Marc Johnson saw trouble in the water.
Dr. Johnson, a virologist at the University of Missouri, had spent much of 2020 studying sewage, collecting wastewater from all over the state and analyzing it for fragments of the coronavirus. People with Covid-19 shed the virus in their stool, and as the coronavirus spread throughout Missouri, more and more of it began to appear in the state’s wastewater.
In January, Dr. Johnson spotted something new in his water samples: traces of B.1.1.7, a more contagious variant that was first detected in Britain. Officially, the state had no confirmed cases of B.1.1.7, but the wastewater suggested that the variant had arrived. By the end of the month, the B.1.1.7 levels in Dr. Johnson’s water samples had risen sharply, and in early February, the state finally found its first case. It has since found hundreds more.
Using some samples of sewage, Dr. Johnson had been able to peer into Missouri’s coronavirus future. “I can’t believe how well it works,” he said. “I feel like an oracle.”
Dr. Johnson is one of many scientists who have been drawn into the once niche field of wastewater epidemiology in the past year. Researchers in 54 countries are now tracking the coronavirus in sewage, according to the Covid19Poops Dashboard, a global directory of the projects.
Their work has validated the idea that wastewater surveillance can be a useful way to track infectious disease across entire communities, revealing epidemiological blind spots and yielding actionable public health information.
It has also helped push wastewater epidemiology into the mainstream. In March, the European Commission recommended that member states establish systems to monitor sewage for the coronavirus. And last fall, the Centers for Disease Control and Prevention and the Department of Health and Human Services established the National Wastewater Surveillance System to help local officials respond to Covid-19. It is the first system of its kind in the United States.
“Wastewater surveillance is not a new idea,” said Amy Kirby, the program lead for the surveillance system. It has been used in low- and middle-income countries in the fight to eradicate polio, for instance, and has been proposed as a way to keep tabs on noroviruses, a common cause of stomach bugs. “But really, the return on investment to build this large new infrastructure was never enough to warrant building the system for any of those other diseases,” Dr. Kirby said. “But Covid and the pandemic really changed the calculus.”
The system, and others like it now emerging around the world, could ultimately usher in a new age of wastewater epidemiology, helping officials track not just the coronavirus, but also other outbreaks and diseases. “I think this is really going to be the beginning of a whole new type of data collection for public health disease surveillance,” Dr. Kirby said.
Although Covid-19 is primarily a respiratory disease, research conducted early in the pandemic revealed that people infected with the coronavirus often shed it in their stool. This finding, combined with the scale and urgency of the crisis, spurred immediate interest in tracking the virus by sampling wastewater.
By searching for, and then counting, certain coronavirus genes in sewage, researchers hoped to determine whether the virus was present in a particular region and how widespread it was. Before long, wastewater surveillance projects were popping up everywhere from Kansas City, Mo., to Kathmandu, Nepal.
The resulting data, now appearing in a flood of scientific papers and preprints, have provided powerful proof of principle. Scientists have detected the virus in all kinds of environments: in treated and untreated water, in sludge and settled solids, in sewers and septic tanks, in pit latrines and open drainage systems. They found it in water flowing into enormous treatment plants and out of schools, dormitories and nursing homes. “It’s just fascinating how robust this tool has become,” said Peter Grevatt, chief executive of the Water Research Foundation.
Teams all over the globe — in the United States, France, Portugal, India, Iran, Brazil, Canada and elsewhere — also found that the wastewater data seemed to be an accurate indicator of what was happening in the real world. When the number of diagnosed Covid-19 cases in an area increased, more coronavirus appeared in the wastewater. Levels of the virus fell when areas instituted lockdowns and surged when they reopened.
Multiple teams have also confirmed that sewage can serve as an early warning system; Wastewater viral levels often peaked days before doctors saw a peak in official Covid-19 cases.
This lead time, which can range from a couple of days to two weeks, depends partly on the robustness of local clinical testing programs, scientists say: When more people are being tested for the virus more frequently, the wastewater data provides less advance warning. The lead time also exists because infected people often begin shedding the virus, SARS-CoV-2, before they feel symptoms and then, once they fall ill, frequently delay seeking medical care.
“I think wastewater has proven itself as one of the most, I would say, objective means of understanding what SARS-CoV-2 is doing in our society,” said Gertjan Medema, a microbiologist at KWR Water Research Institute in the Netherlands.
