Epidemiology and genetic diversity of group A rotavirus in acute diarrhea patients in pre-vaccination era in Himachal Pradesh, India

• Published in: Vaccine 2019-08, Vol.37 (36), p.5350-5356
• Main Authors: Gupta, Shipra, Chaudhary, Sanjeev, Bubber, Parvesh, Ray, Pratima
• Format: Article
• Language: English
• Subjects: Age; Antigens; Children; Developing countries; Diarrhea; Epidemiology; Feces; Gastroenteritis; Genetic diversity; Genotype; Genotypes; Heterogeneity; Himachal Pradesh; Immunization; LDCs; Migration; Morbidity; Prevalence; Ribonucleic acid; RNA; RNA-directed DNA polymerase; Rotavac; Rotavirus; Statistical analysis; Strains (organisms); Surveillance; Vaccination; Vaccine; Vaccines; Viruses; Vomiting
• ISSN: 0264-410X; 1873-2518
• DOI: 10.1016/j.vaccine.2019.07.037

•G12P[6] was the most predominant strain detected during the two years study period.•Detection of G12P[6] in high percentage in children was seen first time in India.•Overall, 17 varying G/P combinations and several unusual RV strains were detected.•Genotypes, G3 and P[11] detected for the first time in Himachal Pradesh.•Both long and short RNA migration patterns was observed within G1P[8] rotavirus. Acute gastroenteritis due to Group A rotaviruses remains the leading cause of mortality and morbidity in children in developing countries. India introduced its indigenous rotavirus vaccine Rotavac® in 2016 and Himachal Pradesh (HP) the first state to launch it. The present study aimed to evaluate rotavirus strain diversity associated with AGE prior to vaccine introduction in HP. A total of 331 fecal specimens collected from diarrheic children hospitalized at RPGMC Tanda, HP between July-2014 and June-2016 were screened for RVA by EIA. Rotavirus RNA was extracted by TRIZOL method and analyzed by RNA-PAGE. G/P typing was performed using semi-nested multiplex reverse transcriptase PCR. Rotavirus was detected in 45% (n = 149/331) of diarrheic children, with highest rate observed in the 6–11 months age group (47%). Vomiting was found more frequently associated with RV-infection. Among G-types, G12 was found most prevalent (33.1%) followed by G1 (28.4%), G9 (12.2%), G2 (9.5%), G3 (3.4%) and G10 (2.7%). G4 (0.7%) strains were rarely detected. Among P-types, P[6] was the most prevalent (40.5%) followed by P[8] (29.1%) and P[4] (14.2%). Of note, genotypes G3 and P[11] were detected for the first time in HP. Among G/P combinations, G12P[6] was most prevalent (30.4%) followed by G1P[8] (20.3%), G2P[4] (4.7%), G1P[6] (3.4%) and G3P[8] (2.7%). Interestingly, our study observed high percentage of unusual strains (14.2%) namely G9P[4], G2P[6], G2P[8], G12P[4] and G1P[11]. The regionally common strains G3P[6], G4P[6], G9P[6], G9P[8], G10P[6], G10P[8] and G12P[8] strains were very rarely detected. Of interest, RNA migration pattern of G1P[8] was DS-1 like and genomic heterogeneity was observed within G12P[4] strains with both long and short electropherotypes. Our study highlights rich genetic diversity with emergence of rare rotavirus strains circulating in HP and provides baseline data prior to Rotavac® introduction that will help to gauge the impact of the Rotavac® vaccine in HP.