Respiratory virus infection dynamics and genomic surveillance to detect seasonal influenza subtypes in wastewater: a longitudinal study in Bengaluru, India

Recent global pandemics have been caused by respiratory viruses found in both humans and animals with zoonotic spillover potential. Many respiratory viruses, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respiratory syncytial virus (RSV), influenza A virus (IAV), and influenza B virus (IBV), have overlapping ecology and share similar symptoms. However, respiratory disease surveillance is often passive and relies on testing clinical specimens. Wastewater surveillance has been widely used as an epidemiological tool for early detection of SARS-CoV-2 variants and can differentiate between respiratory virus infections and SARS-CoV-2 peaks at a community level. In this retrospective longitudinal study covering three SARS-CoV-2 Omicron waves, we conducted a monthly sampling for 28 months (812 samples) between August 2021 and December 2023 at 28 sewershed sites in Bengaluru city (∼11 million inhabitants). Using RT-qPCR kits, we quantified SARS-CoV-2 RNA concentrations, IAV, IBV and RSV to understand community viral infection occurrences. We provide evidence of changes in the relative abundance of influenza subtypes and SARS-CoV-2 variants driving emerging peaks in wastewater data. We found 86% of samples positive for SARS-CoV-2, while the positivity rates for influenza virus and RSV were lower (37% for IAV, 16 % for IBV, and 15% for RSV). We observed an increase in influenza viruses in the post monsoon season (August to December) and remained present in January and February, while being practically absent the rest of the year. RSV showed a similar trend to IAV, with comparable quantities. Furthermore, we identified all eight segments of influenza virus genomes and emerging SARS-CoV-2 variants in wastewater samples. Wastewater surveillance provides data on the abundance of respiratory viruses in urban Bengaluru that would not be reported otherwise. Under the One Health framework, wastewater surveillance can offer early warning signs and enhance the traceability of infectious diseases in both wildlife and humans.