Post-pandemic surveillance of SARS-CoV-2 in wastewater bodies using integrated molecular analysis

Wastewater-based surveillance (WBS) is increasingly used to monitor the spread of various pathogens, including viruses like SARS-CoV-2, bacteria, and protozoa. This work reports a WBS study for SARS-CoV-2 conducted in Jorhat district of Assam, India. A total of 800 samples were collected from diverse locations, such as hospitals, residential areas, and rivers bodies, in two sessions – a) September 2022 to March 2023, and b) September 2023 to March 2024. The samples were collected from water surface and a layer of depth of 30 cm (transitional) of these wastewater bodies during the rainy season (September & October) and dry season (December till March). Though SARS-CoV-2 positive rate was high during the rainy season, results showed that it was more common in the transitional layer in both wet and dry seasons. Notably, positive samples in the second session were detected only during the rainy season. Furthermore, we identified eight (8) distinct lineages, such as XAA, XAB, XAC, BA.2.38.2, BA.2.66, B, XBB.1, and XAJ and among which XAA, XAB, and XAJ have not been detected in routine epidemiological studies in India. This work demonstrates the effectiveness of WBS in tracking SARS-CoV-2 variants, providing crucial data for public health assessment. The seasonal and regional fluctuations in viral detection draw attention to the need of environmental elements in surveillance efforts. • SARS-CoV-2 positivity rate is higher in rainy season • Higher viral load was found in transitional layers of wastewater bodies • Higher positivity rate found in temperatures ranging: 21–28°C and pH: 7.1–8.0 • Recombinant lineages XAA, XAB, XAJ has been reported for the first time from India