With the end of the Covid emergency, surveillance shifts to the sewers

When the United States ends the Covid-19 public health emergency on Thursday, the coronavirus will not go away. But many of the data streams that helped Americans monitor the virus will no longer be available.

The Centers for Disease Control and Prevention will stop tabulating population COVID-19 infection numbers and will no longer require specific case information from hospitals or testing data from laboratories. And as free testing is curtailed, official case numbers, which have become less reliable as Americans have switched to at-home testing, could be even further from reality.

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

People infected with the coronavirus shed the pathogen in their stool, whether they undergo a Covid test or see a doctor. This allows authorities to track virus concentrations in communities over time and watch for the emergence of new variants.

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

And while other tracking efforts are waning, some communities are scrambling to establish wastewater monitoring programs for the first time, noted Dr. kirby “It actually increases interest in wastewater,” she said.

Sewage monitoring will become even more important in the coming months, scientists said, and it should help officials spot emerging outbreaks.

However, wastewater monitoring is still lacking in many communities and more work is needed to transform what started as an ad hoc emergency response into a sustainable national system, experts said. And authorities need to think carefully about how they use the data as the pandemic continues to evolve.

“Sewage needs to get better,” said David O’Connor, a virologist at the University of Wisconsin-Madison. “And we need to get a little smarter about interpreting what the wastewater data is telling us.”

Wastewater monitoring has repeatedly proven its worth over the past three years. When tests became widely available, wastewater trends reflected official Covid-19 case numbers. When testing was scarce, spikes in virus levels in sewage gave early warning of impending spikes, allowing officials to reallocate public health and hospital resources to prepare for an influx of cases.

Sewage samples helped scientists determine when new variants emerged in certain communities and helped doctors make more informed decisions about when to use specific treatments that may not work against all versions of the virus.

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

Houston, for example, now has an extensive wastewater monitoring infrastructure, collecting weekly samples from all of the city’s 39 wastewater treatment plants, as well as individual schools, shelters, nursing homes and prisons. The city has no plans to reduce the decline, said Loren Hopkins, the Houston Health Department’s senior environmental scientist and a statistician at Rice University.

“We really don’t know what Covid is going to do,” she said. “We will continue to examine the sewage to find out how much virus is out there.”

The CDC will continue to track deaths and hospital admissions, but these tend to be lagging indicators. As such, wastewater is likely to remain an important early warning system for both officials and the public.

“It can help immunocompromised people who maybe should be really careful,” said Alexandria Boehm, an environmental engineer at Stanford University and lead researcher of WastewaterSCAN, a wastewater monitoring initiative. “It can help us decide whether to mask up or go to a really crowded concert.”

As clinical testing declines, effluent monitoring will also be a key strategy to keep track of new variants and assess the threat they pose, scientists said. Variants that quickly invade a sewer, for example, or whose spread leads to increases in local hospitalization rates, could require increased surveillance.

Open to interpretation

However, the data will not be available everywhere. Because the existing sewage monitoring system arose rather haphazardly and interested jurisdictions opted in, coverage across the country is inconsistent. In many rural areas and parts of the South and West, wastewater sampling sites are typically sparse or non-existent.

And collecting wastewater data is just the first step. It could be harder to make sense of it, scientists warned.

Among the challenges they cited were that many Americans had now developed some immunity to the virus, that sewage spikes would not necessarily result in the same wave of hospitalizations that some facilities had come to expect. And the scientists do not yet know whether all variants will be equally detectable in the wastewater.

Furthermore, just discovering a new variant in the wastewater does not necessarily mean a problem. For example, since 2021, University of Missouri virologist Marc Johnson 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. So far, however, these variants do not seem to be spreading. They likely come from single supershedding patients with long-term infections with the coronavirus, said Dr. Johnson.

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

And while a reduction in Covid case tracking was likely inevitable, wastewater monitoring is most telling when combined with other sources of public health data, scientists said. “I think of it more as a supplemental stream of data,” said Dr. Eisenberg.

optimization of the system

Wastewater monitoring will continue to evolve, said Dr. kirby The CDC is talking to some states about how to optimize their network of sampling sites. This process could include both adding new sites and reducing in areas where multiple sampling sites provide essentially redundant data.

“We expect the number of locations in some of these states will decrease somewhat,” said Dr. kirby “But we will work with them to be strategic about this so we don’t lose information.”

Officials are also exploring other possibilities. For example, as part of the CDC’s Traveler Genomic Surveillance program, Ginkgo Bioworks, a Boston-based biotechnology company, is now testing wastewater samples from airplanes that land at the international terminal of San Francisco International Airport.

“Establishing these indirect mechanisms that can give you a sense of what’s going on in the world is really important as other forms of testing begin to fade,” said Andrew Franklin, director of business development at Concentric by Ginkgo, the company Department of Biosecurity and Public Health.

The American Rescue Plan has provided enough funding to conduct wastewater monitoring in every state and territory by 2025, said Dr. kirby

However, maintaining wastewater monitoring in the longer term will require continued funding as well as continued support from local authorities, some of whom may lose interest as the emergency phase of the pandemic comes to an end. “We’re going to see some dropouts from college due to fatigue,” said Guy Palmer, an infectious disease pathologist at Washington State University and chair of the National Academies of Sciences, Engineering and Medicine Wastewater Oversight Committee.

Proponents of wastewater monitoring therefore hope to demonstrate its continued usefulness for both Covid-19 and other diseases. Some jurisdictions are already using wastewater to track influenza and other pathogens, and the CDC hopes to roll out expanded testing protocols by the end of the year, said Dr. kirby

“This is part of our monitoring portfolio for the long term,” said Dr. kirby “I think we’ll really see how impactful it can be once we get through this emergency response phase.”