Waste water sequencing analysis picked up key mutations of SARS-CoV-2: Study

The study provides evidence on how waste water sequencing identified mutations, and shows variants in circulation before being observed through clinical data.

Written by Anuradha Mascarenhas

Pune | Updated: June 11, 2021 10:25 AM IST

4 min read

These mutations were absent in samples collected from December 2020 to February 2021. (AP Photo/Representational)

A STUDY in Pune’s open wast water drains from December 2020 to March 2021 has not only been able to assess the presence of SARS-CoV-2 nucleic acid, but also picked up key mutations circulating in the community. The study provides evidence on how waste water sequencing identified mutations, and shows variants in circulation before being observed through clinical data.

Waste water sequencing analysis revealed mutations L452R and E484Q associated with B.1.617 lineage in samples collected during March. These mutations were absent in samples collected from December 2020 to February 2021.

“The study is significant as it is a first-of-its-kind in the country to test capability of waste water sequencing data to provide mutations in circulation before they are observed clinically. Through waste water epidemiology, we could identify mutations associated with SARS-CoV-2, and that can function as an early warning indicator system,” said Tanmay Dharmadhikari, Vinay Rajput and others from researchers from CSIR-NCL. The study was supported by funding from Science Engineering and Research Board (GoI), New Delhi, to researchers of CSIR-NCL.

In their paper ‘High throughput sequencing based detection of SARS-CoV-2 prevailing in waste water of Pune, West India’ posted as a preprint on medRxiV ( a non peer-reviewed platform) on June 9, scientists have said the tracking of genomic variants from waste water was essential to understand the spread. These findings will soon be communicated to a peer-reviewed journal.

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The Indian Express on June 8 reported that a team of scientists from CSIR-National Chemical Laboratory had made an official presentation to Deputy Chief Minister Ajit Pawar on their pilot study that was able to detect the presence of SARS-CoV-2 RNA in sewage samples. Pune Municipal Commissioner Vikram Kumar had also indicated that they would continue the project for another year in anticipation of future waves of the Covid-19 pandemic. The funding for another year has been sanctioned as part of the CSIR project.

The study found all the waste water samples collected between December 2020 and March 2021 were positive for SARS-CoV-2 nucleic acid fragments. The analysis showed several mutations in multiple genomic regions of SARS-CoV-2 , said Dr Mahesh Dharne, scientist, biochemical sciences division, CSIR-NCL, and project coordinator of the pilot study. The Ecosan Services Foundation, an NGO, partnered in the study

In total, 108 mutations, categorised into 40 types based on nucleotide position, were detected in all samples. Notably, nine mutations in the spike region (L452R, C480R, E484Q, D614G, P681R, N801, D950N, Q1071H, P1140) were observed in this study.

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The study also provided instances where there were four mutations (N801:C480R, NSP14:C279F and NSP3:L550del) obtained from waste water sequenced data, which are either not reported in GISAID (Global Initiative on Sharing All Influenza Data) from India or in case of novel mutation, not across the world.

A novel mutation NSP13:G206F mapping to the NSP13 region was also observed from waste water, the study said.

Regular monitoring of waste water is an essential criterion to observe mutations associated with concerned variants in circulation as the required results can be obtained from a smaller sample volume of wastewater than the more significant number of individuals , Dr Dharne said. The team also comprised Dr Syed Dastager and Dr Sanjay Kamble from NCL who ascertained that for polio and rotavirus tracking, waste water surveillance has been useful in the past.

Dr L S Shashidhara, one of the founders of Pune Knowledge Cluster, said it was an important study. “They have identified a variant at least two months before it was reported to be in patients’ samples. Environmental waste water surveillance is a strategy . It is able to predict ahead of time and tell us if a small surge is happening, which is not yet detected via traditional diagnostic methods so that we are better prepared,” he said.

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Anuradha Mascarenhas

Anuradha Mascarenhas is a Senior Editor at The Indian Express, based in Pune. With a career spanning three decades, she is one of the most respected voices in Indian journalism regarding healthcare, science and environment and research developments. She also takes a keen interest in covering women's issues . Anuradha has won several awards including the Press Council of India's national award for excellence in journalism under the gender based reporting category in 2019 and the Laadli Media award (gender sensitivity -2024). A recipient of the Lokmat journalism award (gender category-2022), she was also shortlisted for the RedInk awards for excellence in journalism-2021. Her debut book At The Wheel Of Research, an exclusive biography of Dr Soumya Swaminathan the inaugural chief scientist of World Health Organisation was also nominated in the Popular Choice Category of JK Paper AUTHER awards. She has also secured competitive fellowships including the Laadli Media Fellowship (2022), the Survivors Against TB – New Research in TB Media Fellowship (2023) and is part of the prestigious 2025 India Cohort of the WomenLift Health Leadership Journey.” Professional Background Education: A gold medalist in Communication and Journalism from Savitribai Phule Pune University and a Master’s degree in Literature. Author: She authored the biography At The Wheel Of Research, which chronicles the life and work of Dr. Soumya Swaminathan, the former Chief Scientist at the WHO. Key Focus: She combines scientific accuracy with storytelling, translating complex medical research into compelling public and human-interest narratives. Recent Notable Articles (Late 2025) 1. Cancer & Specialized Medical Care "Tata Memorial finds way to kill drug-resistant cancer cells" (Nov 26, 2025): Reporting on a breakthrough for triple-negative breast cancer, one of the most aggressive forms of the disease. ``Discipline, diet and purpose; How a 97-year-old professor defies ageing'' (Nov 15, 2025) Report about Prof Gururaj Mutalik, the first Head of Department at Pune's B J Government Medical College who at 97 credits his longevity to healthy habits and a strong sense of purpose. 2. Environmental Health (The "Breathless Pune" Series) "Long-term exposure even to 'moderate' air leads to chronic heart, lung, kidney issues" (Nov 26, 2025): Part of an investigative series highlighting that even "safe" pollution levels are damaging to vital organs. "For every 10 µg/m3 increase in PM2.5 level, there was 6-8% jump in medicine sales" (Nov 23, 2025): Using commercial data to prove the direct link between air quality and respiratory illnesses in Pune. 3. Lifestyle & Wellness News "They didn't let cancer, diabetes and heart disease stop them from travelling" (Dec 22, 2025): A collaborative piece featuring survivors who share practical tips for traveling with chronic conditions. ``At 17, his BP shot up to 200/120 mmHG; Lancet study flags why child and teen hypertension doubled between 2000 and 2020'' (Nov 12,2025)--A report that focusses on 17-year-old-boy's hypertensive crisis and reflects the rising global trend of high blood pressure among children and adolescents. 4. Scientific Recognition & Infrastructure "For promoting sci-comm, gender diversity: IUCAA woman prof highlighted in Nature" (Nov 25, 2025): Covering the global recognition of Indian women scientists in gender studies and physics. ``Pune researchers find a spiral galaxy like the Milky Way from early universe'' (December 3, 2025)- A report on how Indian researchers discovered a massive galaxy that existed when the universe was just 1.5 billion years old , one of the earliest to have been observed so far. Signature Beat: Health, Science & Women in Leadership Anuradha is known for her COVID-19 reportage, where she was one of the first journalists to provide detailed insights into the Covishield and Covaxin trials. She has a dedicated interest in gender diversity in health and science, often profiling women researchers who are breaking the "leaky pipeline" in STEM fields. Her writing style is scrupulous, often featuring interviews with top-tier scientists and health experts from various institutions X (Twitter): @runaanu ... Read More

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