Genetic Diversity of Rotavirus Strains in the Era of Vaccination: A Pilot Study from Central Kerala, India

Abstract

Introduction: Rotaviruses cause Acute Gastroenteritis (AGE) in children. Characterisation of rotavirus VP7, VP4 and VP6 genes revealed novel genotypes circulating in the region. Aim: To characterise the circulating rotavirus genotypes in Central Kerala and compare the genotypes with vaccine components to assess the genetic variability. Materials and Methods: We analysed VP6, VP4 and VP7 genes of rotavirus strains from hospitalised children (January-December 2013) by amplification, sequencing and phylogenetic analysis. VP4 and VP7 antigenic epitopes of G1P8 strains were compared with vaccine strains to determine the genetic variations. Results: G1P8 was the predominant strain, G9P8, G1P6, G9P4 were also encountered in the study. VP6 gene analysis revealed that 91.30% of strains belonged to genotype I1 and 8.7% to genotype I2. G1 and G9 strains show low nucleotide and amino acid homology with corresponding vaccine strains. Comparison between the vaccine strain and G1 study strains, eight substitutions were observed in the VP7 epitope region. In the VP4 gene (VP8 region) 22 and 12 substitutions were observed compared to Rotarix with RotaTeq vaccine strains respectively. Conclusion: Study strains clustered closely with other Indian strains, indicating common ancestral link. G1P8 strains showed low homology with vaccine strains, suggesting genetic variability to escape vaccine-derived immune response. This study helped to identify the circulating rotavirus genotypes in the region and explored possibility of emergence of divergent strains.

Keywords

• acute gastroenteritis
• molecular diversity
• vp4
• vp6
• vp7