Bengaluru: Ecologist Farah Ishtiaq knows that the sewage in Bengaluru, India’s Silicon Valley, holds secrets. That’s why, every day, she wades through endless reports and graphs on the city’s detritus. The data she gathers are key to knowing how the SARS-CoV-2 virus travels, and Ishtiaq’s team at the Tata Institute for Genetics and Society are tracking the virus’ movement through the city’s underbelly.
Although most Indians are now immune to Covid — naturally or due to the vaccine — the virus hasn’t been completely tamed. It still can potentially mutate into a new worrying variant.
Such surveillance data can predict the spread of Covid—the clues appear relatively early in wastewater because infected people excrete the virus even before they test positive for it.
The authorities don’t want to be caught unawares again, which is why Ishtiaq is preparing the report that she presents to the Bengaluru civic body Bruhat Bengaluru Mahanagara Palike (BBMP) every week.
This wastewater-based epidemiology (WBE) project has attracted researchers, ecologists, virologists, and water experts in Bengaluru, including Uma Ramakrishnan, a molecular ecologist at the National Centre for Biological Sciences (NCBS), S. Vishwanath, an authority on the waterways in Bengaluru and founder of Biome Solutions, as well as civic officials at the Bangalore Water Supply and Sewerage Board (BWSSB), among others.
Through joint and independent testing, they are monitoring the city’s wastewater and combining the data for the authorities to understand the big picture about how the virus is spreading and mutating in the country.
This WBE project has also been adopted as a pilot for Bengaluru’s One Health initiative, conceived as a Science & Technology (S&T) Cluster and funded by the Principal Scientific Advisor’s office. It aims to find solutions for public health challenges such as tracking infectious diseases, biodiversity loss, and food insecurity.
This month, this One Health pilot WBE project published a study on the data obtained by testing wastewater samples from 28 sewage treatment plants (STPs) in Bengaluru. They found that wastewater data is consistent with clinical data that followed after a lag—like a crystal ball demonstrating advance warning of new waves.
“Before [the] Omicron [variant] came, we could see that the viral load was going up,” says Ishtiaq. “We saw it literally 10 days before South Africa announced their Omicron wave.”
Spurred on by the promising results and seeing the technique’s success in the Netherlands in detecting Covid in advance, the team wants to expand WBE to track other kinds of diseases. Active work is already underway with dengue.
“It has been a good monitoring tool for us, and we are trying to see if other diseases can be covered. In fact, we have set up a One Health cell in BBMP,” says Dr Thrilok Chandra, special commissioner (health) at the civic body.
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A growing team
Cartoons of colourful birds adorn the walls in Ishtiaq’s office — a reminder of her previous research at Bengaluru’s Indian Institute of Science (IISc) where she spent several years studying the transmission of malaria by birds in Asia. She joined TIGS in 2019 to explore new technologies for malaria eradication.
TIGS constitutes one of the four institutes that make up the Bangalore Life Sciences Cluster — Tata Institute of Fundamental Research’s National Centre for Biological Sciences (NCBS), Institute for Stem Cell Science and Regenerative Medicine (InStem), and Department of Biotechnology’s Centre for Cellular and Molecular Platforms (C-CAMP) — all of which are situated inside the sprawling campus of the University of Agricultural Sciences (GKVK).
Ishtiaq had been wanting to change the focus of her research when the pandemic struck in 2020. As doctors, scientists, and governments around the world scrambled to find information, reports of wastewater-based epidemiology started trickling in. And serendipitously, just before India’s deadly second wave in 2021, TIGS changed its mandate to focus on infectious diseases.
Ishtiaq then decided to start a wastewater-based epidemiology project in Bengaluru. Large amounts of treated wastewater go from the city to nearby districts for irrigation purposes.
Uma Ramakrishnan of NCBS, too, had read about the Netherlands’ success with wastewater monitoring. And more importantly, she knew the importance of faecal matter analysis. While researching tigers in the past, she had studied and genetically sequenced their stool samples to learn more about their lives. In late 2020, Ramakrishnan brought S. Vishwanath and Ishtiaq together to work on wastewater monitoring. It helped that Ishtiaq was equipped with a grant to conduct infectious disease monitoring.
With the help of Vishwanath, who is a member of the BWSSB technical committee, the team pushed the idea within the sewage authority and was met with enthusiasm.
The team facilitated the signing of a memorandum of understanding between NCBS and BWSSB in early 2021, which allowed them to access samples from some sewage treatment plants (STPs) on a weekly (or as frequently as necessary) basis. This project then became a part of the One Health initiative, and operates out of the Bengaluru Science & Technology (BeST) centre at IISc.
Three months after the MoU was signed, wastewater testing began.
Wading through waste
The WBE team monitors wastewater at a molecular level to detect particles of RNA from the virus.
“We started with the watersheds at Yelahanka and Allasandra, which are located close to NCBS,” says Ramakrishnan. Water from these locations was sampled every two weeks for three months starting March 2021. “We decided to do it throughout the city and set about sampling them once in 10 days, and then subsequently once a week or so,” she adds.
Bengaluru runs a massive wastewater treatment programme, and the treated wastewater is pumped into neighbouring Kolar (139 lakes) and Chikballapur (70 lakes) districts. This water is rich in nutrients and can provide energy through anaerobic reactions that produce methane. It essentially functions like a “barometer and thermometer for the city’s health”, according to Vishwanath.
