Wastewater testing at the University of Illinois at Chicago

Using samples from local sewage systems is proving to be a useful tool in helping identify COVID hotspots and predict spread throughout communities.

Over the past several months, a group of public health and academic scientists organized by the Discovery Partners Institute have been testing wastewater throughout Chicago and Illinois to monitor outbreaks. The programs could help pave the way for permanent water surveillance that would monitor other dangerous illnesses.

Used alongside clinical testing and hospital admissions data, wastewater samples can be an effective method for public health experts to track COVID-19 among communities, said Charlie Catlett, a senior research scientist at DPI, a University of Illinois-affiliated organization that's helped build COVID-19 water surveillance programs at the local and state levels.

“What wastewater does is give you a snapshot of what’s happening today with about a week lead time on what we might see in terms of volume of cases,” Catlett said.

The earliest evidence of the omicron variant in Chicago wastewater was detected Dec. 12, according to data from DPI. In just the past two weeks, COVID-19 cases have been surging in Chicago. As of Dec. 21, Chicago’s COVID-19 positivity rate was 8.3%, up from 4.2% one week ago, according to the Chicago Department of Public Health. On average there are 2,069 cases a day in Chicago, just over double the week prior.

“Especially with the holidays happening here, now is exactly the time we’re going to start to see those increases,” Catlett said.

SARS-CoV-2, the virus that causes COVID-19, is detectable in human waste nearly from the onset of infection, even when symptoms haven’t appeared. Data collected from wastewater can’t tell officials who has COVID-19 or provide an exact number of people infected, but it can provide information on infection trends over time at a community level. The data helps determine where COVID-19 is rapidly spreading and identify areas that could benefit from mobile testing sites and increased communication about vaccines.

“Nobody yet has cracked the code on what does a viral concentration mean in terms of case count,” Catlett said. “But, having said that, it is a very good measure over time of the growth of a virus.”

Early on during the pandemic, the U.S. Centers for Disease Control & Prevention and the Department of Health & Human Services recommended that states monitor COVID-19 in wastewater. Nearly 80% of U.S. households are served by municipal sewage collection systems, according to the CDC. The agencies created a portal for state and city health departments to submit wastewater testing data, which is used to summarize and interpret data for public health action.

In Illinois, select wastewater surveillance programs were funded by the Walder Foundation, a Skokie-based organization that supports science innovation and environmental sustainability. Others have been funded by the CDC, which earlier this week gave a new grant to DPI and CDPH to continue their water surveillance program for at least two more years.

Besides Illinois, many other states routinely test wastewater for COVID-19. In CDPH’s wastewater surveillance program, samples are taken from water treatment plants as well as sewer locations throughout the city and then analyzed at the University of Illinois at Chicago.

Scientists detect COVID-19 in water the same way they do in humans—using polymerase chain reaction, or PCR, tests, Catlett said. To identify variants, samples undergo genomic sequencing at Argonne National Laboratory in Lemont.

At the state level, DPI has worked with the Illinois Department of Public Health to test wastewater across 65 collection sites in 48 counties.

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At both the state and Chicago levels, health departments prioritize vulnerable communities—those in disadvantaged areas with lower vaccination rates. Identifying high-risk areas helps both CDPH and IDPH choose which treatment plants and sewer locations to test more frequently.

“We’re really looking at vulnerable communities when we think about where to sample in the city of Chicago,” Catlett said. “Some communities are hit much harder than others and they tend to be those that are underresourced.”

DPI has also developed water surveillance programs for Cook County Jail and O’Hare International Airport. At the jail, samples help operators know when to start large-scale testing initiatives.

At O’Hare the situation is a little trickier because the people congregating at the airport change every day. While the data is useful, it’s more difficult to address from a testing standpoint. Researchers mostly use the data for evidence of new variants arriving in Chicago via O’Hare.

Even before the pandemic, testing Chicago’s waterways for dangerous materials was conducted regularly. Lake Michigan has long been tested in the summer for high levels of fecal matter, which if present at dangerous levels sometimes causes Park District officials to shut down Chicago’s beaches.

Additionally, the Metropolitan Water Reclamation District of Greater Chicago routinely checks for toxins like lead and phosphorus. But testing for illnesses is less common. Besides COVID, wastewater can be used to test for dozens of illnesses, like influenza, H1N1, polio, norovirus, Zika virus and hepatitis.

The COVID-19 wastewater surveillance program is providing insight into the feasibility of operating programs like this year-round, even once the pandemic is over, Catlett said.

Once the pandemic subsides, testing wastewater may not be required on a twice-weekly basis as it is now, but testing wastewater even twice a month for COVID or other illnesses could help public health officials keep their finger on the pulse.

“The mechanism for doing wastewater surveillance just wasn’t there before COVID-19 hit,” Catlett said. “It will serve us well in future pandemics, too.”

This story first appeared in our sister publication, Crain's Chicago Business.

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