Wastewater surveillance is not a replacement for clinical testing, experts said, but can be an efficient, cost-effective complement. In one study published last August, researchers calculated that they could test the wastewater from every treatment plant in Germany millions of times for less than it would cost them to test every German resident just once. The approach is likely to be especially valuable in low- and middle-income countries, where testing resources are even more limited.
“Not every population gets tested, not everyone has access to health care,” Dr. Johnson said. “If there’s groups of people that are asymptomatic, they probably aren’t getting tested either. So you aren’t really getting the full big picture. Whereas for our testing, everyone poops.”
Although there is a lot left to learn, even the small pilot projects started over the last year have already helped officials identify hidden viral hot spots and figure out how to target their resources.
For instance, a number of U.S. colleges and universities, including the University of Arizona and the University of North Carolina, have used wastewater surveillance of dorms to find asymptomatic, infected students who had otherwise evaded detection. In the Netherlands, health officials have used wastewater data to determine where to send their mobile testing buses, Dr. Medema said.
In Australia, where case numbers have been relatively low, the wastewater monitoring has helped reassure authorities that their pandemic controls are working. “Almost all the samples come back with nothing in them,” said Daniel Deere, the project manager for ColoSSoS, a coronavirus sewage surveillance project in Australia. “It’s been good to give confidence to allow the economy to stay open, to allow movement to continue between states.”
(On the occasions when a water sample has come back positive, the government has ramped up testing and launched media campaigns to alert people who live in the region, he said.)
Wastewater analysis has also allowed scientists to detect the arrival of certain variants in a region weeks before they are found in actual patients — and to identify mutations that have not yet been detected in patients anywhere.
Dr. Johnson and his colleague John Dennehy, a virologist at Queens College, recently identified novel combinations of mutations, which might suggest the presence of new variants, in New York City wastewater. “We don’t know what it means yet,” Dr. Johnson said, noting that the new sequences could be coming from animals, not people. “We can see a little bit into the future, but you know, the crystal ball is always a little cloudy.”
Waste not, want not
This flurry of research and investment has been a boon to wastewater epidemiology. “This has been just an amazingly huge catalyst for the field,” said Tim Julian, who leads the pathogens and human health group at the Swiss Federal Institute of Aquatic Science and Technology.
Over the last year, scientists have refined their methods, and water utilities, environmental laboratories and public health agencies have forged new connections. “The big question mark on everyone’s mind is what happens next,” said Christopher Mason, a geneticist at Weill Cornell Medical College who is part of a team tracking the coronavirus in wastewater samples collected from sites around the world. “How long does this go? How do we really sustain it?”
The C.D.C.’s new wastewater surveillance system is one answer.
“A lot of the initial efforts were coming from academic researchers, commercial laboratories and a few utilities that were able to do the testing themselves,” Dr. Kirby said. “And they have done great work to develop these methods. But routine, long-term surveillance work is not what any of those groups were designed to do.”
The National Wastewater Surveillance System provides funding, technical support, a national data repository and other resources that will allow state and local health departments take over this long-term monitoring. Since its founding last year, the system has grown to include 33 states, four cities, one county and three U.S. territories.
Some health departments were initially skeptical that wastewater data could be useful, but they have since come to embrace it, Dr. Kirby said, using it to figure out where to target their testing resources or to forecast hospital demand. “When you see an increase in wastewater data, we know that within a couple of weeks, you’re going to start seeing an increase in hospitalizations,” she said.
In the next three to five years, the agency plans to expand the system to include monitoring for other pathogens, including antibiotic-resistant bacteria and microbes that frequently contaminate food, Dr. Kirby said.
The European Union is also developing a “sewage sentinel system” that aims to monitor the wastewater in roughly 6,000 cities, Dr. Medema said. Although Covid-19 is the immediate priority, researchers are also assessing the feasibility of using such a system “in a post-pandemic E.U. for antibiotic resistance, infectious diseases, use of pharmaceuticals and illicit drugs and maybe more on the horizon,” he said.
These systems could ultimately help officials stay ahead of emerging threats, providing early warnings about whatever pathogen is poised to cause the next pandemic. An Italian team recently found that the new coronavirus was already present in the wastewater in northern Italy in mid-December 2019, days before the first Covid-19 cases in Wuhan, China, were publicly reported.
“This isn’t the last infectious disease that will come through our water supplies,” said Belinda Sturm, an environmental engineer at the University of Kansas. “This is a tool that we should make sure that we keep sharpened.”