Evolutionary analysis of rotavirus G1P[8] strains from Chennai, South India

Rotaviruses by virtue of its segmented genome generate numerous genotypes. G1P[8] is the most common genotype reported globally. We intend to identify the evolutionary differences among G1P[8] strains from the study with vaccine strains. Stool samples collected from children <5 years were screened for rotavirus antigen by enzyme linked immunosorbent assay. The samples that tested positive for rotavirus were subjected to VP7 and VP4 semi-nested RT-PCR. Sanger sequencing was performed in randomly chosen VP7 and VP4 rotavirus strains. Phylogenetic analysis showed less homology between study strains and vaccine strains and they were placed in different lineages. The VP7 and VP4 proteins of rotavirus were analyzed by two different platforms to identify the amino acid substitutions in the epitope regions. Nine amino acid substitutions with respect to Rotarix (R), RotaTeq (R) and Rotasiil (R)-V66A, A/T68S, Q72R, N94S, D100E, T113I, S123N, M217T, and I281T were observed in VP7. There were five amino acid substitutions-S145G, N/D195G, N113D, N/I78T, E150D in VP4 (VP8 portion) with respect to Rotarix (R) and RotaTeq (R) vaccine strains. M217T substitution in VP7 (epitope 7-2) and N113D, D195G substitution in VP4 (epitope 8-3, 8-1) confer changes in polarity/electrical charge with respect to vaccine strains, thus indicating the need for continued surveillance.