and VP4 gene of the virus. The samples positive for group A rotavirus were subjected to G and P type determination by nested- multiplex RT PCR as well as nucleotide sequencing of VP7 and VP4 gene. Nested- multiplex RT PCR revealed the presence of porcine group A rotavirus in the genotypic combination of G1P[6], G3P[6], G8P[6] and G4P[6] in the two states of North East India. Nucleotide sequencing of VP7 and VP4 genes however, revealed emergence of an unusual genotypic combination G26P[13]. VP7 and VP4 nucleotide and its deduced amino acid sequences when compared with global isolates, showed that the present strains shared closest similarity to the porcine rotavirus strain TJ4-1from Japan and hp140 from Eastern India. Identification of a novel genotype G26P[13] in the RVA infected pig population of Tripura and Assam, suggested presence of a greater diversity in rotavirus strains in the region. Thus, it evokes the need for continuous monitoring to assess and consider the strain variability in the design of a suitable vaccine candidate against the virus. SUPPLEMENTARY INFORMATION: The online version of this article (10.1007/s13337-021-00659-6) contains supplementary material, which is available to authorized users.