Philly’s effort to find viruses in poop is still backed up

Three years ago, Philadelphia led the region in rolling out new technology using wastewater to track COVID-19.

But coming out of the pandemic, the city lags behind its neighbors in identifying emerging health threats in what gets flushed down toilets.

Locations in several Pennsylvania counties, including in Montgomery, Bucks, and Delaware Counties, are now able to use wastewater to track mpox, the virus formerly called monkeypox responsible for a concerning outbreak last summer, according to the Centers for Disease Control and Prevention, though it is not the counties themselves necessarily running that testing.

The Delaware County Regional Water Quality Control Authority is testing wastewater for influenza, RSV, and norovirus.

» READ MORE: Philly’s wastewater testing for COVID is up and running, but city has yet to share data

New Castle County, Del., announced last month that it would begin testing for drugs, including opioids, amphetamines, and nicotine, in wastewater. County officials said this will provide a better understanding of where these substances are used most often.

Meanwhile, Philadelphia in April began getting COVID test results that health officials were confident were accurate. The city’s three wastewater sampling sites are not among the 22 in the state, including locations in Philadelphia’s four neighboring Pennsylvania counties, currently sharing wastewater testing data to help the CDC monitor COVID. However, city officials said they will begin routinely sharing data this week.

Health department officials said the wastewater testing program’s rollout has been slow because they decided to manage it in-house, a complicated endeavor that they hope will enable the department to respond more nimbly to emerging public health threats in the future. Many other communities contract out the scientific analysis to private companies.

“This capacity has taken time to develop but puts us in a much better place to address future infectious risks to Philadelphia promptly without being dependent on sending specimens to outside labs,” Cheryl Bettigole, the city’s health commissioner, said in a statement.

Still, the approach has limited the health department’s ability to offer meaningful data on current public health threats, such as COVID. The health department hasn’t updated its public dashboard showing the results of wastewater testing for COVID since Jan. 23. Officials said they weren’t confident enough in the results to publicize them.

In November, the city was one of two locations in the nation selected by the CDC to test wastewater for polio, which has shown signs of rebounding nationally. Philadelphia’s lab likely won’t be ready to test for polio until 2024, health officials say.

The other participant in the pilot program, Oakland County, Mich., expects to start testing for polio soon, said a spokesperson from the Michigan Department of Health and Human Services.

Charles Haas, a Drexel University professor, described the progress of wastewater testing as, “disappointingly slow for a city of our size.”

As public health officials scrambled for ways to continue tracking COVID, wastewater testing seemed promising. Hospital data on treatment and illness rates can be skewed by how many people report test results or seek treatment. Wastewater screening can identify where and when the virus is circulating and may give an early warning of its resurgence.

“Maintaining a national wastewater surveillance system ensures readiness to respond to evolving risks,” a National Academies of Science, Engineering, and Medicine study released this year found.

Philadelphia’s health department launched a wastewater testing pilot in 2020, and started a full-fledged program, drawing sewage samples from three sites in the city, in January 2022.

By late spring the program was generating reliable results, health officials have said. But it quickly began to run into problems.

The city had a $700,000 contract with Temple University to run analysis. But concerns about data collection and interpretation methods kept the health department from sharing data publicly until last October.

Temple routed wastewater samples from Philadelphia to Michigan State University for processing. It sometimes took weeks to get results and occasionally, samples got lost in the mail, undermining the value of wastewater testing as an early alert system.

» READ MORE: Testing sewage for COVID is providing valuable data, but Philly seeks to get faster results

When the contract with Temple ended in January, the department moved the entire operation in-house — but did not yet have a lab ready to take on the task. Everything from sample collection to testing is now conducted through the department’s genetic sequencing lab, which opened in August.

They have spent $615,000 paid for through CDC grants to hire and train staff and buy equipment and chemicals.

“The data continued to be collected, but we couldn’t publish it before we were confident that our results were valid,” health department spokesperson Jim Kyle said.

The health department anticipates its wastewater testing program won’t be prepared to test for anything other than COVID for months.

The process of building a lab should have begun years ago, if the city wanted to process its own wastewater test samples, said Drexel’s Haas, a national expert who was on the committee that authored the National Academies of Science, Engineering, and Medicine study.

“I think they should have planned in advance if they intended to move this all in-house,” Haas said.

Boston is among the cities that decided to conduct wastewater testing through a company, Biobot Analytics in Cambridge, Mass., which processes samples from about 1,000 locations nationally.

New Castle County recently contracted with Biobot to scan wastewater samples for drugs, said Jennings Heussner, Biobot’s director of government business. Wastewater samples in Delaware County are processed by a testing initiative from Stanford University, WastewaterSCAN, the county water authority reported.

“It’s pretty difficult to stand up these kinds of operations,” Heussner said, noting that conducting testing in-house does give the health department more flexibility in deciding what it tests for.

The city’s lab is also getting results faster than when Michigan State processed Philadelphia’s samples. Test results consistently arrive in four days, Kyle said.

The health department is in the process of applying for additional federal grants to keep the program running when CDC funding runs out in July.

“We believe that having this capability in-house is an important part of the preparedness for the future,” Kyle said, “and will enable us to have much more rapid turnaround in the event of a future emergency.”