New York is scouring its sewers for COVID-19. Are we learning enough from what we flush?

December 4, 2020 Rachel Holliday Smith, THE CITY
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As the COVID-19 positivity rate rises across the five boroughs, city scientists are working to get the lowdown on the virus, straight from New Yorkers’ poop.

Unlike many municipalities, New York is testing wastewater for the coronavirus in an effort to trace — and stop — the spread. But experts on sewage monitoring say the city could be using the technology to do more to contain the virus.

Microbiologists working for the city’s Department of Environmental Protection test samples taken twice a week by DEP staff at 14 wastewater treatment plants.

At the plant at Newtown Creek in Greenpoint, Brooklyn, the largest facility by volume in the city, sampling means walking down four stories to large concrete basins that open to a river of raw sewage.

From there, a worker lowers two empty bottles — held securely inside a contraption made of cut PVC pipe, heavy bolts and a long rope — into the smelly stream, waits for them to fill and hoists them back out to deliver to the DEP’s on-site laboratory.

Still, some experts emphasize those samples are mere drops taken from a waste ocean. Each of New York’s treatment plants treat sewage from more people than the entirety of many smaller cities.

DEP Commissioner Vincent Sapienza noted the Newtown Creek plant collects the waste of about a million New Yorkers. Even the city’s smallest facilities handle “a couple hundred thousand,” he told THE CITY.

The Newtown Creek Wastewater Treatment Plant in Greenpoint services parts of Manhattan, Brooklyn and Queens. Photo: Ben Fractenberg/THE CITY

“The data we collect isn’t that granular. We can’t say it’s a specific neighborhood or a specific block where things may be happening,” he said. “Right now, we’re using the data, sharing it with the health department to say, ‘Hey, there may be something there.’”

At that point, the DEP data hopefully points the health experts in the right direction to then use results from individual COVID tests to further monitor the virus, he added.

‘Everybody uses the restroom’

No municipality should rely solely on wastewater monitoring when trying to trace the spread of the coronavirus and the method should not replace laboratory testing of individuals, said Adam Gushgari, CEO of AquaVitas, a wastewater testing group affiliated with Arizona State University.

“Ideally, the best case scenario is you have both going in tandem because, frankly, one cannot replace the other,” he said.

But the scientific community is increasingly looking at the wastewater approach as a more comprehensive, equitable way of monitoring the virus.

“Everybody uses the restroom. We collect everybody’s sample through this method. And that’s the way that we can catch the asymptomatic cases,” Gushgari said.

Just last week, the federal government reportedly took a major step toward implementing wastewater epidemiology in the U.S.

On Nov. 27, AquaVitas said it was chosen by the U.S. Departments of Health and Human Services and the Centers of Disease Control and Prevention to run a national wastewater testing study. The initiative aims to include up to 100 treatment plants in the first phase, which could begin by the end of the month, Gushgari told THE CITY.

Rolf Halden, director of the Center for Environmental Health Engineering at the Biodesign Institute at ASU, encouraged New York to join the national study — and to increase the frequency and locations of its sewage testing scheme.

To him, wastewater monitoring is critical to keeping the virus in check. In Tempe, Ariz., Halden was part of a team from ASU that created a testing program in 2018 to track opioid usage in the city — then switched gears last year to start monitoring the common flu.

When COVID-19 hit, the team was set to begin tracking the virus, he said. Earlier this summer, ASU researchers monitored a growing outbreak in the town of Guadalupe, which helped local leaders tamp down the spread.

“It will never supplant clinical testing. But if you find the right balance between screening for clusters of infections, and then doing individual tests right there where you have a cluster, and then you do contact tracing, then you are on your way to doing everything you can in order to contain the pandemic,” he said.

An ‘equitable’ approach

Specificity is key, however, he said. To improve accuracy and “to be equitable to the population of New York,” Halden believes the city must collect samples from more locations — and a lot more often.

Often, it can take the better half of a day for the contents of a toilet to reach a treatment plant, and the “signal” from the virus diminishes with time, Halden said.

He encouraged New York to join the HHS study, and to do “more refined monitoring.”

“I think it would be highly desirable to supplement the sampling,” he said.

Department of Environmental Protection microbiologist Alexander Clare helps test wastewater samples for the coronavirus inside at a lab at the Newtown Creek facility in Brooklyn. Photo: Ben Fractenberg/THE CITY

Besides that, doing wastewater testing is, in his view, gets a big bang for the buck. In a cost-benefit analysis he co-wrote and published this summer, Halden found that using wastewater-based epidemiology in combination with clinical testing would be a much cheaper option than using traditional testing alone.

“The tests that we use [for wastewater testing] are essentially identical to the saliva tests or the nasal swab. So, for the cost for one test — if you test one individual, you could also test a neighborhood,” he said. “It’s orders of magnitude more effective.”

Waiting for the future

For now, the city health department and DEP are watching, learning and waiting.

Sapienza said the DEP is “still in the early stages of understanding how this technology works” and sees it as too soon to start thinking about how to get “into more specific neighborhoods.”

Dr. Jay Varma, senior health advisor to Mayor Bill de Blasio, said the wastewater testing happening in the city helps officials get a handle on methodology, data interpretation and what the statistics look like “when levels are high,” as a baseline for the future.

But when, or if, the city may do more wastewater testing is up in the air, he said, partly because of the administration’s confidence in individual laboratory tests.

“We made a tremendous investment in building up human testing,” Varma told THE CITY. “As a result of that, our data from humans being tested — you know, getting a sample from your nose — is really good and gives us a lot of geographically targeted information that we can act on.”

Varma and Sapienza both said wastewater testing could be much more effective in the future, as vaccines come into use and widespread personal testing ebbs.

“After the pandemic kind of wanes, and the vaccine comes out next year, and people are inoculated, the sewage testing may be more beneficial at that time, because then we can say, ‘Hey, there’s truly zero infection going on,’ or ‘Hey, you know, it looks like people are getting infected again, what’s going on?’” the DEP commissioner said.

Varma said health officials are discussing other ways to use wastewater science down the road, including testing in “a very defined geographic area” or specific facility.

Some are already doing just that. The Ohio prison system has started testing sewage at correctional sites in 36 cities, and many colleges and universities are doing the same on their campuses, including Columbia University.

Even if New York wanted to increase its testing capacity, logistic hurdles remain. Because of the demand for testing equipment from all over the world, getting basic parts to test the samples has been a battle, Sapienza said.

“We had a three-month delivery time on this large centrifuge. We’re still waiting for another piece of this PCR machine,” he said, referring to the polymerase chain reaction machines typically used for laboratory COVID-19 tests. “We have to get in line with everybody else to get this stuff.”

‘Ending this damn thing’

Halden of ASU knows how long it can take to get a testing system up and running. He said it took years for him and his colleagues to cajole Tempe’s leaders to allow researchers to implement their opioid-monitoring scheme.

Now, there is more awareness of sewage testing all over the country, but few experts available and rarely a clear path for how best to implement the method.

“The issue with the science is it is in no man’s land between medicine, public health and environmental engineering,” he said.

To Gushgari, the effort to help find a solution for managing the pandemic is worth it.

“The important part here is ending this damn thing. I’m so sick of it. It’s time. We’ve got to get data in the hands of the decision makers,” he said.

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