Wastewater data mining evolving
Method that tracks virus may detect opioid use, resistance factors
With COVID -19 here to stay — albeit in a less lethal, endemic form — scientists hope the monitoring of traces of the virus in wastewater will eventually serve as an early warning system, enabling governments to better anticipate, track and respond to outbreaks.
Since the New York State Wastewater Surveillance dashboard went live in January, some county health officials, including in Albany, have used it to alert communities of elevated coronavirus rates, but the science is still limited, experts say.
The state Department of Health-run program shows whether a pathogen causing COVID -19 is present in a community and whether community levels are rising or falling, according to Syracuse University researcher Dustin Hill, who designed the dashboard. Humans shed the virus in feces, even if they are asymptomatic, according to the Centers for Disease Control and Prevention.
Similar monitoring systems have cropped up on the municipal level — New York City is working on its own wastewater testing project — and several college campuses, including
Loudonville’s Siena College, have been experimenting with the program on a smaller scale.
But the data is still patchy, varying based on the method and frequency of sample collection, the coverage area of a particular sewage treatment plant and the weather, which can dilute the sample, according to Hill.
“Sometimes outbreaks may happen in the suburbs and if we are monitoring a treatment plant in the city, we may not get that outbreak ahead of time and that’s why the expansion of this program will be important,” Hill said.
The two-week trend line is often more important than a single point in time, as evidenced by the state’s most recent COVID-19 surge, driven by new omicron variants BA.2.12.1 and BA.2, that emerged in central New York in early April and has since spread to most counties north of New York City.
Three weeks ago, “we had three sites in central New York where there’s been this hotbed of activity and it seemed like we were heading downward, but the next week, we were back up,” Hill said.
In order for its full utility to be realized, the technology must be streamlined across a broad geographic area, experts say.
In New York, wastewater surveillance began in August 2020 as a six-week pilot program in Erie, Onondaga, Albany and Orange counties and gradually expanded across the state.
Now samples are drawn from 88 waste treatment plants in 48 New York counties. The dashboard is managed by the state Department of Health, Syracuse University and the SUNY College of Environmental Science and Forestry and the state Department of Environmental Conservation.
The map estimates the probability of transmission (low, moderate or substantial to high) in participating counties based on levels of RNA in the sewer system and the state’s estimated number of cases in that community.
Currently, RNA levels in wastewater across the state correlate with a substantial to high risk of transmission or greater than 50 cases per population of 100,000.
“It’s not a perfect science yet and we are still working to improve it ... but what we are seeing now is that levels are higher than we’d want them to be from a public health perspective,” Hill said.
Several other states are tracking the virus in wastewater and the CDC recently created its own dashboard to aggregate the state-level data.
Wastewater surveillance has been around for decades but it had never been used for respiratory diseases.
Pre-COVID -19, public health experts searched for environmental causes of a disease based on the way the pathogen was transmitted, according to David Larsen, an epidemiologist and Syracuse University professor who directs the state’s wastewater surveillance network.
Wastewater testing made sense for polio and cholera, for example. Those diseases are transmitted fecally and orally, he said.
In early 2020, Dutch scientists found that the pathogen causing COVID -19 could be detected in wastewater using DNA testing methods before an outbreak.
Using wastewater to track a respiratory illness is “a paradigm shift” for epidemiologists that will have implications for the management of influenza, tuberculosis and other communicable diseases, according to Larsen.
“Wastewater surveillance provides intelligence; it provides an understanding of the burden, it provides an understanding of direction,” Larsen said.
But the data is only as good as the frequency of samples drawn. To refine the program and make it more efficient, scientists are looking to incorporate in-stream “biosensors” that supply real-time data and DNA analyzing techniques that can indicate the severity of an infection.
Once the infrastructure is in place, experts predict that wastewater testing has the potential to become a powerful and costeffective public health tool that, in addition to monitoring disease, can track things like opioid use and antimicrobial resistance.
Over the course of the pandemic, the wastewater dashboard has gotten more attention from public health officials as the state’s clinical testing metrics became less reliable, due to asymptomatic cases and the availability of at-home tests, which are rarely reported. COVID -19 hospitalizations and deaths are now seen as more accurate indicators of an outbreak than the number of positive tests in a community, but those figures tend to lag infection rates by weeks.
College campuses, as smaller, more-controlled environments, offer a model of how wastewater testing can be incorporated into a robust COVID -19 mitigation strategy.
When Siena College environmental studies professor Kate Meierdiercks first approached Siena officials in September 2020 with the idea of creating a wastewater monitoring program on the campus, she imagined it would be a one-semester educational experiment.
But as the pandemic evolved, so did the campus wastewater surveillance program.
The program was useful as an early warning system in the early days before COVID -19 tests were widely available on the 3,300-student campus.
Wastewater samples were drawn at each dormitory. When the water in a particular building turned up “hot,” or with detectable levels of the virus, the college would direct resources to students in that building.
At the time, the only way to manage the virus was with measures like masking, contact tracing and quarantining after exposure.
Now that the campus population is vaccinated, the system is used to observe campuswide trends rather than to locate outbreaks, according to Meierdiercks.
With untraceable athome tests widely used, “it’s more of a check on whether or not the clinical tests that are being reported to the college match what we see in the wastewater,” she said.
There are pros and cons to the method. The wastewater monitoring system is less invasive and more cost-effective than other types of surveillance testing used at colleges and universities.
Unlike the batch testing used to catch infections on State University of New York campuses, wastewater surveillance cannot link an infection to a specific person or even identify how many in a particular building are infected.
“We use the Swiss cheese analogy,” she said. “The wastewater data is not going to be 100 percent, but we also know that clinical testing is not perfect. Neither method is perfect but when we use them together, it can be a pretty powerful tool to understanding what’s happening on campus.”