Genetic diversity and prevalence of group A rotavirus infection in children of Imphal, Manipur, India: A hospital-based surveillance study conducted during December 2015 to March 2019

Rotavirus is the most common cause of acute gastroenteritis in infants and children worldwide. The study is hospital-based surveillance of rotavirus diarrhea in children from Imphal, Manipur, India conducted from December 2015 to March 2019. The positivity rate was found to be high ∼69.25% (358/517) and proportion of diarrhea cases and rotavirus diarrhea was peak in winter months and mostly in children from 6 to 24 months. G3 (43%) was the most widely circulating genotype in Imphal followed by G1 (16%), G2 (8%), G9 (5%), G8 (3%), G10 (1%), and G4 (1%), while G12 (0.26%) was rarely detected. Among P-types, P[6] (22%) accounted for the highest prevalence followed by P[8] (11%) and P[4] (4%), P[11] (4%), P[10] (3%), P-type mixed infection 3%, while 53% were untypeable. In G/P combinations, we detected 22 different rotavirus strains at varying frequencies. Globally distributed G3P[8] and G1P[8] strains were observed in the study. G3P[6] emerged as the most predominant rotavirus strain followed by G3P[8], G1P[6], G1P[8], and G9P[6]. The common rotavirus strains distributed across the region namely G3P[8], G1P[8], G2P[4], G9P[4], G1P[4], G1P[6], and G9P[6] were also observed. Interestingly, our study has observed a high percentage of unusual strains namely G9P[4], G1P[11], G2P[11], G3P[10], G3P[11], G4P[11], G9P[10], G9P[11],G10P[6], and G10P[8]. Of note, the high frequency of non-typeable rotavirus P-types (56%) are suggestive of point mutations that might have accumulated in the primer-binding region of VP4 gene. The findings of the present study revealed the hospital-based prevalence of rotavirus disease and the circulating genotypes during the pre-vaccination period and highlights the need for continuous surveillance of rotavirus infection post-rotavac vaccine introduction in the state of Manipur, India. • A hospital-based surveillance of rotavirus-associated acute gastroenteritis in children of Imphal, Manipur, India was conducted during December 2015 to March 2019. • The rotavirus positivity rate was found to be high ∼69.25 % (358/527) in stool samples collected during the study period from December 2015 to March 2019. Rotavirus diarrhea peak in winter months and mostly in children from 6 months to 24 months. • G3 was the most widely circulating genotype (43 %) followed by G1 (16 %), G2 (8 %), G9 (5 %), G8 (3 %) and G10 (1 %), G4 (1 %) while G12 (0.26 %) was rarely detected. • Among P-types, P [6] accounted for highest prevalence (22 %) followed by P [8] (11 %) and P [4] (4 %), P [11] (4 %), P [10] (3 %), P type mix infection 3 % while 53 % were untypeable. • Interestingly, our study has observed a high percentage of unusual strains namely G9P [4], G1P [11], G2P [11], G3P [10], G3P [11], G4P [11], G9P [10], G9P [11], and G10P [6], G10P [8].