In NYC sewers, a tool for fighting the virus
Labs track outbreak in wastewater samples
New York City ’s sewers, whose lore has spawned films, children’s books and fantastical tales of alligator infestation, have now seized a role in the pandemic: Scientists are tracking outbreaks by monitoring the smelly, gray effluent that flows through underground pipes in hopes of identifying coronavirus clusters days before they appear through patient testing.
The undertaking, which has ramped up in recent weeks, has mirrored efforts across the country to surveil waterways for viral components, flushed down toilets by infected Americans who are excreting it in feces, even when asymptomatic or pre-symptomatic.
Rising traces of the virus were detected in New York in recent months in wastewater samples scooped from sewage treatment plants near coronavirus hotspots in Brooklyn, Queens and Staten Island. But now, scientists say, increases are being seen citywide, as infection rates reach their highest levels since the spring.
“At first, we thought it was a testing error, but then we kept seeing it,” Dr. Dimitri Katehis, a scientist with the city ’s Department of Environmental Protection, said of the initial heightened readings.
This kind of wastewater testing is especially challenging in New York, a sprawling and dense city that is served by the nation’s largest combined water and wastewater utility.
In smaller towns, such testing is easier to conduct. But in New York, 7,500 miles of pipes handle 1.3 billion to 3 billion gallons of wastewater a day, depending on rainfall levels, making it nearly impossible for the scientists to pinpoint exactly which neighborhoods the viral remnants are actually coming from.
This is one reason that city health officials say person-byperson testing is still the best tracking tool. On Tuesday, the seven-day average positive test rate was 4.94 percent, according to Mayor Bill de Blasio.
Still, Katehis and his team remain optimistic that the sewers will be helpful in detecting new outbreaks — especially when cases are not as widespread.
The city ’s health and water departments were working out how the current wastewater data could best be incorporated into the tracking of the virus, said Dr. Jay Varma, the mayor’s senior adviser for public health.
“It’s just one piece of a much larger puzzle, and we are still trying to figure out where it fits,” Varma said. “It is absolutely worth pursuing.”
The virus breaks down too rapidly to spread through sewage, Katehis said, but its surviving genetic components can be measured as viral indicators, which provide a type of earlywarning system. For instance, officials recorded heightened readings at the two treatment plants that serve Staten Island, corresponding to the increase in cases there early last month.
The city began planning out wastewater sampling sites and testing protocols in the spring, when New York was a global epicenter of the pandemic. By April, workers were collecting specimens. These early samples were frozen to be tested later to see if they aligned with sections of the city that had been recording large numbers of virus cases. (Preliminary tests indicated that they had.)
By September, the agency was taking six wastewater samples per day at each of its plants and testing them twice a week — its current testing rate. The agency provides the results to city health officials.
The samples are all analyzed at Newtown Creek, the wastewater treatment plant in North Brooklyn that is the city ’s largest and is notable for its huge, gleaming digestion tanks that break down organic materials in sewage.
A microbiology lab that was long used to measure bacteria in wastewater, as well as viruses like the poliovirus and norovirus, was expanded to include the coronavirus analyses.
Several academic partners helped the agency develop the lab methodology. Department officials said they have spent $250,000 on new equipment, acquired $300,000 from grants and academic partnerships and hired a handful of new staff members.
The recent spikes in cases that they detected provided a proving ground for the system, city officials said. The outbreaks in Brooklyn and Queens, identified through lab and rapid coronavirus tests of individual people, were also being borne out by heightened sewer readings at nearby plants, said Pam Elardo, a deputy commissioner who oversees the 14 plants.
Other municipalities in New York state have emulated the city ’s model and also send samples to the city ’s Department of Environmental Protection for testing, when it has extra room in its centrifuge.
In the lab, Katehis pointed to newly arrived wastewater samples from Plattsburgh.
He said that even when the pandemic was over, the testing system could be used to detect the flu and other outbreaks.