To Detect COVID Trends, Including DELTA’S Emergence, CUNY Scientists Turn To The Sewers

By Lida Tunesi

In early 2020, Professor John Dennehy (GC/Queens, Biology) was searching for a way to help battle the growing pandemic. As a researcher of virus ecology and evolution he was in a good position to help, but needed to find the right avenue.

The answer, it turned out, was in the sewers. With Professor Monica Trujillo from Queensborough Community College, Dennehy established a partnership with the city and began looking at concentrations of the coronavirus in samples of New York City wastewater. Over a year later the work continues: Dennehy’s lab receives samples every week from all 14 of the city’s wastewater treatment plants, analyzes the samples, and sends the data back to city agencies. The next week, the process starts again. Dennehy and Trujillo also monitor wastewater from a Queens College dorm that houses about 130 people.

“I was looking for ways to contribute my skills to this global crisis,” Dennehy said. “My friend Monica Trujillo sent me a paper about monitoring SARS-CoV-2 in sewage and we decided to pursue this.”

Testing wastewater allows scientists to monitor large populations in a cost-effective way, Dennehy explained. It can also help the city take preemptive measures, since viral material from infected people can show up in the wastewater before those people get tested. Similarly, wastewater testing data captures asymptomatic people who might not get tested at all. However, the method can’t precisely estimate a total number of cases and is better suited to identifying trends. For example, the group has been monitoring the presence of the delta variant.

“We first observed delta in mid-April at slightly the detection threshold in a single sewershed,” Dennehy said. “It quickly spread to all areas of the city and now every area of the city is dominated by the delta variant.”

The work has two parts. First, Dennehy and his colleagues determine how many virus particles, including all variants, there are per liter of wastewater in each sample. This data goes to the city’s Department of Environmental Protection, or DEP. Next, they do targeted sequencing of viral RNA in the samples to see which variants are present, and send this info to the Department of Health and Mental Hygiene. As part of their contract with the city, Dennehy’s group also trains the DEP Newtown Creek microbiology lab in the testing protocols they have developed.

“Previously, my lab had been working on extracting virus and bacterial genetic material from environmental samples such as outflow from combined sewage pipes,” Dennehy said, “so we had the right skills and equipment for this type of work.”

Dennehy has been sequencing RNA in search of variants since January 2021, but started analyzing samples for virus concentrations back in June 2020.

“We reached out to a lot of people from various city agencies but weren’t getting much traction,” he said. “Finally, Monica sent an email to Pam Elardo, the deputy commissioner of the DEP. Pam responded within two hours and got us in touch with the right people. Within days, we were analyzing samples.”

Published by the Office of Communications and Marketing.