Wastewater surveillance is the way to catch and counter disease-causing pathogens early and effectively
I n March 2014, the World Health Organization declared India (and Southeast Asia) to be polio-free. So when in June 2022 traces of polio were found in sewage in Howrah in West Bengal, there was understandable panic. The Howrah municipal authorities played it down, saying the traces were from a round of vaccinations and that no polio cases had been reported.
Be that as it may, the incident proved one thing: sewage samples don’t lie (and that they can sometimes be even more reliable than clinical data). The environmental surveillance and disease ecology team at the Tata Institute for Genetics and Society (TIGS) knows this. In August 2020, when the Delta variant of Covid was raging, the team began studying wastewater samples in Bengaluru to assess the viral load of SARS-CoV-2 in various neighbourhoods.
Viruses and bacteria found in the wastewater of a particular area indicate if there is an ailment among people residing there. For instance, in April this year the surveillance team found a peak in Covid cases — the highest ever seen — from wastewater samples. But there were no clinical cases to corroborate this. With widespread vaccination, no one was getting tested anymore, and the virus found in sewage was likely from asymptomatic people.
“Wastewater surveillance becomes even more important when you don’t have much clinical testing,” says principal scientist Farah Ishtiaq, who heads the team. “[The April peak] showed that Covid still exists, even though people were not showing symptoms and therefore not getting tested.”
“Enteric pathogens [which live in the intestines of the host, like the SARS-CoV-2 virus] find their way into wastewater through human faeces,” says senior scientist Shivranjani C Moharir. “We can find these pathogens if we concentrate the wastewater and extract DNA/RNA fragments.”
The TIGS team uses genome sequencing to detect ‘signatures’ of bacteria or viruses present in the sample. It has also come up with a mathematical formula to calculate exactly how many people in a particular neighbourhood have been affected.
This is helpful in several ways. First, it shows the efficacy of any preventive measures taken. For example, the large presence of Covid in April — without corroborative evidence from clinics — revealed that the majority of the populace had been vaccinated and had, consequently, become asymptomatic.
“Another advantage is that we can detect variants of a particular disease from wastewater samples,” says Ms Ishtiaq. “During Covid, while Delta and Omicron 2 cases were being tested by clinics, our wastewater tests also showed the presence of Omicron 2.1, even though no clinical cases of this were reported.”
Today, if there is a fresh disease outbreak in, say, China, South Africa or the United States, the surveillance team will know from wastewater samples if the new variant has reached India. Which brings us to the most important advantage: with sufficient data points and the use of predictive AI tools, the team can also project what is going to happen.
“You can develop an early-warning system based on wastewater samples, and alert municipal authorities if there is another pandemic around the corner,” says scientist Sanjay Lamba, who has devised the mathematical tools for the process. “With sewage samples, our system enables us to detect a possible outbreak at least 14 days before clinical cases begin to be reported. With samples from open drains, we can detect it seven days earlier.”
In Bengaluru, the surveillance team collects and studies samples from 28 sewage treatment plants that cover about 80% of the wastewater generated by the city. Working closely with the city’s municipal body, the team reports back every week with its findings. TIGS is doing a similar exercise in Hyderabad, where it is collecting and examining wastewater from open drains (there is a 15% margin of error here since samples tend to get contaminated more easily or diluted during rainy days).
The TIGS team can, additionally, provide microlevel data. Based on calculations, its scientists can share the ward-wise prevalence of an ailment, identify hotspots and see where the spike in the viral load is. Whether it is 7 days or 14, this provides enough of a head start for civic and healthcare authorities to take necessary measures.
And they do. After initial hesitation about the data shared by TIGS, the Bengaluru municipal authorities have come around and even provided the team with a list of 12 other pathogens to look for in the wastewater. TIGS is also working with the National Institute of Veterinary Epidemiology and Disease Informatics to study
The team visits cattle fairs across Karnataka to collect samples to identify ailments like blue tongue and tuberculosis in cows. “We are trying to set up protocols to detect other pathogens present in wastewater, as well as the anti-microbial resistance [AMR] of these pathogens,” adds Ms Moharir.
The team has, from wastewater, found AMR signatures in the genes of pathogens causing malaria, hepatitis, rotavirus and such. This indicates an overuse of antibiotics, both in humans and animals, leading to the genes becoming resistant to regular lines of treatment. Over time, the usual medicines will stop working and clinicians will be forced to prescribe stronger and stronger alternatives.
When a wastewater sample shows substantial AMR signatures, it means that an entire neighbourhood or community has developed antibiotic resistance. Informed civic authorities and healthcare professionals can act accordingly and start scaling back on antibiotic recommendations.
“There is no healthcare body recording this kind of information, so it’s important to put things in perspective,” says Ms Ishtiaq. “Our data can tell municipal authorities what infections are dominant in the population and where they should focus their efforts.”
The TIGS team is now looking at air surveillance. This, too, started with Covid, which was initially thought to be transmitted through surface contact and droplets before being found to be airborne. “We wanted to explore if it was indeed airborne, and we collected air samples from hospitals, Covid wards and even patients’ homes,” says Ms Moharir. “For air surveillance, we have standardised certain parameters in terms of air flow rate, how much volume of air to collect, for how long, etc.”
There are two approaches in the process. First, the metagenomics approach, by which one has to DNA sequence everything, see what signatures can be found in the air and then look for specific pathogens. The second is to directly look for the pathogens (like tuberculosis in a hospital ward), or look for diseases that are not known to spread through the air but may well could.
The objective with wastewater surveillance and air surveillance is the same: to provide early warnings to authorities so that outbreaks can be prevented or minimised.