Decade-long temporal analyses of circulating rotavirus genotypes during 2008–2017 in Eastern India: Phylodynamics during the pre-vaccination scenario

Abstract

Background: Group-A human rotaviruses (GARV) are among the leading etiological agents causing acute childhood gastroenteritis, worldwide. Despite the significant reduction in global infantile death toll due to rotaviral diarrhea, developing countries like India still contributes substantially to rotavirus-related hospitalization and mortality rates. In on-going hospital based diarrheal-disease surveillance in Kolkata, eastern India (2008–17), GARV was identified as the most common cause of infantile gastroenteritis. The circulating strains were genotyped and phylogenetically analysed to understand their dynamics and evolution prior to the vaccine introduction in eastern India. Methods and materials: Stool samples were screened from children (≤5 years) with diarrhea, seeking health care facilities at two hospitals in Kolkata. Preliminary screening for rotavirus VP6 antigen was done by ELISA. GARV positive samples were genotyped by multiplex semi-nested PCR. DNA sequencing of VP7 (G-type) and VP4 (P-type) gene segments were done followed by phylogenetic analyses by MEGA 7 software. Results: Among 7092 stool samples, 3020 (42.5%) were found to be GARV positive. Children of 6–12 months age group were found most susceptible to infection (57.3%). GARV incidence peaked during the winter months each year (November–February). G1, G2, G3, G9 and G12 in conjunction with P[4], P[6] and P[8] genotypes were seen to co-circulate in the study-population. G1 strains predominated during 2008–10, while G2 and G9 genotypes eventually upsurged during 2011–13. G1 re-established its lead during 2013–15, while polymorphic G3 strains emerged for the first time in eastern India in 2015 and rooted itself as the cardinal strain during 2016–17. All the strains clustered distantly from the vaccine strains in the phylogenetic dendrograms, depicting less genetic relatedness. Differences in amino-acid residues encompassing the antigenic epitopes of VP4 and VP7 capsid proteins between the vaccine and Kolkata strains were observed. Conclusion: GARV shows a tendency towards directional selection under persistent immunological pressure that might promote natural selection of one genotype over another in an endemic setting. These decade-long temporal data during the pre-vaccination period revealed high hospitalization rates, along with dynamic circulation of multiple genotypes in addition to sporadic occurrence of zoonotic strains like G10P[6] and G11P[25].