James Andriano, laboratory manager at the Schenectady wastewater treatment plant, displays a beaker of untreated sewage on Friday, April 15, 2022. Samples are being shipped out twice weekly for analysis that helps determine the risk of COVID transmission in the community.

SCHENECTADY — Hidden within the millions of gallons of sewage flowing each day through the Schenectady wastewater treatment plant are microscopic clues about the direction the COVID pandemic is taking in the community.

People who have the virus in their systems excrete viral genetic material in their poop. 

So each time the toilet is flushed in tens of thousands of homes and businesses in Schenectady, Scotia, Glenville, Niskayuna and Rotterdam, any of these tiny biomarkers in the bowl flow to the northernmost corner of the city, where the sewage plant sits on the bank of the Mohawk River.

It’s one of dozens of sewage plants across the state that are collecting samples for lab analysis. 

And with more people using at-home COVID tests, which often aren’t included in official statistics, wastewater provides another, perhaps more-accurate way to quantify the pandemic as it appears to be on another upswing in many parts of the state.

David Larsen of Syracuse University, who’s coordinating the initiative in cooperation with the state Department of Health, uses an iceberg as a metaphor for the situation.

Positive tests, hospitalizations and deaths due to COVID are visible and can be counted, for the most part. Actual infections are much less visible.

“What’s lurking in the general population is much greater than what we see on the surface,” Larsen said.

Gathering, blending and testing dozens of small samples a day from a community’s sewers gives epidemiologists a look at what is not otherwise visible, as people without symptoms excrete fragments of the virus they are unknowingly carrying.

In mid-April, more sewage treatment plants across the state are seeing increases in COVID genetic markers than are seeing declines. Meanwhile, as of Thursday, the number of newly confirmed infections each day across New York has doubled from a month earlier and the number of people hospitalized with COVID has increased 50% over the month.

The crew that runs the Schenectady wastewater treatment plant is accustomed to collecting and testing samples to show state and federal regulators that they’re doing an effective job cleaning the water they dump into the Mohawk River.

On an average sunny day, 13 million gallons of sewage will flow through the plant, the combined effluent of 78,000 residents and many hundreds of non-residential users. 

If it rains all day, the volume could double to 25 or 30 million gallons.

Sampling is an automated process, plant manager Andy Coppola said. Every 15 minutes, about 3 ounces of water is diverted from the inflow into a jug. Once a day, an empty jug is swapped in. The full jug is given a few shakes and becomes a 24-hour composite sample.

The contents are about what you’d expect: cloudy water with little specks of assorted solid material settling out on the bottom. Not appetizing, but also not revolting, nor even smelly.

The treatment plant has its own laboratory on site, but lab manager Chris Andriano said it’s focused on the business of cleaning up sewage, not monitoring a pandemic. It tests for one specific type of organism — fecal coliform bacteria — and measures the amount of suspended solids in the treated water it is discharging.

To check for the ribonucleic acid of the COVID virus, a liter or so of water is poured off into a wide-mouth beaker, then into a plastic lab bottle for temperature-controlled shipment to one of three labs in New York that are doing the analysis for 77 wastewater plants in 45 counties through the state wastewater surveillance program.

Analysts will look at the number of gallons coming through each plant during the 24-hour period to adjust for volume, and they’ll measure the amount of crAssphage — a biomarker of human poop — to see how dilute the samples are. 

With these two variables quantified, they can tell how much COVID genetic material local residents are dropping into the toilet, and track how it is increasing or decreasing over time.

In this manner, the sewage of roughly 3.96 million New Yorkers outside New York City is used to predict COVID trends.

It has become a valuable addition to the effort to track the pandemic that hit the state more than 25 months ago. 

“New York’s robust COVID-19 wastewater program is proving to be another important public health tool as participation continues to expand statewide with nearly 80 sampling locations in more than 40 counties implementing surveillance sampling to date,” state Department of Health spokeswoman Erin Silk said via email Friday.

Wastewater sampling is not a new technique, said Larsen, an epidemiologist who is an assistant professor of public health at Syracuse University. It was previously used to track polio in the 20th century, he said. 

“We see a really good correlation” between rises in COVID genetic material in wastewater and rises in COVID infections in the population that generated that wastewater, Larsen said.

The wastewater surveillance project is a joint effort by the state departments of Health and Environmental Conservation, Syracuse University, several SUNY colleges and the federal Centers for Disease Control National Wastewater Surveillance System.

It’s an evolving joint effort.  “There’s a lot more to do,” Larsen said. 

A major focus now is to form an accurate prediction of hospitalization rates, he said, which would give the overstretched medical system some advance notice of increased demand. There’s also a search for more funding to realize the full potential of wastewater screening for other purposes, such as measuring the intensity of the annual influenza outbreak, the presence of drug-resistant bacteria, and the local severity of opioid abuse.

