India’s sewage surveillance for SARS-CoV-2 going down the drain

Manupati Hemalatha has been testing water samples from Hyderabad’s sewage treatment plants, drains and lakes to look for viral remains of SARS-CoV-2 that infected people pass out in their faeces. Since July 2020, her lab at the CSIR-Indian Institute of Chemical Technology (IICT) is surveying the spread of the virus in the south Indian city, home to nearly 10 million people.

At daybreak, Hemalatha and her co-researchers drive through a locked-down city to reach the treatment plants, donning protective overalls, gloves and N95 masks. They collect wastewater in sterilised bottles. “Initially, it was quite adventurous, even scary, when we didn’t know if we could get infected through aerosols or the viral remnants,” she says.

In January 2021 the PhD student, part of a team of scientists led by IICT’s S Venkata Mohan, published results from these early samples. They found that around 6% of the city’s population was shedding the virus in their faeces¹ – a figure that later loosely matched the trend of regional viral infection reported in official figures,

“It is quite possible to get an early warning through these viral RNA copies obtained from wastewater,” says environmental engineer Venkata Mohan. Symptoms of SARS-CoV-2 infection could take about 2 weeks to show up. In many, there are no symptoms at all. However, people start shedding the virus in their faeces from the first day of infection. So, by simply detecting the viral genome load in sewage water reaching the treatment plants weeks beforehand, scientists are able to predict with a fair degree of accuracy the number of future infections for a region, he says.

Collaborating with the city-based CSIR-Centre for Cellular and Molecular Biology (CCMB), Venkata Mohan’s team analysed samples from all the major sewage treatment plants in Hyderabad and detected the viral genome using the standard Reverse Transcription Polymerase Chain Reaction (RT-PCR) method.

“Interestingly, the samples that came to the treatment plants were positive for SARS-CoV-2, while the ones that went out of the plants were negative, showing that the treatment efficiently eliminates viral particles,” he says. They calculated viral gene copies seen per litre of water and from that estimated viral particle shedding per individual in the regions they sampled. This gave them an idea of the number of people exposed to SARS-CoV-2.

Hemalatha and her colleagues slowly replaced their cumbersome overalls with simple aprons, after studies established² that the live virus cannot be transmitted through sewage. “It was a relief to get confirmation that the SARS-CoV-2 remnants in wastewater are non-infectious,” she says of the evolving evidence around the new virus.

Venkata Mohan’s team is now collaborating with other scientists to establish a protocol for nation-wide wastewater epidemiology, an arm of surveillance grossly underutilised in India’s COVID-19 fight.

Globally, more than 200 projects are now tracking virus particles and viral fragments in faeces. Countries have successfully used this method to monitor illicit drug abuse and detect stress biomarkers or viruses like poliovirus and norovirus circulating in communities. In Brazil, infection hotspots of COVID-19 were studied retrospectively by testing sewage water³. In the US, a National Wastewater Surveillance System is part of pandemic tracking. Other countries leading the trend are Australia, Netherlands and Spain.

“Indeed sewage surveillance helps spot the emergence of new disease outbreaks in real time from population pooled wastewater,” says Sudipti Arora, an environmental scientist at the Dr. B. Lal Institute of Biotechnology in Jaipur, India.

India lags behind

Though the awareness around waste-water-based epidemiology (WBE) among scientists working in the field has grown during COVID-19, the discipline itself is not yet an established one in India, Arora says.

There are several reasons for this, she says, especially the lack of awareness about the field among public health officials, the government and municipal corporations.

“The Indian sewerage system is fragmented unlike western countries, and testing could be incredibly challenging,” she says. India’s sewage network is only about 33% connected. Of the rest, only 38% use septic tanks. “How does one capture these disconnected areas, especially when trying to detect a hotspot?” she asks. Surveying ‘unsewered’ networks such as open drains, nullahs, informal settlements in rural & urban areas, and catchments independently could help bridge this gap.

