A lapse in COVID wastewater detection is worrying scientists about distorted data

One of the last tools for tracking the pandemic is shifting hands. Experts warn it could reduce our surveillance

Published October 19, 2023 12:45PM (EDT)

Swetlana Rot prepares water samples in a laboratory of the Saxony-Anhalt State Office for Environmental Protection in Halle/Saale. The scientists here examine wastewater for the coronavirus pathogen. (Hendrik Schmidt/picture alliance via Getty Images)
Swetlana Rot prepares water samples in a laboratory of the Saxony-Anhalt State Office for Environmental Protection in Halle/Saale. The scientists here examine wastewater for the coronavirus pathogen. (Hendrik Schmidt/picture alliance via Getty Images)

The expiration of the public health emergency in May also ended national test-sharing mandates that helped the Centers for Disease Control and Prevention (CDC) track the spread of SARS-CoV-2, the virus that causes COVID-19. As tests became more expensive and harder to come by, the CDC turned to wastewater testing — or collecting samples of pathogens in our poo — to monitor the national and regional spread of COVID-19

As Anne Zink, president of the Association of State and Territorial Health Officials and Alaska’s chief medical officer, told the New Yorker: Alaska is relying on wastewater testing because it “doesn’t have the money or political backing to set up daily nasal-swab testing sites.”

However, there is currently a lapse in data in one of the only COVID-19 monitoring systems remaining essentially due to a business deal. Last month, the CDC ended its contract with Biobot, the Cambridge, Massachusetts-based bioanalytics company that generated data for the wastewater monitoring system. The contract was transferred to Verily, which is owned by Google’s parent company, Alphabet. Some scientists — who have taken on the responsibility of monitoring and organizing Biobot’s data to keep the public aware of increasing cases — are concerned the transfer will throw a wrench in the modeling they’ve been sharing.

“Comparing the validity of their existing data, it's not as strong as Biobot's, but they haven't brought on all of the CDC-funded Biobot wastewater sites yet,” said Michael Hoerger, Ph.D., a psychologist at Tulane University who has been using Biobot’s data to post about the spread of COVID-19 on X (formerly Twitter) since January. “It's possible once they bring that over that they'll actually have much stronger [data] in some ways.”

“The biggest issue to me doing wastewater modeling is just its disruption. People rely on this data.”

Perhaps more concerning is that Biobot’s dashboard continues to track some wastewater facilities but is operating at only a fraction of its prior capacity — and Verily’s dashboard hasn’t yet picked up the slack, with about 350 sites involved in the transfer going back online in the next few weeks on a rolling basis. That's reflected in a lapse in the CDC’s wastewater data used to track COVID-19.

“The biggest issue to me doing wastewater modeling is just its disruption,” Hoerger told Salon in a phone interview. “People rely on this data.”

In 2020, the CDC launched the National Wastewater Surveillance System (NWSS) to track the spread of infectious diseases by testing for pathogens in sewage. However, the initial launch was criticized for being a patchwork rollout, and some counties, especially rural ones with less funding, faced barriers in implementing wastewater tracking systems. To beef up surveillance, the CDC partnered with private companies to expand access. In the spring of 2022, the agency partnered with Biobot, which added hundreds of new wastewater treatment facility sites to the dashboard.

Biobot CEO and cofounder Mariana Matus said the company will continue to monitor some of its sites but had to cut 35% of its employees due to losing the contract. The company is experiencing delays in getting back to its regular updates but will be “back to business as usual as soon as possible,” she shared in a statement. Neither Biobot nor Verily's press teams responded to Salon's request for comment before the publication of this story.

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“CDC NWSS is viewed by many citizens, public health officials, and politicians as a rare pandemic success story — a smart combination of public policy and private sector innovation in response to a national crisis,” Matus said. “Despite this setback, we remain committed to our company’s vision of transforming wastewater infrastructure into real-time data observatories — a vision that existed years before we started working with CDC.”

The CDC’s contract with Biobot expired on Sept. 15, 2023, and its new contract with Verily, which will test for not just SARS-CoV-2 but also mpox virus, will provide testing for up to 400 treatment plants across the U.S, including territories and tribal nations, said Tom Skinner, a CDC Public Affairs Officer.

Skinner told Salon in an email that wastewater results will be provided to public health agencies to support the COVID-19 response as well as the public, and that it was "testing with all previously participating sites is expected to restart soon." When the CDC similarly transferred contracts in the spring of 2022 from LuminUltra to Biobot, data was unavailable for 150 wastewater sites in 29 states for several weeks.

The “bumpy” transfer is reducing an already insufficient surveillance system.

One 2022 survey from the Rockefeller Foundation found two-thirds of state agencies planned to continue wastewater surveillance post-pandemic as part of a strategy to enhance preparedness for future ones, as it could potentially be used to test for any number of pathogens. There are certain aspects of Verily’s system that seem more promising than Biobot’s, like the ability to separate data by specific wastewater sites, Hoerger said.

Skinner said health equity is an ongoing priority for the NWSS moving forward.

"We work directly with health departments to respect their priorities and needs in wastewater surveillance," he wrote. "These may vary by community."

Time will tell how the CDC and local health departments use the data provided from the new contract with Verily to make recommendations about the spread of COVID-19. Data suggests cases are on the decline but some project they will once again rise in November. Although 7 million Americans have gotten the new batch of vaccines rolled out last month, uptake is also slower than this time last year.

Andrew Wang, Ph.D., a health equity researcher at Northwestern University Feinberg School of Medicine, said he is concerned the switch in contracts may change the sample processing and analyses in a way that prevents Verily’s data from being directly compared with Biobot’s hundreds of sites. The “bumpy” transfer is reducing an already insufficient surveillance system, Wang said.

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“The danger that exists during a lapse in national and local reporting prevents public health agencies and the general public from being able to have timely awareness of changes in COVID transmission in the community, especially when changes are significant during increases or surges in COVID transmission,” Wang told Salon in an email.

Skinner said methodologies may change with the new contract but that the agency's COVID tracker is designed to integrate these different methodologies "to provide a national picture of wastewater surveillance trends."

Still, Hoerger said he’d like to see the CDC’s wastewater system ramp up the number of testing sites it includes and make its data more readily available.

“It would have been great if they used their funding to do the sorts of analyses that I'm doing and that others are doing to estimate cases, to make forecasts and to take their raw wastewater data and put it into metrics that people actually care about,” Hoerger said.

By Elizabeth Hlavinka

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Covid-19 Mpox Pandemic Public Health Wastewater