Tempe, Arizona, and some European cities already are monitoring drug abuse by measuring opioid compounds and their metabolites in raw sewage, Larsen said.

It’s a tool that can indicate whether more help is needed in a community, or whether the help being rendered is effective.

There’s no need to opt-in and there’s no way to opt out — everybody who poops potentially contributes to the test data. There’s also complete privacy — samples are submitted anonymously and are combined in the same jug.

Wastewater monitoring of COVID began in New York soon after the pandemic hit the state, both on the large scale (whole cities) and on the small scale (individual college dormitories).

But gathering data has been easier than using it as a wide-scale population health tool.

In mid-December, when Hochul announced expansion of the surveillance program, Health Commissioner Dr. Mary Bassett noted there was still much to learn about the tool.

The heavy lift in all this is not gathering and testing sewage, it’s understanding what the sample results mean in the real world, correlating the number of microscopic bits of COVID or fentanyl in a beaker of dirty water to the number of people falling ill or overdosing in the community.

“A lot of the work is trying to understand how to relate findings to clinical indicators,” Larsen said.

Gathering the samples is easy, said Coppola, manager of the Schenectady plant. There’s only a few extra minutes’ labor involved. The shipping materials are provided at no cost and postage is prepaid.

It’s also safe, said Andriano: The staff wears gloves and goggles to protect against microorganisms, COVID isn’t a waterborne disease, and COVID genetic material isn’t infectious.

Sewage treatment plant operators in general have been very cooperative, said Larsen, adding: “We’re hoping to get a treatment plant in every county.”

Shaila Raymond is one of six people working for the CDC Foundation on the New York wastewater project. She provides analysis to ten counties in the Capital Region and Mohawk Valley, and says the data gathered have been beneficial.

“Wastewater has the ability to predict three to five days before cases rise,” she said. “When we provide this data to county health departments, it allows them time to notify the community.”

Late Friday, the state’s online dashboard indicated the following two-week trends at area sewage treatment plants:

“All of my counties are very interested, they reach out with questions,” Raymond said. “Albany County is definitely into it, they’re constantly calling me and emailing me.”

Albany County on April 8 issued a community warning based on the recent spike in test data provided by the surveillance program. It said:  

“Measuring COVID levels in wastewater is a leading indicator of the coronavirus infection rate and a more accurate estimation, as it is not dependent on individuals making the choice to be tested. A spike in COVID intensity will likely mean a corresponding spike in COVID case counts and percent positivity in the near future.”

Six days later, Dr. Elizabeth Whalen, the county health commissioner, said the early warning had been accurate.

“This week we are certainly seeing an uptick in the number of cases,” she said Thursday via email.

Schenectady County spokeswoman Erin Roberts said the county Public Health Services has only recently begun receiving the data and is seeking insight on what the numbers mean and how best to use them.

“Wastewater surveillance can be incredibly useful in identifying case trends, especially with a significant reduction in the numbers of people being tested through the resources we’re accustomed to,” she said. “It can also be used to locate potential clusters of cases, enabling SCPHS to better focus their prevention, vaccination, and other response efforts.”

The increasing quality and quantity of data and foresight gained from wastewater testing is countered at times by decreasing interest within a population that has gone through three major surges of the virus in 25 months and is tired of taking precautions against it.

“I see people are just tired, they want to get out there,” Raymond said.

She’s hoping that people with COVID fatigue will take time to listen to what the data mean, and said efforts are underway to bring that message to more people.

With COVID numbers on the upswing across New York, some public health professionals were worried about the chances of transmission this weekend. 

It was a rare confluence of Easter, Passover and Ramadan, with the potential for close contact by a lot of people.

“Overall, I would say that for those who have been vaccinated and boosted per guidance, the risk of severe COVID illness is small. However, with increased community transmission we remain concerned about the unvaccinated, as well as those who are immune-compromised and elderly. With the increase in cases, it is prudent to consider wearing a mask indoors to prevent transmission, and to consider testing if symptomatic or before large gatherings — especially this holiday weekend.”

The positive lab test rate has jumped substantially in the Capital Region in the past month. But the positive test rate was never the best metric, and its value may be further diminished now, with widespread use of self-test kits.

Two other metrics tracked by the state Department of Health help show the course of the pandemic so far in 2022 in the eight-county region:

And the Capital Region is tied for best in the state at the moment. Eight of the nine other regions had higher infection rates as of Thursday, led by Central New York at 53.1 per 100,000. 

At the Schenectady wastewater plant on Anthony Street, which processes the poop of about half the county’s 158,000 residents, the COVID tests began to tick upward on March 29, said Coppola, the plant manager.

State DOH data show Schenectady County’s average daily new infections increasing more than 50% since then.

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