Doing the dirty work
Scientists have been tracking wastewater to keep tabs on COVID-19, flu, monkeypox and polio viruses
The COVID-19 pandemic has turned sewage into gold.
People infected with the coronavirus shed the germ 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 COVID19 testing has increasingly shifted to the home.
The institutions and localities that invested in wastewater surveillance during the past two years are discovering that it can track other health threats, too. The Sewer Coronavirus Alert Network has been tracking the monkeypox virus in wastewater. And New York City officials said that polio had been detected in the city’s sewage.
Earlier this year, health care system NYC Health + Hospitals began piloting its own wastewater surveillance system to track the coronavirus and the flu.
There are various approaches to wastewater surveillance. Here is a description of how coronavirus tracking works at one New York hospital.
New York City was the epicenter
of the nation’s first COVID-19 wave, and its hospitals were hit hard in the pandemic. In late 2021, Health + Hospitals decided to build a sustainable, long-term virus surveillance system to get ahead of future outbreaks, said Leopolda Silvera,
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 a number of hospitals.
Coronavirus fragments deposited into hospital toilets travel through the plumbing system and enter a sewage pipe in the basement.
“This is our baby,” John Reilly, 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 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.
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 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 doublebag the waterlogged tampon to ensure it does not leak. Then they put the sample on ice and click the cooler shut. The dirty work is done.
The technicians carry the cooler to the car and drive the sample to Queens College.
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,” he said.
In 2020, 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. Dennehy’s lab at Queens College is the first stop for the hospital samples.
First, 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.
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. Finally, they add a bright pink chemical, TRIzol, to extract the RNA from the viral pellet.
To determine how much virus is present in the sample, the researchers use a polymerase chain reaction, the same method used to test people for the virus. They put the RNA they have extracted into the tiny wells of a PCR plate and then slide the plate into a machine known as a thermal cycler.
The machine will 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.
Dennehy, 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-19 and flu patients.
“When you are testing everything and everybody, the wastewater doesn’t give you such a big lead,” 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.
Silvera, the global health deputy at Elmhurst, ferries the Queens College samples, and some additional bottles of wastewater, to a laboratory and deposits them in a refrigerator until they are ready to be processed.
Opentrons Labworks,
a laboratory robotics company, created the Pandemic Response Lab in 2020 to provide highvolume, 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 BrennanBadal,
CEO of Opentrons.
The Queens College laboratory isolated the virus’s RNA. To sequence the material, the Pandemic Response Lab first converts the RNA into DNA using certain chemicals and enzymes.
Copies are made of the viral DNA and then chopped into fragments that are short enough to be read by the sequencer.
These fragments are marked with molecular bar codes, which allow the scientists to later distinguish individual samples from a pool of them. Finally, the samples are cleaned and then combined.
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. The results are uploaded to a server and processed. Findings are reported to hospitals weekly.
The sequencing results “reflect what has been seen with clinical data,” 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 citywide wastewater surveillance system, which involves collecting sewage samples from municipal wastewater facilities.
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,” Silvera said.
And all it takes is a flush.