Philly’s been testing wastewater for COVID for months but isn’t using the data

Editor’s note: After this article was published, the Philadelphia Department of Public Health said it had misinterpreted The Inquirer’s questions and given wrong information about its use of wastewater data to track COVID-19. The department now says it uses the data internally but has not yet shared the data publicly or with the CDC.

Philadelphia isn’t using one of its best tools for tracking COVID-19 and other infectious diseases: wastewater.

By analyzing genetic material in the poop of people infected with the virus, health officials can determine whether COVID cases are rising and can even identify what variants are circulating. Other cities, including Houston, are using the technology to track viruses like monkeypox or polio. All told, some 1,000 jurisdictions across the country, including Montgomery County, are increasingly relying on the stuff we flush down the toilet to monitor COVID, as fewer test results are reported to public health agencies.

Since May, Philadelphia has been collecting COVID wastewater samples that the health department considers reliable, city officials said, but the data aren’t being used to shape the city’s COVID response or being shared with the federal government and the public. And the city has not yet expanded testing to viruses other than COVID.

Officials from the Philadelphia Department of Public Health say they want to fine-tune their testing system to improve accuracy and address data processing delays before using or releasing data. They plan to publish their numbers and share them with the Centers for Disease Control and Prevention soon.

Experts argue, though, that even an imperfect testing and data program would be a valuable tool for policymakers and the public — especially as at-home test results are increasingly unreported.

“Just because we don’t have the best shouldn’t be enough to keep us from starting,” said Charles Haas, a professor of environmental engineering at Drexel University. “This is the last tool available to get a broad picture of what’s going on in the community.”

Wastewater testing simply requires the public to use the bathroom to be effective.

The CDC data compiled from 1,155 wastewater sampling sites across the country give perhaps the most accurate picture of COVID’s spread, showing the prevalence of COVID and whether COVID’s presence is increasing or decreasing.

Philadelphia launched a wastewater testing pilot program in 2020, but it was discontinued. The city resumed wastewater collection in January and by May was gathering samples that program leaders felt were reliable.

» READ MORE: The clues are in the poop: COVID-19 sewage testing is coming to Philly

Still, health officials are withholding data as they work through processing delays. They’ve also expressed methodological concerns with their collection and interpretation of their data.

For instance, they are trying to update the tests run on wastewater samples to capture the latest variants.

The CDC is currently gathering wastewater data from 987 sites, but Philadelphia isn’t one of them right now. Providing data on several fields required by the CDC took longer than expected, the health department said. The city is finalizing efforts to share data with the federal agency, said Matt Rankin, a health department spokesperson.

The department is also concerned that wastewater data can’t predict the number of COVID cases in a community.

“Setting up surveillance systems like this and looking for opportunities to improve them is challenging,” said Rankin.

But experts said Philly has delayed the release of useful, if flawed, information in an unnecessary effort to perfect science in an emerging field.

“There is a definitely a trade-off in a new and developing area” between refining methods and sharing results, said Scott Olesen, an epidemiologist at the wastewater testing company Biobot Analytics, which publishes its data online. But “is this what they think is a reasonable and timely response in a pandemic scenario?”

He applauded the city’s desire for accuracy but said the level of precision the city is seeking is “extra-credity.”

Olesen said he doubts wastewater testing will ever provide an accurate measure of case counts because the amount of virus a sick person sheds in the wastewater is highly variable.

“I don’t know that anyone will be able to really crack it, absent some new data sources,” he said.

The city doesn’t need to be able to precisely translate wastewater measures into case counts, Olesen and Haas said. Wastewater is invaluable for identifying trends and will show whether the virus is becoming more or less prevalent.

“If you see a spike of what’s coming in the wastewater, it’s going to be indicative that you’re going to have a rise in cases,” Haas said.

As it was when COVID broke out in 2020, testing for monkeypox has been hard to access, particularly in the early weeks of the outbreak, and health officials believe current case numbers are an undercount.

Using wastewater to test for monkeypox is an even newer field of study than COVID-19 testing in sewage.

“The science behind monkeypox testing in wastewater is not settled at all,” Rankin said.

Biobot is still conducting research to see how to test for monkeypox in its labs, Olesen said.

Scientists at Verily Life Sciences, Stanford University, and Emory University are testing for monkeypox in wastewater across the country, including in Harrisburg, as part of a national initiative called WastewaterSCAN. The initiative posts results online and shares them with the CDC. Philadelphia is not part of the project.

“We are entirely funded by CDC. We felt it best to await their guidance for anything related to monkeypox testing,” Rankin said.

The city isn’t using its testing technology to look for polio either, though New York City has used wastewater testing to identify the virus.

“We currently don’t have that capability to test for polio, as all of our testing has been COVID-specific,” Rankin said.

Polio testing — in wastewater and otherwise — is handled by the CDC, he said, and the federal funding that supports the wastewater testing program currently requires the technology be focused on COVID. Philadelphia has not identified any polio cases this summer.

» READ MORE: Philly health department’s new lab a key resource for tracking COVID

By limiting its $700,000 wastewater contract with Temple University to COVID testing, Haas said, the city isn’t taking full advantage of its wastewater testing capacity.

“Once you’ve got the sewer sample and you’re bringing the sample in to test it for new organisms, that level of effort is minor,” he said. “Once you have an oven in your house and you’ve been cooking cakes, you can cook a beef roast. You just need a different temperature and time.”

Haas reached out to Philadelphia Health Commissioner Cheryl Bettigole when she began her term and offered to help set up a wastewater testing program. He didn’t hear back, he said.

The city didn’t want to switch partnerships midproject, Rankin said, but other experts have questioned whether the city could have rolled out surveillance more efficiently by choosing local partners.

Temple and Michigan State University currently test Philadelphia’s wastewater, though the city eventually plans to run the program without help. The city debuted this month its own genetic sequencing lab, which can test COVID samples to identify variants from nasal swabs and can be used to evaluate other kinds of bacteria and viruses, but that lab has not yet been used to process wastewater test samples.

Building internal testing capacity is worthwhile, Olesen said, but the trade-off is withholding valuable data.

The city’s program, Olesen said, “doesn’t seem to have served the citizens of Philadelphia very well, at this point in time.”