When the Covid-19 public health emergency expires in the United States on Thursday, the coronavirus will not disappear. But many of the data streams that have helped Americans monitor the virus will go dark.

The Centers for Disease Control and Prevention will stop tabulating community levels of Covid-19 and will no longer require certain case information from hospitals or testing data from laboratories. And as free testing is curtailed, official case counts, which became less reliable as Americans shifted to at-home testing, may drift even further from reality.

But experts who want to keep tabs on the virus will still have one valuable option: sewage.

People who are infected with the coronavirus shed the pathogen in their stool, whether or not they take a Covid test or seek medical care, enabling officials to track levels of the virus in communities over time and to watch for the emergence of new variants.

This approach expanded rapidly during the pandemic. The National Wastewater Surveillance System, which the C.D.C. established in late 2020, now includes data from more than 1,400 sampling sites, distributed across 50 states, three territories and 12 tribal communities, Amy Kirby, the program lead, said. The data cover about 138 million people, more than 40 percent of the U.S. population, she said.

And as other tracking efforts wind down, some communities are racing to set up wastewater surveillance programs for the first time, Dr. Kirby noted. “This is actually driving more interest in wastewater,” she said.

In the months ahead, wastewater surveillance will become even more important, scientists said, and it should help officials spot some incipient outbreaks.

But wastewater surveillance is still missing many communities, and more work is needed to turn what began as an ad hoc emergency effort into a sustainable national system, experts said. And officials will need to be thoughtful about how they use the data, as the pandemic continues to evolve.

“Wastewater has to get better,” said David O’Connor, a virologist at the University of Wisconsin-Madison. “And we have to get a bit more savvy about interpreting what the wastewater data is telling us.”

Over the past three years, wastewater surveillance repeatedly proved its worth. When testing was widely available, the wastewater trends mirrored the official Covid-19 case counts. When testing was scarce, spikes in the viral levels in sewage provided early warnings of coming surges, allowing officials to redistribute public health resources and hospitals to prepare for an influx of cases.

Wastewater sampling helped scientists determine when new variants arrived in particular communities and helped clinicians make more informed decisions about when to use certain treatments, which may not work against all versions of the virus.

“For SARS-CoV-2, our wastewater surveillance system is pretty solid now,” Marisa Eisenberg, an infectious disease epidemiologist at the University of Michigan, said. “We’ve kind of put it through its paces.”

Houston, for instance, now has an extensive wastewater surveillance infrastructure, collecting samples weekly from all 39 of the city’s wastewater treatment plants as well as from individual schools, shelters, nursing homes and jails. The city has no plans to scale back, said Loren Hopkins, the chief environmental science officer for the Houston Health Department and a statistician at Rice University.

“We really don’t know what Covid will do,” she said. “We’ll be continuing to look to the wastewater to tell us how much of the virus is out there.”

The C.D.C. will still track deaths and hospitalizations, but those tend to be lagging indicators. So wastewater is likely to remain a critical early warning system for both officials and members of the public.

“It can help people who are immunocompromised, who might want to be really cautious,” said Alexandria Boehm, an environmental engineer at Stanford University and a lead investigator for WastewaterSCAN, a sewage surveillance initiative. “It can help us make decisions about whether we want to mask or go to a really crowded concert.”

As clinical testing drops off, wastewater surveillance will also be a key strategy for keeping tabs on new variants and for gauging the threat they pose, scientists said. Variants that quickly take over a sewershed, or whose spread is followed by a rise in local hospitalization rates, for instance, might warrant increased monitoring.

Open to interpretation

Still, the data will not be available everywhere. Because the existing wastewater surveillance system emerged in a somewhat haphazard way, with interested jurisdictions opting in, coverage of the country is uneven. Wastewater sampling sites tend to be sparse — or absent — in many rural areas and parts of the South and West.

And collecting wastewater data is just the first step. Making sense of it can be trickier, scientists cautioned.

Among the challenges they cited: Now that many Americans have developed some immunity to the virus, wastewater spikes might not necessarily lead to the same wave of hospitalizations that some facilities have come to expect. And scientists still don’t know whether all variants will be equally detectable in wastewater.

Moreover, simply spotting a new variant in wastewater does not necessarily portend a problem. For instance, since 2021, Marc Johnson, a virologist at the University of Missouri, and his colleagues have found dozens of unusual variants in wastewater samples across the United States.

Some of these variants are radically different from Omicron and could theoretically pose a new public health risk. But so far, at least, these variants do not seem to be spreading. They are probably coming from individual, supershedding patients with long-term coronavirus infections, Dr. Johnson said.

“Wastewater is really good because it can give you a comprehensive view of what’s going on,” Dr. Johnson said. But there are times, he said, “where it can mislead you.”

And although a reduction in Covid case tracking was probably inevitable, wastewater surveillance is most informative when combined with other sources of public health data, scientists said. “I like to think of it more as being a complementary data stream,” Dr. Eisenberg said.

Optimizing the system

Wastewater surveillance will continue to evolve, Dr. Kirby said. The C.D.C. is talking with some states about how to optimize their network of sampling sites, a process that could involve both adding new sites and scaling back in areas where multiple sampling locations are providing essentially redundant data.

“We do expect some reduction in the number of sites in some of those states,” Dr. Kirby said. “But we’ll be working with them to be strategic about that, so that we’re not losing information.”

Officials are exploring other possibilities, too. As part of the C.D.C.’s Traveler Genomic Surveillance program, for instance, Ginkgo Bioworks, a Boston-based biotechnology company, is now testing wastewater samples from planes landing at the international terminal at San Francisco International Airport.

“Putting in place these indirect mechanisms that can give you a sense of what’s going on in the world are really important, as other forms of testing start falling off,” said Andrew Franklin, the director of business development at Concentric by Ginkgo, the company’s biosecurity and public health arm.

The American Rescue Plan has provided enough funding to conduct wastewater surveillance in all states and territories through 2025, Dr. Kirby said.

But maintaining wastewater surveillance will require ongoing funding over the longer term, as well as continued buy in from local officials, some of whom might lose interest as the emergency phase of the pandemic winds down. “We’re going to see some fatigue-based dropouts,” said Guy Palmer, an infectious disease pathologist at Washington State University and the chair of the wastewater surveillance committee of the National Academies of Sciences, Engineering and Medicine.

So proponents of wastewater surveillance are hoping to demonstrate its continued utility, both for Covid-19 and other diseases. Some jurisdictions are already using wastewater to track influenza and other pathogens, and the C.D.C. hopes to roll out expanded testing protocols by the end of the year, Dr. Kirby said.

“This is part of our surveillance portfolio for the long haul,” Dr. Kirby said. “I think we’re really going to see how powerful it can be once we’re out of this emergency response period.”