But a thickly populated country like India needs this arm of epidemiology the most, says Manish Kumar, an assistant professor of earth sciences at the Indian Institute of Technology, Gandhinagar. Kumar, who has been leading a team testing wastewater samples in the state of Gujarat, says their results could provide early warning of outbreaks, spikes and waves of a pandemic.

“A pandemic can be better managed by zoning cities or regions and identifying infection hotspots,” he says. Scientists can also look at ambient water to gauge the rise of antibodies (IgG) in response to vaccination or natural immunity after recovery from the COVID-19 infection.

Arora says another bottleneck that scientists are facing in India is corroborating sampled data with government figures since granular, regional-level infection data is difficult to get. Plotting trends of infection with sewerage data could complement public surveillance data. Venkata Mohan echoes this saying they found no regional level seroprevalence data to correlate their findings with.

India may be losing out on a never-before opportunity to record data at this scale, Kumar says. “There is a wrong notion that we are already in a mess and so no early warning advantage is not possible,” he says. “But even if we are able to record a dissipation curve, it would be precious for future pandemic management.” Kumar recommends immediate biweekly sewerage monitoring, at least in the ‘smart cities’ equipped with analytical facilities. Besides SARS-CoV-2 genes, measuring the concentration of pharmaceutical and personal care products would be useful to track the level of antimicrobial resistance, he says.

Just before the second wave of the pandemic hit India, a multi-institutional group of researchers proposed a model they called ‘Surveillance of Wastewater for Early Epidemic Prediction’ (SWEEP). Lead author Vinay Kumar Tyagi, a professor in IIT Roorkee’s Department of Civil Engineering, who has been monitoring wastewater studies extensively in states of Uttarakhand and Rajasthan, says the pandemic presents an opportunity to include such protocols in routine urban water management. “We can start small, say with educational institutes or planned cities like Chandigarh.”

Tamil Nadu-based SRM Institute of Science and Technology created a set of standard operating procedures for wastewater-based surveillance, which India’s planning body NITI Aayog passed on to the states and union territories for possible implementation. “However, before the states could take action, the second wave of COVID-19 hit us,” says Paromita Chakraborty, an associate professor in the institute’s civil engineering department.

Lack of a uniform protocol for viral detection, the heterogeneous nature of sewage and variation in environmental and operational conditions also become challenges for epidemiologists to make perfect projections. For instance, viral fragments may disintegrate quickly in hotter conditions of north India during the peak of summer, thus obscuring the actual scale of the outbreak, Tyagi says.

Given that large scale clinical testing of COVID-19 has proven difficult in India due to costs, limitations of manufacturing and accessibility of remote areas, WBE could be a quick and efficient way forward. “By identifying populations likely to be negative, WBE can help make each diagnostic test count,” Arora says.

Contrary to popular notion, monitoring wastewaters is not expensive. Venkata Mohan says each weekly sample analysis could cost up to Rs 3000 and is easily implementable in urban settings. However, since very few people work in this area in India, Arora says the key reagents for the analyses have to be imported adding to the expenses.

Epidemiological workforce

Specialist wastewater epidemiologists are hard to come by in India.

“I am aware of none,” says Manish Kumar. At present epidemiologists, virologists or wastewater experts, civil engineers or environmental scientists are pooling together resources to feed into this greenfield research area. “Only a few like us at the interdisciplinary interface are doing the job of wastewater epidemiologists,” he says.

Chakraborty says a national consortia of epidemiologists, environmentalists, microbiologists and field engineers could lead the action.

Public-facing epidemiological research can be tricky to execute in the middle of a pandemic. People could panic when hazmat-suit wearing researchers come to collect water samples from drains in their locality. “You have to be discreet about the purpose,” says Hemalatha. But there are fun moments too. “Like when children get excited seeing us work by the lakes — they think we are 'fish-catchers’,” she says.