Wastewater surveillance can get more specific than entire sewersheds

The first page from a comic about wastewater surveillance in K-12 schools, developed for UC San Diego’s SASEA program

This week, I had a new article published in The Atlantic about how COVID-19 wastewater surveillance can be useful beyond entire sewersheds, the setting where this testing usually takes place. Sewershed testing is great for broad trends about large populations (like, an entire city or county), the story explains. But if you’re a public health official seeking truly actionable data to inform policies, it’s helpful to get more specific.

My story focuses on one wastewater testing setting that’s been in the news a lot lately: airplane bathrooms, from which researchers can identify new variants arriving with international travelers. But airplanes are far from the only place where specific wastewater surveillance can be valuable. Here are some of those other places, highlighting some information that I learned in reporting this story (but couldn’t fit in the final article).

K-12 schools

Early in the pandemic, colleges and universities became a hub for wastewater surveillance innovation. At campuses like Columbia University in NYC, researchers tested the sewage at individual dorms in order to determine exactly which students were getting sick—and take quick action, usually by requiring students at the infected dorm to get PCR-tested and quarantining the people who tested positive.

But the same technique can apply to schools with younger students. In late 2020, the University of California San Diego expanded its testing program to elementary schools, in an initiative called the Safer at School Early Alert System. The program started with 10 schools in the 2020-21 school year, then expanded to 26 in the 2021-22 year. Wastewater testing at specific sewershed points next to the schools led researchers to identify asymptomatic COVID-19 cases with high accuracy, program leader Rebecca Fielding-Miller told me.

The San Diego program isn’t alone: other public school systems have tried out building-level wastewater testing, usually in collaboration with nearby research groups. While the research projects tend to successfully show that wastewater surveillance can pick up infections, it’s challenging for school systems to get the funding to do these programs long-term. (Unlike universities, which are in total control of their funding, public schools need to rely on local governments).

As a consequence of these funding challenges, the San Diego program wasn’t renewed for the 2022-23 school year. “We really would have wanted to keep doing it, but funding ran out,” Fielding-Miller said.

Hospitals, other healthcare facilities

Much of the U.S.’s health strategy throughout the pandemic has focused on keeping hospitals from becoming overwhelmed—or at least helping hospitals weather COVID-19 surges. Wastewater surveillance can help accomplish this, by giving hospital administrators warnings about potential increased transmission; wastewater trends usually predict hospitalization trends by a week or more. And when wastewater surveillance is happening at hospitals themselves, these warnings can be really specific.

At NYC Health + Hospitals, the city’s public hospital system, administrators can get these warnings from wastewater testing at the system’s eleven hospitals. The surveillance program includes weekly tests for COVID-19, flu, and mpox (formerly called monkeypox), in collaboration with local researchers. The resulting data “gives us better situational awareness,” said Leopolda Silvera, a global health administrator at Health + Hospitals. If the health system notices a coming surge at one hospital, they can adjust resources accordingly—such as sending more staff to the emergency department.

The Health + Hospitals wastewater program has been running for about a year, Silvera said. At this point, it’s the only program she knows of that does building-level surveillance at hospitals. In the future, the hospital system might start testing for other pathogens and health threats like antimicrobial resistance.

Congregate facilities

Congregate facilities like nursing homes and senior living facilities can include a lot of vulnerable people who are at higher risk for severe COVID-19, all living in close quarters. As a result, this is another category of settings where it could be helpful to have building-level wastewater surveillance: facility administrators could learn quickly about upcoming surges and respond, by doing widespread PCR testing or instituting a temporary mask mandate.

The state of Maryland used to have a program doing exactly this, with a focus on correctional facilities throughout the state—particularly facilities housing the most vulnerable residents. The wastewater surveillance program ran through May 2022, at which point it “quietly ended,” according to local outlet the Maryland Daily Record. An initial $1 million in funding for wastewater testing in Maryland ran out; while the CDC National Wastewater Surveillance System picked up testing at wastewater treatment plants, no new entity was able to continue testing at the congregate living facilities.

