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
Authors: Giri Sidhartha , Kumar C. P. Girish , Khakha Shainey Alokit , Chawla-Sarkar Mamta , Gopalkrishna Varanasi , Chitambar Shobha D. , Ray Pratima , Venkatasubramanian S. , Borkakoty Biswa Jyoti , Roy Subarna , Bhat Jyothi , Dwibedi Bhagirathi , Das Pradeep , Paluru Vijayachari , Ramani Sasirekha , Babji Sudhir , Arora Rashmi , Mehendale Sanjay M. , Gupte Mohan D. , Kang Gagandeep ,   National Rotavirus Surveillance Network investigators, Agarwal A. , Aneja S. , Simon Anna , Aundhakar S. C. , Bavdekar A. , Baveja S. , Biswas D. , Bora C. J. , Chatterjee S. , Chaudhary S. , VNR Das , Desai K. , Dhongade R. , Dwivedi R. , Dzuvichu K. , Ganguly N. , Gathwala G. , Ghosh C. , Gupta D. S. , Jadhav A. R. , Jali S. , Kalrao V. R. , Kar S. K. , Khuntia H. K. , Kumar P. , Kumar S. S. , Lal B. G. , Manglani M. , Manohar B. , Mathew A. , Mathew M. A. , Mehariya K. M. , Mishra S. K. , Panda S. , Pandey K. , Patankar M. , Purani C. S. , Sahoo G. C. , Singh N. , Singh P. , Singh T. , Sundari S. , Thakur A. K. , Topno R. K. , Upadhyay A. , Singh Utpalkant 
Published: October 2020

Abstract
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.