NEW YORK >> 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 hot spots 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 and on college campuses, 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-by-person testing is still the best tool to track the virus. On Tuesday, the seven-day average positive test rate was 4.94%, 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 early-warning 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.

This was the case, for example, at the Owls Head plant in Brooklyn, which treats wastewater from Borough Park, Gravesend and Bensonhurst — all of which had outbreaks. The Bowery Bay plant in Astoria, Queens, showed increases linked to outbreaks in Kew Gardens and other areas, agency officials said.

“We were definitely seeing a parallel,” Elardo said as she entered an intake location at the Newtown Creek plant where wastewater is strained for stray objects — which included on this day a dead pigeon, a $20 bill and clumps of sanitary wipes.

A deputy chief at the plant, Michael Radano, lowered a sampling container down with a rope into an open pipe bearing a river of pungent wastewater from Brooklyn and Queens sewers.

Vincent Sapienza, commissioner of the Environmental Protection Department, watched Radano and said his agency was eager to be on the front lines of fighting the virus.

Sewer work is not glamorous, but the department’s employees take pride in maintaining a system that most New Yorkers know little about yet rely heavily upon. After pulling up the sample, Radano said he was a third-generation worker for the department.

Sapienza chuckled and said, “He’s got sewage running through his veins.”

In the lab, technicians conduct the sewage testing in protective biosafety cabinets. The samples are pasteurized and put through a centrifuge to remove other pathogens, so that the traces of the virus can be measured, according to Katehis.

Experts say that ideally, the concentration of viral components in a sample can indicate the rough number of infected people in a broad area. But the testing has limitations in such a large system. The Newtown Creek plant, for example, handles about 300 million gallons of wastewater a day from parts of Brooklyn, Queens and Manhattan that have a combined population of roughly 1 million people. Even the city’s smallest plant, the Rockaway facility in Queens, handles waste from about 90,000 people.

Also, New Yorkers’ household sewage is combined with runoff from storm drains, which dilutes viral components in the wastewater.

So, while city health officials say sewer surveillance may prove helpful, they are measured in their public assessment of it — especially when comparing it with simply testing patients for the coronavirus.

Varma, of the mayor’s office, said that since the city’s health department only began receiving samples in September, it was still too early to gauge how vital it might be.

Dr. Dave Chokshi, the city’s health commissioner, said in a statement that the testing was “promising and may prove to have great value for disease surveillance and decision-making in the months to come.” But, he added, “We have to follow the science in determining how to use the data from this innovative program.”

Still, New York City seems to be testing in more locations than many other municipalities.

Newsha Ghaeli, president of Biobot Analytics, a wastewater epidemiology company that handles testing for roughly 200 municipalities nationwide — including agencies that handle Boston and Miami — said that while New York’s 14 sampling sites were far more than most of their municipal clients, New York City could increase its number of sites and do more localized sampling around communities that have had a history of outbreaks.

Katehis said his department was planning to perhaps expand the testing to nearly 100 pumping stations. The department has begun acquiring more equipment and hiring researchers and microbiologists to allow for sampling from sewers further upstream, to zero in on the source of heightened levels.

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, New York, which were sitting next to a deep freezer where the specimens are kept.

He said that even when the pandemic was over, the testing system could be used to detect the flu and other possible outbreaks.

“We’re using the sewers,” he said, “to keep people healthy.”