Epidemiology and Surveillance of Influenza, RSV and SARS-CoV-2 in Children Admitted with Severe Acute Respiratory Infection in West Bengal, India from 2022-2023

Background Evaluating the burden of respiratory syncytial virus (RSV) and influenza among young children in LMICs is crucial, given the importance of maternal influenza and RSV vaccination which may not yet be widely available. This study established a one-year surveillance of severe acute respiratory infection (SARI) from June 2022-2023 in hospitalized children 1-24 months from rural West Bengal India. Methods We tested nasopharyngeal swabs collected from children admitted with SARI using multiplex real-time PCR for influenza, RSV, SARS-CoV-2, with a subset (N=81) tested for additional respiratory pathogens and analyzed clinical features, virus seasonality, factors influencing infections, and hospitalization duration. Results Of 1842 children admitted with SARI, 77% (1419) were between 1-24 months. Of 191 sampled, 21 required intensive care, and 3 died. Infants under 6 months more frequently required referrals and oxygen support (p=0.02). The majority of mothers (83.7%) were vaccinated against COVID-19, but none against influenza, pertussis, or RSV. Viruses were detected in 44% (84/191), with RSV being the most common 60/190 (31.6%), followed by influenza 16/190 (8.4%), and SARS-CoV-2 2/191 (1%). Influenza subtypes included influenza A/H3 (6/16), A/H1N1pdm (5/16), Influenza B (4/16), and Influenza C (1/16). RSV peaked during autumn, influenza during winter and monsoon. Influenza was more common in infants <6 months (13.4%, p=0.03). RSV affected both infants under 6 months and over similarly (34% vs 29.6%, p=0.5). RSV infection was associated with 19% of ICU admissions and influenza with 14%. Additional pathogens included Haemophilus influenzae (23.45%), Streptococcus pneumoniae (22%), rhinovirus (13.6%), Staphylococcus aureus (8.6%), Moraxella catarrhalis (5%), bocavirus (3.7%), adenovirus (3.7%), parainfluenza virus [PIV-1 (2.47%); PIV-3, (2.47%); PIV-2, (1.2%)], Chlamydia pneumoniae (1%), Acinetobacter baumannii (1%), Bordetella (1%) and enterovirus (1%). Viral-bacterial co-detection occurred in 34%, especially in infants <6 months. RSV was commonly co-detected with S. pneumoniae and H. influenzae . Rhinovirus cases were associated with ICU admission, mechanical ventilation, and longer length of stay. Conclusion High SARI levels were observed in children under two, with RSV and influenza being key contributors. Findings highlight the need for diagnostics to guide vaccination, reduce antibiotic use, and improve indoor air quality for alleviating the SARI burden in rural settings.