The first signs of the most recent Covid-19 waves have often been detected in our sewers instead of nasal swabs.

But in the future, the potential for human waste to tell us about what is happening with our community’s health could extend far beyond the novel coronavirus.

“This has been its coming-out party. We’ve realized the power in this pandemic,” John Dennehy, a biologist at the City University of New York who has been assisting with NYC’s wastewater surveillance program, told me. “Now there’s great interest in developing an infrastructure to sustain this capability beyond the pandemic.”

Sewage surveillance is becoming more valuable right now as conventional testing is becoming less transparent. More people have been using rapid at-home tests and might not report results to a public health agency. That means the number of positive cases being reported by official sources might not actually provide a full picture of what’s happening with the pandemic.

But no matter how or if they’re testing, infected people — whether they have symptoms or not — flush out the virus when they go to the bathroom, leaving viral RNA that can be detected in wastewater samples. It requires careful collection and testing, but sewage can provide a less biased look at the viral trends in a given community.

Science has not yet reached the point where we can say that X amount of viral load in a community’s sewage means Y number of people are infected in that community. But still, knowing which way viral loads are trending is useful. If they are going up, even before the number of positive tests starts increasing, it could in theory allow public health authorities and the local health system to start preparing for a surge. If they are going down, public health officials (and the general public) can be confident that any waning in official case numbers is real and not the byproduct of, say, less testing.

So far, health authorities have not been using wastewater levels to trigger a public health response — ordering people to mask up again once viral loads hit a certain level, for example. But experts say a more direct link between sewage surveillance and public health policies might be established in some places in the coming year.

Covid-19 has shown the value of public health sewage surveillance

The pandemic has revealed the potential for wastewater surveillance — and the shortcomings in the current US infrastructure.

Dennehy told me that his team in NYC had noticed an unusual iteration of the virus back in November, but it wasn’t until South Africa announced the presence of the omicron variant in people there a month later that they realized they had been seeing the mutations that would soon start a new wave of infections worldwide.

South Africa has been commended for its genomic surveillance system, which is what allowed it to be the first to identify omicron as a threat, even though, as the New York example shows, the variant was likely already present in other parts of the world. The US, on the other hand, lagged behind other countries for much of the pandemic in that work, and integrating sewage into that surveillance system remains a work in progress.

Before the pandemic, using wastewater for disease surveillance was not unheard of, but it was generally limited to monitoring for diseases like polio, where the appearance of any amount of virus would be cause for alarm.

Covid-19 has shown that wastewater can provide an even more nuanced and varied picture of a community’s health. Since researchers showed the ability to detect the coronavirus in sewage in early 2020, wastewater surveillance has spread across the globe. More than 470 sites in the US and nearly 3,400 sites worldwide are reporting the amount of virus they are detecting in the waste we flush.

Wastewater has its limitations, including challenges with proper collection and adjusting for the concentration of human waste in the sewage. Some rural areas don’t have a community wastewater system, relying instead on individual homes’ septic tanks, which makes broad monitoring impossible. Across Montana, Wyoming, North and South Dakota, and Nebraska, only two wastewater sites are reporting their coronavirus levels to the CDC.

Setting up a strong wastewater monitoring program also requires political support and coordination between public health departments, environmental agencies, and local water authorities, which may not be accustomed to working together.

In spite of those obstacles, sewage monitoring has become more integrated into the global pandemic response over time. And experts don’t expect it to stop there. They are already imagining how else we might use all the information that can be gleaned from our waste to get ahead of future outbreaks and target public health interventions.

“Most people believe wastewater testing is not going away,” Marc Johnson, a University of Missouri virologist who has helped lead that state’s wastewater monitoring program, told me. “It’s too nice of a tool. It can give us an unbiased readout of a community’s health, without having to worry about individual patient confidentiality.”

All the ways wastewater surveillance could help us improve public health

For the foreseeable future, sewage surveillance could help the country keep ahead of Covid-19. Not only can the general trends — an increasing or decreasing amount of virus being found — give a warning about emerging or fading waves, but wastewater can also provide scientists clues about new variants that may soon appear.

After wastewater is collected and taken to a laboratory, scientists run the same kind of test that is conducted for an individual diagnostic PCR test. Beyond identifying whether or not the virus is present, the lab can also determine how much of it there is depending on how many testing cycles they need to run to detect it. (Fewer cycles means more virus.)

Then scientists can also take the sample and analyze the genetic make-up of the virus found therein. If it’s different from the most common variant at the time, that may be a signal that another variant is lurking out there with the potential to take over. Johnson said that, in Missouri, his team has seen Covid-19 variants that have not been detected in humans yet. They may have found their way into the wastewater system from animals, he told me, and we know that animal-to-human transmission is one way for new variants to emerge.

US scientists are also starting to use wastewater in more targeted ways to combat Covid-19. Dennehy said an NYC hospital had asked his team if they could start analyzing the sewage coming out of their facility specifically so they could get an early warning if the virus was appearing more frequently in their patients and staff. Continuous diagnostic testing would be expensive to maintain, and this population-level surveillance would allow the hospital to institute more rigorous testing only when the viral load in the wastewater suggests that it’s necessary.

That kind of creative approach can be applied to other public health problems as well.

Johnson described a similar proposal in Missouri prisons that want to monitor for tuberculosis outbreaks. They have asked for their sewage to be regularly tested for TB, which they could use to determine when to conduct individual diagnostic tests, which are both costly and logistically cumbersome.

“They don’t have to waste money on testing when they know there is nothing there,” he said.

Surveillance programs could watch for other pathogens, too, such as influenza, hepatitis, and norovirus for early warnings of emerging outbreaks. Julianne Nassif, an expert on wastewater surveillance with the Association of Public Health Labs, said we could also monitor for bacteria, viruses, and other microbes that are resistant to current treatments. Public health officials could try to get ahead of an outbreak of antibiotic-resistant bacteria in a nursing home, for example, with the information gleaned from downstream sewage.

Johnson envisioned communities monitoring for narcotics, to better tailor their public health campaigns. Wastewater could be tested to determine whether cocaine or opioid use is rising in a given sewage shed. It could even determine what kind of opioids are being used, which could be helpful to health departments. Widespread heroin use might require a different intervention than diverted prescription opioids or black-market fentanyl.

The possibilities sound almost endless, extending to research that could help us better understand human health. Dennehy described to me one hypothetical experiment that could be run with sewage monitoring, looking for the viral markers associated with colon cancer. By comparing the results from one community with, say, a nearby nuclear power plant and another community somewhere else, we could get a better understanding of how the surrounding environment affects people’s health.

But for all of this potential to be realized, these efforts would require sustained support. The CDC bet on the wastewater boom, launching a national Covid-19 surveillance system in the fall of 2020. But dedicated investments in infrastructure and a workforce would be necessary if the country were to begin conducting wastewater surveillance on a more permanent basis.

In general, the US has not appeared willing to make big investments in public health. Scientists working on these programs hope that the same may not be true of wastewater surveillance, given the opportunities it presents.

“We learned a lot of hard-won lessons with the Covid pandemic. We got caught with our pants down at the beginning. A lot of things that we did were too late,” Dennehy told me. “The hope is we can remember these lessons for the next time this comes around, which may not be that long.”