Environmental engineer Smruthi Karthikeyan started her postdoc with Rob Knight at the University of California San Diego (UCSD) in March 2020 only days before the state implemented its first Covid lockdown.
“I haven’t met most of my colleagues,” she told me.
Starting a new job during a pandemic is not ideal, but Karthikeyan was soon offered an unexpected opportunity. “I was mostly working on computational stuff, and then one day, my principal investigator called me saying, ‘You're an environmental engineer. We're looking at environmental surveillance of SARS-CoV-2 virus, because apparently, they found it in wastewater. Is this a project you want to build from the ground up?’ So I said, ‘Yes, that sounds exciting.’”
With that, Karthikeyan joined the ranks of scientists trying to find quick and inexpensive ways to screen large groups of people for the SARS-CoV-2 virus by testing wastewater for signs of viral genetic material. The emerging field has one overarching goal: identify new infections and stop them before they become outbreaks.
When you flush the toilet or wash your hands, that water contains more than just waste; for years, scientists around the world have been trying to figure out what it could tell us.
For instance, a group of researchers have tested wastewater to track the use of illicit drugs across more than a dozen European cities, while others have been testing it for pharmaceuticals and alcohol. But in the last year, the concept of large-scale wastewater monitoring has taken off, for one simple reason: many viruses (including Covid-19) are shed from the gut of infected individuals, and therefore, wash down the drain when people use the toilet.
In February 2020, weeks before the first case of Covid-19 was reported in The Netherlands, Dutch experts began testing sewage in five cities and an airport. By mid-March, all but one location had detected the virus.
The European Commission is pushing additional countries to monitor wastewater for signs of Covid-19, and the U.S. has established the National Wastewater Surveillance System, which collects data from local communities to track Covid-19 patterns.
All of this suggests that wastewater monitoring will be an essential tool for future disease detection as part of an artificial immune system for the planet. Wastewater-based epidemiology (WBE) “can serve as a ‘virus radar’ to identify hotspots of infections that then can be more quickly localized and managed with clinical testing and contact tracing,” said Rolf Halden, director of the Center for Environmental Health Engineering at the Biodesign Institute of Arizona State University. Halden is also Chief Scientific Officer of wastewater monitoring company Aquavitas, which he said has monitored wastewater from more than 100 U.S. cities. “Post-COVID, the WBE technology is expected to be used routinely as a public health surveillance tool that can be applied to biological and chemical agents alike.”
According to Jeffrey Ram, a biologist at Wayne State University, the goal of the “post-vaccine era” is to increase the chances of detecting new outbreaks before they spread. Recently, his lab became part of a statewide effort in Michigan to create a massive infrastructure for wastewater testing. “Our plan is to work closely with the local health department in Detroit so that at the first sign of a new spike in Covid-19 in neighborhood sewersheds, prompt and timely public health measures can be taken at those locations.”
It’s one of many WBE projects from around the globe that are being tracked by COVIDPoops19, a database and interactive map created by Colleen Naughton, an assistant professor at University of California Merced. The project lists more than 2,200 sites in 54 countries. “I definitely anticipate more widespread adoption of wastewater monitoring in the future,” Naughton told me. “We see it happening already.”
Wastewater monitoring may be particularly helpful in low-income countries, she noted, because it can track infections in many more people than individual tests, and is cheaper and faster. But in order to become more widespread, wastewater monitoring has some hurdles to overcome.
For one, there are “concerning gaps,” Naughton told me. Of the 54 countries where wastewater is being monitored for SARS-CoV-2, none are low-income countries.
Another issue is that many wastewater monitoring projects are not sharing their data. “Of the over 200 universities, 2,000 sites, and 54 countries we now have tracked...about 16 of those have downloadable data,” said Naughton.
She’s also heard that monitoring projects have struggled to get access to supplies, testing kits, and autosamplers. Still, she has been heartened by how hard everyone is trying to make this work. “There are still methodological challenges and differences like filtration type, extraction from liquids versus solids, etc. but the research community has been very active in testing and comparing the different methods,” she said. “It is inspiring to see how everyone is sharing methods and results.”
Another inherent limitation of wastewater monitoring is that it cannot identify individuals who have Covid-19, just that someone from whom the wastewater originated has contracted it. Ideally, that should be enough to go on.
