Marc Johnson saw trouble in the water. Johnson, a virus expert at the University of Missouri, had spent much of 2020 studying sewage, collecting waste water from all over the state and analysing 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 waste water. In January, 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 waste water suggested that the variant had arrived. By the end of the month, the B.1.1.7 levels in 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, 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.” Johnson is one of many scientists who have been drawn into the once niche field of waste water 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 waste water 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 waste water 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. 

“Waste water 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,” 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 waste water 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,” 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 waste water. 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, waste water surveillance projects were popping up everywhere from Kansas City, Missouri, 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, CEO 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 waste water 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 waste water. 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: Waste water 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 waste water 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 waste water 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. Waste water surveillance is not a replacement for clinical testing, experts said, but can be an efficient, cost-effective complement. In one study published in August, researchers calculated that they could test the waste water 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. 

This flurry of research and investment has been a boon to waste water 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 past 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 waste water samples collected from sites around the world. “How long does this go? How do we really sustain it?” 

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. 

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 waste water in northern Italy in mid-December 2019, days before the first COVID-19 cases in Wuhan, China, were publicly reported.