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• Differences between G9 RV strains from North India and vaccine strain 116E. • North Indian G9 rotavirus strains clustered in different lineage than vaccine strain. • Analysis of antigenic epitopes showed mutations between North Indian and vaccine strains. • Substitutions in antigenic epitopes of G9RV were responsible for neutralization escape. • Substitutions were found in the most exposed residues on 3D VP7 trimer. The parental rotavirus strain 116E (G9P[11]) used to generate Rotavac® vaccine was isolated in 1986 in New Delhi. Thenceforward, there is no comprehensive report on diversity of G9 rotavirus strains from 116E; therefore, the present study evaluates the VP7 gene sequence diversity of G9 strains (retrieved from GenBank) from different geographical regions (1987–2016). Additionally, 22 recently collected G9 strains from Himachal Pradesh and Delhi (2013–2016) were included in the phylogenetic analysis. Interestingly, unlike 116E which belong to lineage-II all other G9 rotavirus including these 22 samples clustered together in a separate lineage (III). Further, six amino acid substitutions including one novel, K143M (epitope 7-2) different from 116E were detected mostly in the neutralization epitopes of VP7 protein (neutralization escape mutants). Overall, the accumulation of identified substitutions in VP7 epitopes and evolution of G9 strains in India may have impact on Rotavac® efficacy. [ABSTRACT FROM AUTHOR]