In the initial stages of their research, the 3,600 decentralised wastewater treatment plants spread out in the city were of particular concern. These plants are managed by apartment complexes.
Additionally, about 20 per cent of wastewater from the city ends up in open drains. Forty-six of those are tracked by Varsha Sridhar, CEO and co-founder of Molecular Solutions. “When the Netherlands findings showed that sewage data could predict Covid four days before people reported symptoms, it was clear that this could potentially be an early warning, a surveillance tool,” says Sridhar. She is also part of Precision Health, an environment surveillance platform that has been independently monitoring wastewater in Bengaluru.
“In May 2020, I just went to the drain behind my house and collected a sample,” she says. “At the time, there weren’t many cases in my part of town, but I was shocked to see the amount of viral RNA material in the sample.”
Apart from these two, there are also other independent projects that are performing wastewater-based epidemiology such as the Infectious Disease Research Foundation (IDFR).
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Collection and testing
To obtain viral fragments from sewage, the sewage board authorised a person to collect samples from the inlets of some of the 28 STPs with unique inlets in the city. These samples were taken to TIGS directly to Ishtiaq’s lab in 200ml bottles placed in cool boxes because RNA is prone to easy degradation.
Sewage samples carry infectious pathogens, so only Biosafety Level-2 labs are authorised to work with them. In such labs, various physical and chemical procedures are performed to concentrate viral particles and extract their RNA.
The samples are then sent to the labs where Ishtiaq works with her students.
“These are PCR machines,” says Ishtiaq, casually pointing to devices that resemble large printers. Students feed RNA samples into the machines, analyse them for the density of particles, and sequence them.
Ishtiaq’s lab collects data on the different variants and mutations, which are then uploaded to the global sequence database GISAID. Her team is then able to identify where cases are spreading, where new mutations are occurring, whether immune evasive variants are evolving, and so on.
“Farah was able to predict 10 to 14 days in advance which strain was emerging in which area,” says Vishwanath.
All hands on board
Building a comprehensive understanding of Covid spread is the first step, but just the data isn’t enough. Civic authorities need to act on it too.
When Ishtiaq took her analysis to the municipal corporation, officials were immediately interested. Since then, she has held weekly meetings to brief them about the status of viruses found in ward-wise wastewater and locations.
The granularity of data helps the BBMP prepare for resource allocation, should the need arise.
“BBMP integrated our data in its Covid war room,” says Sridhar, recalling mid-2021. “We [Precision Health Alliance] also joined forces in late 2021 [with Ishtiaq and Ramakrishnan] and decided to have a single dashboard that incorporated STP and open drain data and provide information from that to BBMP.”
“Work like this requires multidisciplinary and multi-institutional partnerships,” says Vishwanath. “We’re crafting that base now with a focus on building trust and scaling at the ward level.”
Others in the city and the consortium are doing the same.
The next step is to get all sorts of environmental surveillance experts on board. “There is no point to everybody working at cross purposes,” Ramakrishnan says.
Ishtiaq, Ramakrishnan, and Vishwanath’s team also recently published a paper with all their findings on SARS-CoV-2 surveillance and infection dynamics.
“Over the past 15 months, the data has been shifted from macro-level to micro-level with more details to gain a better understanding of the viral spread at a ward level,” says BBMP’s Chandra. “This data helps us with environmental surveillance, public health, and clinical monitoring.”
There are more who are scouring Bengaluru’s sewage. City-based non-profit Infectious Disease Research Foundation (IDRF) is also working on testing wastewater from airports and hospitals. Their team is working on the samples in its BSL-2 lab independent of the One Health consortium.
“We are able to capture raw sewage from apartment buildings and institutions that have their own STPs,” explains Chitra Pattabiraman, virologist and founder of IDRF. “We know the catchment area (sources of wastewater) for each of them, and when such granular data can be obtained, everyone should be able to know what is circulating around them so they can take appropriate precautions.”
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Future of environmental surveillance
One Health hopes to scale up wastewater monitoring to track more infectious diseases as well as keep an eye on Covid patterns and SARS-CoV-2 virus mutations. Ishtiaq and her team continue to track variants and upload sequences on GISAID, as does IDRF.
“This process should be embedded in the institutional system such that this kind of environment monitoring becomes routine,” says Vishwanath. When diseases such as dengue peak, such monitoring can be expanded.
WBE is not a new idea; countries all over the world, including India, have conducted environmental surveillance in the past, especially through wastewater sampling, for diseases such as cholera and polio.
Today, WBE is being conducted internationally in many countries such as the Netherlands, Finland, US, South Africa, and Ghana, and in Hyderabad, Pune, and Mumbai’s Dharavi in India.
The One Health consortium also plans to track antibiotic resistance, mosquito-borne diseases, and other illnesses carried by other vectors such as ticks as well as diseases reported by the Integrated Disease Surveillance Project (IDSP).
Currently, such projects are academic in nature, with only researchers (mostly ecologists) sampling and obtaining data. But the team hopes this scales up into a large centralised model or be outsourced to other entities for testing through the year.
“We’ve seen this happen already with Covid,” explains Ramakrishnan. “Before the pandemic began, there were only one or two labs in India that could test for the virus. Now, such labs are everywhere and Covid testing is routine.”
With the enthusiasm from Bengaluru’s civic bodies and the reliability of data, there is increasing interest and investment in WBE, say the scientists.
“When we put our hearts and souls into something, we can do really good stuff,” says Ishtiaq.
(Edited by Humra Laeeq)