Tracking viruses can be tricky.

Sewage provides a solution.
(All you have to do is flush.)

Here’s how a scrappy team of scientists, public health experts and plumbers is embracing wastewater surveillance as the future of disease tracking.

Aug. 17, 2022

The Covid-19 pandemic has turned sewage into gold.

People who are infected with the coronavirus shed the pathogen in their stool. By measuring and sequencing the viral material present in sewage, scientists can determine whether cases are rising in a particular area and which variants are circulating.

People excrete the virus even if they never seek testing or treatment. So wastewater surveillance has become a critical tool for keeping tabs on the virus, especially as Covid-19 testing has increasingly shifted to the home.

The institutions and localities that invested in wastewater surveillance over the last two years are discovering that it can be used to track other health threats, too. The Sewer Coronavirus Alert Network has already begun tracking the monkeypox virus in wastewater. And last week, New York City officials announced that polio had been detected in the city’s sewage.

Six months ago, NYC Health + Hospitals, a large, local health care system, began piloting its own wastewater surveillance system to track the coronavirus and the flu. Monkeypox and polio monitoring will start as soon as next week. There are a variety of approaches to wastewater surveillance. Here’s a visual guide to how the coronavirus tracking process works in one New York hospital.

Part 1: In the Hospital Basement

In which the toilets are flushed, sewage flows through a basement pipe and two intrepid scientists come to collect it.

New York City was the epicenter of the nation’s first Covid wave, and its hospitals were hit hard by several surges in the pandemic. In late 2021, Health + Hospitals decided to build a sustainable, long-term pathogen surveillance system to get ahead of future outbreaks, said Leopolda Silvera, the global health deputy at Elmhurst Hospital Center in Queens, which is part of the health care network.

The wastewater surveillance initiative is now running at 10 hospitals, but it began, in February, at Elmhurst.

Coronavirus fragments deposited into hospital toilets travel through the plumbing system and enter a sewage pipe in the basement.

Two plumbers in blue jackets wearing face masks lean against one of two large green pipes in a basement. One pipe is partially cut open, and one of the plumbers peers in, while the other plumber looks at the camera.

“This is our baby,” John Reilly, the supervisor plumber at Elmhurst, said, banging on the outside of the pipe. Every Monday, a member of the wastewater team drops a collection device, which the team calls the Contraption, into an opening in the pipe.

Over the next 24 hours, the wastewater will rush over, around and through the device.

The next day, two researchers arrive to check on the Contraption. “I must warn you that it’s going to be gross,” said Sherin Kannoly, who was on collection duty with Justin Silbiger.

A lab technician in a hair net, white jacket and blue rubber gloves holds the Contraption, a porous metal cylinder with a wire attached to it, and guides it into the hole cut into the large green basement pipe.

Wearing masks and gloves, they carefully remove the device from the pipe and then use tweezers to extract a tampon – yes, a tampon – from the mesh tube.

The researchers have experimented with different designs for the Contraption; one day this spring they were using a porous metal cylinder that contained a tampon to absorb the wastewater. Their current design uses charcoal water filters instead.

The technicians double-bag the waterlogged tampon to ensure it does not leak on the 15-minute drive across Queens.

A wide view of two lab technicians in the basement, one on the right placing a plastic bag containing a tampon sample into a plastic bag held open by the technician on the left. There are coolers and water bottles in the foreground on the floor, as well as the red waste bag.

Then they put the sample on ice and click the cooler shut. The dirty work is done.

A researcher in a face mask and white lab coat and green rubber gloves holds a tray of wastewater samples that have blue tops.
A street-level view of the Queens College building that contains the wastewater processing lab under an overcast sky. A person strolls by on the sidewalk.

Part 2: In the Queens College Lab

In which the levels of the virus are measured.

Before the pandemic hit, John Dennehy spent his time studying bacteriophages, or viruses that infect bacteria, often isolating them from wastewater. “When the pandemic came, I felt like I had an obligation as a virologist to contribute my skills,” Dr. Dennehy said.

In 2020, Dr. Dennehy, with colleagues including Monica Trujillo, a microbiologist at Queensborough Community College, began testing samples of the city’s wastewater for the coronavirus. When they heard that the hospitals wanted to create their own surveillance system, they were eager to help. Dr. Dennehy’s lab at Queens College is the first stop for the hospital samples.

The sample is pasteurized in a hot water bath, making it safe for scientists to handle. Then, the water is filtered to remove solids and debris.

The scientists add two compounds, polyethylene glycol and sodium chloride, to help the virus form a solid precipitate.

A close-up view of a white refrigerator door adorned with many magnets and signs. The most prominent signs read, “Not for flammable material storage,” and “Important! This laboratory refrigerator is not intended for storage of unsealed materials of corrosive materials.” The magnets are mostly colorful souvenir magnets from places like Las Vegas, Sri Lanka, Oregon, Machupiccu and Sevilla.

The sample incubates in the fridge overnight and then spins in a centrifuge. When the process is complete, the researchers are left with a tiny pellet of virus.

