National Journal of Laboratory Medicine (Jan 2020)
Predominance of G12 Genotype in Rotavirus Strains Causing Diarrhoea in Hospitalised Children of a Tertiary Care Centre in Lucknow, Uttar Pradesh, India
Introduction: Currently available vaccines for rotavirus are based on the common genotypes of neutralisation antigens Viral Protein 7 (VP7) and Viral Protein 4 (VP4). Prevalence of uncommon genotypes may result in lower immune response due to homotypic immunity. Aim: To ascertain the genotypes of VP7 and VP4 in rotavirus strains causing diarrhoea in northern India. Materials and Methods: The cross-sectional study was conducted from January 2010 to June 2012 at a tertiary care centre in Lucknow, Uttar Pradesh, India. Consecutive stool samples from children under the age of five years hospitalised for acute dehydrating diarrhoea were screened for rotavirus antigen by Enzyme Linked Imunosorbent Assay (ELISA). VP7 and VP4 genes were amplified by Reverse Transcriptase Polymerase Chain Reaction (RT-PCR), sequenced (Big-Dye terminator kit using 3130 ABI, Genetic analyser) and genotyped by Rota C software. Molecular Evolutionary Genetics Analysis (MEGA) 5.05 Software was used for phylogenetic analysis. Results: Of the 260 samples, 58 (22.3%) samples were positive by ELISA. Thus the prevalence of rotavirus infection was 22.3% [95% CI (27.59-17.41)]. Out of these VP7 gene was amplified by RT-PCR from 35 strains of which 32 amplicons were sequenced. Total 14 (43.7%) strains belonged to genotype G12, 3 (9.3%) strains to genotype G9, 7 (21.8 %) to genotype G2 and 8 (25%) were G1. Of the 18 VP4 genes sequenced 7 (38.8%), 6 (33.3%) and 5 (27.7%) strains were genotype P(4), P(6) and P(8) respectively. Conclusion: Prevalence of rotavirus diarrhoea was 22.3%. Presence of G12 an emerging genotype was the most common VP7 genotype and a rare reassortment strain G9 P(4) was the most significant finding. As G12 genotype is not present in the current vaccines, it could be included in future versions to improve effectiveness.