When Karthikeyan and her team set up a pilot project at UCSD, they tested wastewater coming from the local hospital, and selected one campus building as a negative control. “It was all fine, until we got a positive from our negative control,” she told me. “We weren't prepared for that.”
UCSD administrators asked anyone who had used the bathrooms in the building around the time the sample was taken to take a Covid test. After screening around 600 staff and students, two asymptomatic employees tested positive. They didn’t even know they were infected.
To scale up the pilot project to cover more of the university, Karthikeyan’s team set up more automatic samplers, which collect water every 15 minutes from wastewater flowing from specific buildings around the campus, including student dorms. They adapted a machine present in the lab to prepare samples for testing more quickly, which dramatically increased their throughput. When a wastewater sample tests positive, the team sends notices only to buildings where it originated. To make testing extra convenient, UCSD became the first US college to install vending machines containing self-tests throughout the campus. Students get a free test kit by swiping their university ID card, swab their noses, then leave their samples in collection bins, which are collected and analyzed by on-campus labs. “It’s just much easier,” said Karthikeyan. Any positive results are updated in an interactive map, which also flags buildings that have been tested.
In a recent paper, Karthikeyan and her colleagues reported that they can now process more than 100 samples per day, and their tests are sensitive enough to pick up a single asymptomatic infection in a building with over 400 residents.
UCSD’s high-tech setup is out of reach for many regions, so scientists are exploring ways to scale up monitoring wastewater more cheaply. Automatic samplers can be bulky and expensive, so a simpler and cheaper alternative is to lower a bottle on a string into wastewater and take a sample. But this only collects a brief few minute snapshot of water passing through the pipes, and so it would be unlikely to detect a virus.
To democratize sampling technology, David McCarthy, an Australian civil engineer and associate professor at Monash University, created small bullet-like “sewage submarines” that are filled with Qtips, medical gauze, and a filter membrane, which can collect up to three days of sewage water per use. McCarthy’s lab has kept the designs for the passive sampler open source so people can make their own. This makes it hard to track how many people are using it, but he told me he has made more than 6,500 subs and shipped them to countries all over the globe. He knows of users in Indonesia, the UK, Europe, New Zealand, and, of course, Australia. “In Victoria alone, from January to April, we deployed and analyzed 1,862 passive sampler submarines,” he said. His team is now tweaking the design and materials to make his invention smaller, more versatile, and more efficient.
Even if regions can make use of inexpensive sampling tools, they still have to invest in wastewater monitoring infrastructure, personnel, and equipment, Ram said. In the first few months of the Michigan project, he struggled to obtain PPE, chemicals, and plasticware for testing—some are still back-ordered.
“I think it is likely that [Michigan] will want to see a long-term ‘payoff’ for this investment by testing for other pathogens when the current emergency passes,” said Ram. One way to recover the infrastructure investment is to expand wastewater testing beyond Covid-19. For example, McCarthy is exploring whether his passive samplers could work in other water systems, perhaps monitoring pathogens in drinking water reservoirs, rivers, and creeks. Naughton’s team is now involved in a global wastewater data center, which they hope to expand for other pathogens in the future.
Even if regions focus solely on Covid-19, and find the resources to build the necessary infrastructure, the payoff would be enormous. A recent analysis by Halden found that WBE for Covid-19 at 105,600 sewage treatment plants around the world could monitor 2.1 billion people.
“This testing is expensive, but we think the long-term benefit of stopping new outbreaks makes it worthwhile,” said Ram.
Helen Albert is a freelance science journalist based in Berlin. She has written for publications including Forbes, the BMJ, New Scientist, Chemistry World, GEN, Clinical Omics, and Cosmos magazine. She was previously Editor-in-Chief at Labiotech.eu, an English-language publication based in Berlin that focuses on the European biotech industry. She worked as a Senior Reporter at medwireNews and served as Editor of The Biochemist. Helen has academic degrees in genetics and bioanthropology, and also spent some time early in her career working in a genetics lab in Cambridge before becoming a journalist.
Cite This Essay
Albert, Helen. “Prophet in the Sewer.” Biodesigned: Issue 7, 19 May, 2021. Accessed [month, day, year].