They add a bright pink chemical called TRIzol to extract the RNA from the viral pellet. (In real life, science rarely looks the way it does in the movies – the shockingly pink concoction is an exception, the researchers noted with enthusiasm.)

A wide, slightly elevated view of the Queens College lab space, whose shelves are replete with beakers, pipettes, weighing machines, notebooks and other assorted equipment and materials. At left, a lab technician in a white coat with her back to the viewer works at a lab bench.

To determine how much virus is present in the sample, the researchers use P.C.R., the same method used to test people for the virus. They put the RNA they’ve extracted into the tiny wells of a P.C.R. plate and then slide the plate into a machine known as a thermal cycler.

The machine will amplify – make copies of – the viral RNA and measure how much is present. The more RNA there is, the more virus presumably is present in the wastewater and, by extension, in the hospital community.

The researchers share the results with hospital officials. The program has already proven promising.

A double-portrait taken in a brick-walled hallway lit from above by skylights, showing John Dennehy, in a lab coat, left, and Monica Trujillo, who stand in a square of light cast from the skylight.
A close-up of a computer monitor showing various figures plotted on a graph in several colors. Hands belonging to a person out of view with white lab coat sleeves points to the graph.

Dr. Dennehy, Dr. Trujillo and their colleagues have found that the amount of coronavirus and influenza in the hospital’s wastewater often began rising 10 to 14 days before the hospital saw an increase in Covid and flu patients.

“When you are testing everything and everybody, the wastewater doesn’t give you such a big lead,” Dr. Trujillo said. But once coronavirus testing in the city dropped off, the wastewater data became especially valuable. “It’s really something that we are hoping that will be incorporated as another tool for public health,” she said.

Leopolda Silvera, wearing a black suit jacket and a black shirt, leans against the railing of an accessibility ramp, looking directly at the viewer.

Ms. Silvera, the global health deputy at Elmhurst, ferries the Queens College samples, and some additional bottles of wastewater, to a commercial laboratory …

A close view of a small refrigerator on the floor, bearing a paper sign that reads “Sample drop off here.”

…and deposits them in the fridge…

A close view of two plastic bottles containing sample water sit in a greenish tray in some ice. One of the bottles has a hand-written label reading “Queens Hospital Grab Sample, 5-11-22, Manhole.”

…to keep them cool until they’re ready to be processed.

Part 3: In the Pandemic Response Lab

In which variants are identified.

Opentrons Labworks Inc., a laboratory robotics company, created the Pandemic Response Lab in 2020 to provide high-volume, high-speed coronavirus testing and, later, coronavirus sequencing of patient samples. The search for viral variants in wastewater involves essentially the same process.

“It just so happens that that sample is not coming from a person but from wastewater, which, you know, has some elements that came from people,” said Jonathan Brennan-Badal, the chief executive of Opentrons.

The Queens College laboratory isolated the virus’s RNA. To sequence the genetic material, the Pandemic Response Lab first converts the RNA into DNA, a process known as reverse transcription.

A metal shelf contains two rows of thermal cycler machines, each with a small touch-screen window and a bright orange label bearing names like “Dopey,” “Doc,” “Snow White,” etc., with a technician to the left mostly out of view except for her sleeves, which are blue, and her hands, which wear black rubber gloves. A number of the machines have fluorescent magenta Post-It notes affixed to them with hand-written notes.

A pipetting robot adds the necessary chemicals and enzymes to a plate containing small amounts of the viral RNA. The plate is then placed into a thermal cycler – each one emblazoned with a Snow White-inspired name – and the enzymes convert the RNA into DNA.

The scientists shuffle the sample back and forth between a small army of laboratory robots.

The robots add chemicals and enzymes, and the samples are manipulated in a variety of ways. The viral DNA is amplified and then chopped up into fragments that are short enough to be read by the sequencer.

These fragments are then amplified and marked with molecular barcodes, which allow the scientists to later distinguish individual samples from a pool of them. Finally, the samples are cleaned and then combined, sometimes by hand.

After all the humans and robots have completed their respective tasks, the pooled samples are loaded into the sequencer, which determines the genetic sequence of each fragment, allowing scientists to determine what mutations and variants are present.

In the lab space, a diverse group of seven researchers in blue lab jackets pose for a portrait, four in the front row, three in the back.

The results are automatically uploaded to a server and processed. The findings are reported to the hospitals weekly.

The sequencing results “reflect what has been seen with clinical data,” Ms. Silvera said. As the BA.4 and BA.5 variants of the coronavirus spread, for instance, they began to “dominate” the wastewater samples, she added.

The hospital project is just one of many springing up across the country and around the world. New York City has its own city-wide wastewater surveillance system, which involves collecting sewage samples from municipal wastewater facilities, including the Newtown Creek Wastewater Treatment Plant.

A ground-level view at dusk of the Newtown Creek Wastewater Treatment Plant, looking up at its large, bulbous and reflective “digester eggs” and a catwalk above them. There is a tall metal fence in the foreground, and a streetlight lit at right.

And the hospital team is already looking toward the future, considering how the same system might be harnessed to monitor a variety of potential health threats. “The information is invaluable, honestly,” Ms. Silvera said.

And all it takes is a flush.

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