Wastewater surveillance of open drains for mapping the trajectory and succession of SARS-CoV-2 lineages in 23 class-I 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. Leveraging Wastewater-Based Epidemiology (WBE), our study examined the proliferation, dissemination, and evolution of the virus across urban, suburban, and densely populated regions in Maharashtra state, India. Over the course of 12-months, from June 2022 to May 2023, SARS-CoV-2 RNA was consistently detected in wastewater samples collected from open drains across various regions of the state. Whole genome sequencing revealed the presence of 22 distinct SARS-CoV-2 lineages, with the Omicron variant dominating from July to September 2022, followed by the XBB variant from February to April 2023, along with 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 before clinical reporting, highlighting the potential of WBE for early detection. Our findings underscore the importance of WBE in tracking and managing the spread of COVID-19, especially in areas with limited clinical testing. This study highlights the significance of WBE in global infectious disease surveillance especially under low to middle-income countries (LMICs).