Full genomic analysis of Indian G1P[8] rotavirus strains

Abstract

Rotavirus G1P[8] strains are the most predominant cause of rotavirus diarrhea, worldwide and are an important component of currently licensed RotaTeq and Rotarix vaccines. Despite a significant contribution of these strains in causing diarrhea in Indian children, none of them has been characterized completely, to date. This issue was addressed in the present study by sequencing and phylogenetic analysis of complete genomes of 3 Indian rotavirus strains (06361, 0613158 and 061060) of G1P[8] specificity. Genotype of G1P[8] I1R1C1M1A1N1T1E1H1 respectively, for the VP7, VP4, VP6, VP1, VP2, VP3, NSP1, NSP2, NSP3, NSP4 and NSP5 genes was assigned to all of the three strains. The sequence analysis of structural and nonstructural genes indicated genetic relatedness (94–99.5%) with recently circulating strains and divergence (2.4–15.6%) with old prototype strains. Phylogenetic analysis revealed that new strains (Western Indian rotavirus strains and recently isolated strains – Dhaka16-03 (G1P[8]), Dhaka25-02 (G12P[8]), Matlab13-03 (G12P[6]), B3458 (G9P[8]), Matlab36-03 (G11P[8]), and B4633-03 (G12P[8]) and old prototype strains (KU and Wa) clustered in the same lineages of VP1, VP2, VP3, NSP2 and NSP4 genes however, grouped separately in VP6, NSP1 and NSP5 genes with 10–11%, 15.6–16.7% and 6.3–7.5% nucleotide sequence divergence, respectively. These results suggest that the rotavirus VP6, NSP1 and NSP5 genes of Wa-like rotaviruses are more prone to temporal mutations. Both structural and nonstructural genes of the Western Indian rotavirus strains shared nucleotide and amino acid substitutions with the Bangladeshi strain, Dhaka16-03 (G1P[8]) in the year 2003. This study documents for the first time the phylogenetic and evolutionary relationships of Indian G1P[8] rotavirus strains with the rotavirus strains from other parts of world and provides data useful for the evaluation of rotavirus vaccine programs.