Wastewater surveillance of open drains for mapping the trajectory and succession of SARS-CoV-2 lineages in 23 cities of Maharashtra State (India) during June 2022 to May 2023

Abstract

The timely detection of SARS-CoV-2 is crucial for controlling its spread, especially in areas vulnerable to outbreaks. However, due to a lack of sustainable and low cost methods, early detection of such outbreaks is impacting low to middle-income countries (LMICs). Leveraging Wastewater-Based Epidemiology (WBE), we examined the dissemination and evolution of the SARS CoV2 virus in open drains across urban, suburban and densely populated cities in selected regions in the state of Maharashtra, the third largest state of India. In the period from June 2022 to May 2023, 44.89% of SARS-CoV-2 RNA were positive in RT-qPCR in wastewater samples collected from open drains across selected regions. Whole genome sequencing revealed 22 distinct SARS-CoV-2 lineages, with the Omicron variant, followed by the XBB variant, dominating, alongside other variants such as BF, BQ, CH, and BA.2.86, albeit with lower frequencies. Wastewater surveillance provided early insights into viral transmission, complementing clinical surveillance. Notably, our study detected emerging variants prior to clinical reporting, highlighting the potential of WBE for early detection. Findings underscore the correlation between population density and the trend of viral load. This study also highlighted the significance of using open drains for WBE as a low-cost, and sustainable tool, especially in LMICs, where adequate methods are lacking or difficult to deploy for accessibility.