Seasonal dynamics and genetic diversity of non-polio enteroviruses in hospitalized children with acute gastroenteritis in Pune, India

Abstract

Acute gastroenteritis (AGE) in children is primarily associated with pathogens such as Human Rotavirus A (HRVA), Human norovirus (HNoV), Human adenovirus (HAdV), Human astrovirus (HAstV), Human parechovirus (HPeV) and increasingly, Human enteroviruses (EVs). EVs are non-enveloped RNA viruses belonging to the Picornaviridae family, comprising over 100 subtypes classified into four species. Despite their clinical relevance, the prevalence of EVs in AGE remains underexplored in India, resulting in limited data on their epidemiology and molecular diversity. A total of 450 stool samples were collected from hospitalized children under five years of age with AGE in Pune, India, between 2017 and 2023. Molecular characterization was subsequently performed to identify and confirm the types of EVs present. EVs were detected in 11.3% (51/450) of AGE cases. HRVA remained the most frequently detected pathogen overall. Among EV-positive cases, 58.8% were viral mono-infections, while 41.2% occurred as co-infections with other enteric viruses. EVs detection was highest in children below two years of age and occurred year-round, with a marked increase during the monsoon months. Molecular characterization identified 16 distinct EVs genotypes among 28 genotyped samples, predominantly belonging to EV-B species, followed by EV-A and EV-C. Phylogenetic analysis demonstrated clustering with contemporary global strains, indicating sustained circulation and genetic diversity. Replication-competent EVs were successfully isolated from representative samples, confirming the presence of viable viruses in clinical specimens. Although rotavirus remained the predominant viral pathogen associated with pediatric AGE, EVs were consistently detected across multiple years and age groups, either as viral mono-infections or in combination with other enteric viruses. These findings suggest that non-polio EVs may contribute to the viral etiology of pediatric gastroenteritis, although their precise etiological role requires further investigation. Continued molecular surveillance and broader diagnostic approaches may help clarify their epidemiological relevance and contribution to gastroenteritis in settings with high disease burden.