Most people would turn away at the mention of sewage sludge, the semi-solid residual material that’s left behind after wastewater has been processed at a water treatment plant. But a team of researchers led by Yale Professor of Chemical and Environmental Engineering Jordan Peccia has found that the presence of SARS-CoV-2 RNA in wastewater sludge can track community infection dynamics—and do so a few days in advance of test results.
The study, published in Nature Biotechnology, found a correlation between viral concentrations in wastewater and testing and hospitalization data in New Haven over 10 weeks of sampling, from March 19 to June 1. The study showed that wastewater sludge is a reliable indicator—and even predictor—of rates of coronavirus infection. The team continues to sample sewage sludge daily from six water treatment plants across Connecticut. Their research currently informs the statewide coronavirus response plan, with data made publicly available on the YaleCOVIDwastewater.com website.
“Not only are you able to see this increase in wastewater concentrations during an outbreak that you might not necessarily see in the cases quite yet, but we can take that case data and we can adjust it, so that you can kind of predict what’s going to [happen] and get a week’s head start on things,” Peccia said.
Through their research, the team found that sludge results led the number and percentage of positive tests by date of specimen collection by zero to two days, hospital admissions by one to four days, and the number of positive tests by report date by six to eight days.
Peccia explained that there is a history of looking to sewage sludge for the presence of pathogens, most recently to monitor polio infections, because pathogens are often passed from humans to their wastewater. Early on in the coronavirus pandemic, testing shortages and delays made it difficult to accurately represent true rates of coronavirus infection, and wastewater is widely representative of large populations. Nearly everyone’s sewage ends up at a centralized water treatment plant—New Haven’s plant alone, for example, serves two hundred thousand people. Further, according to Peccia, coronavirus had been detected in wastewater through other, unrelated, projects. Thus, using sewage sludge to track coronavirus infections was “only natural,” Peccia said.
It typically takes the research team about twelve hours for the team to get from a sewage sludge sample to a number of copies of viral RNA present in that sample, with daily sampling and deliveries four times a week, according to Peccia. On delivery days, before 7 a.m., the team’s courier drives around the state to pick up sewage sludge samples from each site—an almost-three-hundred-mile route that includes New Haven, Stamford, Hartford, Norwich, Bridgeport and New London—before the samples are dropped off at the lab around 11 a.m. Then, it takes four to five hours to extract RNA from the samples through a complex filtration process. Isolated RNA pellets are dissolved in ribonuclease-free water, and total RNA concentration is calculated by spectrophotometry, a type of electromagnetic spectroscopy that tests how much a chemical substance absorbs light to determine the amount present. Using qRT–PCR, the team then measures the presence of SARS-CoV-2 RNA and calculates a final number, in copies per milliliter, by late that evening.
According to Peccia, data from sludge results comes a week in advance of testing reports because infected individuals start shedding pathogens into wastewater before they even “know to get tested”—and when they do get tested, it takes days for results to be reported back to them. Peccia added that the current wastewater data is an alarming indicator of yet another wave of coronavirus infections in Connecticut.
Monitoring sewage sludge, according to the paper, is a “broadly applicable strategy.” Currently, the team shares its data with state officials and their virus response teams to inform the state’s sampling, analysis and monitoring of the virus. The team is also funded by the CDC to inform additional broader projects.
 Peccia, J., Zulli, A., Brackney, D.E. et al. Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics. Nat Biotechnol 38, 1164–1167 (2020). https://doi.org/10.1038/s41587-020-0684-z