Epidemiological and Full Genomic Analysis of the Sapoviruses Circulating During Post Rotavirus Vaccination Period (2021–2023) in West Bengal, India

During the diarrheal disease surveillance to assess the impact of rotavirus vaccine, re-emergence of sapoviruses was observed in 2021 after a decade of no positive case in West Bengal, India. Sapoviruses are a diverse group of enteric viruses that infect different mammalian species. Thus, the study was undertaken to estimate the prevalence, clinical characteristics, and genetic diversity of the circulating sapoviruses. A total of 1203 stool samples were collected from children (≤ 5 year) with acute gastroenteritis attending both inpatient and outpatient departments of two hospitals in Kolkata, during 2021–2023, were screened for sapovirus using reverse transcription PCR. Full-length genome sequencing of 22 sapovirus positive samples was performed to analyze their genetic diversity. Over 3 years, 1.8% children with acute gastroenteritis had lab confirmed sapovirus infection, with the highest prevalence in 36–60 month age group. Diarrhea, vomiting, and dehydration were common clinical symptoms. Sapovirus infection was identified throughout the year at low frequency. Sequence analysis of sapovirus strains showed co-circulation of three different genogroups (GI, GII and GIV) and seven genotypes (GI.1, GI.2, GI.5, GII.1, GII.6, GII.8 and GIV.1). GI.1 circulated as a major genotype, followed by GIV.1 and GI.2. Phylogenetic and amino acid analysis revealed limited diversity among the circulating GI.1 strains compared to GIV.1 and GI.2 strains. Co-infection of two distinct genogroups (GII.6 and GIV.1) and co-circulation of multiple sapovirus genotypes indicate complex epidemiological landscape in this region which may influence their evolution. Additionally, the study is the first report of whole genomic sequences of sapoviruses from India.