According to the Daily Record, the building-level wastewater testing was incredibly helpful for informing COVID-19 measures at correctional facilities and helped keep cases down. I hope the Maryland program isn’t the last example we see of this testing in the U.S.

Large, communal workplaces

Early in the pandemic, some of the U.S.’s worst COVID-19 outbreaks happened at factories, particularly large food processing plants. People in these settings are often working in close quarters, easily able to infect each other—and when an outbreak happens, there are ramifications for both individual employees and the company’s business.

These large facilities could be another target for wastewater surveillance: if company administrators see a warning about rising COVID-19 from their buildings’ sewage, they could institute basic public health measures to curb the spread. Such is the strategy for some mine companies in rural Canada, which work with biotech company LuminUltra to test their wastewater. People often live and work at these sites, making them relatively closed settings for transmission.

At these locations, COVID-19 was previously “kind-of out of control, clinical testing was very reactive,” said Jordan Schmidt, director of product applications at LuminUltra. With wastewater testing, the mining companies can keep outbreaks “to a handful of people.” Fewer people get sick and there’s less interruption to business, he said.

Neighborhood-level testing

As public health agencies face lower budgets and overall lower awareness about COVID-19, some officials want to maximize their limited resources. If you only have the funding and staff for two mobile PCR testing sites this week, you’d want to make sure they go to a neighborhood where the testing would be most helpful, right?

The Boston Public Health Commission had this goal in mind when they launched a new neighborhood-level wastewater testing program, in collaboration with Biobot Analytics. The program includes testing twice a week at 11 sites across Boston, selected to provide good coverage of the city and also enable testing without too much disruption to traffic. While testing just started in January, the program is already helpful for identifying specific COVID-19 patterns, said Kathryn Hall, deputy commissioner for the health agency.

Boston’s program is focused on COVID-19 right now, but could expand to other diseases as needed, Hall said: “Now that we have the infrastructure in place, it allows us to be really be prepared and also to ask novel and interesting questions.”


Airplane surveillance fits into a slightly different category than the other settings I described here. When researchers test airplane wastewater, they aren’t seeking to get advanced warnings of new surges or inform public health policies. Instead, the goal is to track variants—with a focus on any new coronavirus mutations that might come into the U.S. from abroad. (Read the Atlantic story for more details on how this works!)

Other transportation hubs could be useful for tracking variants too, experts told me. This could mean large train stations, bus stations, shipping ports—any location that involves a lot of people moving from one place to another. After all, variants can evolve in the U.S. as easily as they can in other parts of the world.

Overall, the specific wastewater testing settings described here could be valuable pieces of expanding the U.S.’s overall surveillance network, along with the more-traditional sewershed testing. But all these testing sites need sustained funding to actually provide valuable data in the long run, something that could be in jeopardy as the federal public health emergency ends.

More wastewater surveillance

Wastewater surveillance expands beyond COVID-19
I have a new story up this week at Science News, describing how the field of wastewater surveillance exploded during the COVID-19 pandemic and is now looking toward other public health threats.
National numbers, September 24
The COVID-19 plateau that I’ve described over the last couple of weeks continues, with wastewater and test positivity data showing that viral spread has slowed in much of the U.S. However, this is likely just a …
COVID source shout-out: Wastewater surveillance in Wyoming
Wastewater surveillance is re-starting in some Wyoming sewersheds after an earlier iteration of the program ended in December 2021, according to local news reports. This monitoring is a good sign for expanded coverage across more rural …
Wastewater surveillance is crucial for tracking new variants, BA.2.86 shows us
This week, the health department in New York City, where I live, announced that they’d identified new variant BA.2.86 in the city’s wastewater. I covered the news for local outlet Gothamist/WNYC, and the story got me …
National numbers, August 27
This week, our limited COVID-19 data picture suggests that transmission may be starting to level off. But if BA.2.86 or another newer variant enters this high-spread environment, the outlook could get less rosy.
COVID source callout: Nebraska stops reporting wastewater data
The Nebraska state health department has discontinued its wastewater surveillance data page, depriving residents of important COVID-19 updates at a time when cases are rising.

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