Diversity of rotavirus genotypes circulating in children < 5 years of age hospitalized for acute gastroenteritis in India from 2005 to 2016: analysis of temporal and regional genotype variation

BMC Infect Dis. 2020 Oct 9;20(1):740. doi: 10.1186/s12879-020-05448-y.


Background: From 2016, the Government of India introduced the oral rotavirus vaccine into the national immunization schedule. Currently, two indigenously developed vaccines (ROTAVAC, Bharat Biotech; ROTASIIL, Serum Institute of India) are included in the Indian immunization program. We report the rotavirus disease burden and the diversity of rotavirus genotypes from 2005 to 2016 in a multi-centric surveillance study before the introduction of vaccines.

Methods: A total of 29,561 stool samples collected from 2005 to 2016 (7 sites during 2005-2009, 3 sites from 2009 to 2012, and 28 sites during 2012-2016) were included in the analysis. Stools were tested for rotavirus antigen using enzyme immunoassay (EIA). Genotyping was performed on 65.8% of the EIA positive samples using reverse transcription- polymerase chain reaction (RT-PCR) to identify the G (VP7) and P (VP4) types. Multinomial logistic regression was used to quantify the odds of detecting genotypes across the surveillance period and in particular age groups.

Results: Of the 29,561 samples tested, 10,959 (37.1%) were positive for rotavirus. There was a peak in rotavirus positivity during December to February across all sites. Of the 7215 genotyped samples, G1P[8] (38.7%) was the most common, followed by G2P[4] (12.3%), G9P[4] (5.8%), G12P[6] (4.2%), G9P[8] (4%), and G12P[8] (2.4%). Globally, G9P[4] and G12P[6] are less common genotypes, although these genotypes have been reported from India and few other countries. There was a variation in the geographic and temporal distribution of genotypes, and the emergence or re-emergence of new genotypes such as G3P[8] was seen. Over the surveillance period, there was a decline in the proportion of G2P[4], and an increase in the proportion of G9P[4]. A higher proportion of mixed and partially typed/untyped samples was also seen more in the age group 0-11 months.

Conclusions: This 11 years surveillance highlights the high burden of severe rotavirus gastroenteritis in Indian children < 5 years of age before inclusion of rotavirus vaccines in the national programme. Regional variations in rotavirus epidemiology were seen, including the emergence of G3P[8] in the latter part of the surveillance. Having pre-introduction data is important to track changing epidemiology of rotaviruses, particularly following vaccine introduction.

Keywords: Diarrhoea; Enzyme immunoassay; Gastroenteritis; Genotypes; India; Polymerase chain reaction; Rotavirus.

Publication types

  • Multicenter Study

MeSH terms

  • Acute Disease
  • Antigens, Viral / immunology
  • Child, Preschool
  • Feces / virology
  • Female
  • Gastroenteritis / epidemiology*
  • Gastroenteritis / prevention & control
  • Gastroenteritis / virology
  • Genotype*
  • Genotyping Techniques
  • Hospitalization*
  • Humans
  • Immunization Programs
  • Immunization Schedule
  • Immunoenzyme Techniques
  • India / epidemiology
  • Infant
  • Infant, Newborn
  • Male
  • Prevalence
  • Reverse Transcriptase Polymerase Chain Reaction
  • Rotavirus / genetics*
  • Rotavirus / immunology
  • Rotavirus Infections / epidemiology*
  • Rotavirus Infections / prevention & control
  • Rotavirus Infections / virology
  • Rotavirus Vaccines / immunology


  • Antigens, Viral
  • Rotavirus Vaccines