Genomic surveillance of SARS-CoV-2 from community and hospital wastewater treatment plants in Udupi

Title of the project: Genomic surveillance of SARS-CoV-2 from community and hospital wastewater treatment plants in Udupi

Duration: 2022-23

Funds/Grant name: Science and Engineering Research Board (SERB)

Brief description of the project:


Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) has caused a global catastrophe worldwide. For timely monitoring and effective control of outbreak's wastewater-based SARS-CoV-2 surveillance strategy has been implemented in many countries. SARS-CoV-2 is primarily transmitted through small respiratory droplets; however, recent studies have reported the presence of live virus and shedding through faeces and urine. Faeces and urine from COVID-19-infected patients discharged into sewer systems and subsequently into wastewater treatment systems are considered the primary means for SARS-CoV-2 transmission in water and wastewater. Another mode is through used face masks that are disposed of without disinfection into surface water or sewers.


The proposed study is under Science and Engineering Research Board (SERB), planned in four Wastewater Treatment Plants (WWTPs) of Udupi district, Karnataka. Udupi is situated in a coastal region with a population of about 11.7 lakhs. During the 1 year of project duration, a total of 1000 inlet samples will be collected from the 4 WTTP. Collected samples will be transported to the Manipal Institute of Virology (MIV). MIV has a Biosafety level-2 (BSL-2) laboratory that adheres strictly to the biosafety guidelines. Collected WWTPs samples will be processed and tested for SARS-CoV-2. Samples positive for SARS-CoV-2 in real-time RT-PCR will be further subjected to whole genome sequencing (WGS). WGS data will be subjected to further analysis in comparison to reference strains to determine mutant residues and identify variants


Wastewater-based epidemiological (WBE) study will provide insights about the application of WBE of SARS-CoV-2 as a complementary approach for effective COVID-19 surveillance in India. It might serve as a promising approach to detect early warning of COVID-19 outbreaks and provide evidence for public health policymakers to allocate resources and plan large-scale environmental surveillance studies in multiple states. Wastewater-based genomic surveillance might also be a potential tool for monitoring circulating variants of SARS-CoV-2. Assessing the population's immunity to emerging SARS-CoV-2 variants may help design better vaccines and drugs. Since about 40% of COVID-19 patients are asymptomatic, continuous environmental surveillance might be the only feasible way to detect transmission in the community in future.