Annabelle Pan, a research scientist in Jordan Peccia's lab at Yale University, examines sludge samples. Steven Geringer/Yale University Photo

Of all the methods of measuring the progress of the coronavirus pandemic, one has been consistently reliable: the amount of the virus in sewage.

Yale University researchers have been sampling wastewater plants in Connecticut since the early stages of the pandemic, and the latest numbers from that testing have one official “cautiously optimistic” the omicron wave has finally crested in the state.

The recent data provide a clear example of the valuable insight that the sewage testing can provide to public health officials who are trying to deal with a pandemic that has stretched into its third year. But that type of analysis may not last much longer if Yale doesn’t find additional financing for its work.

Up until late last year, the state of Connecticut was paying the researchers at Yale to track the spread of COVID-19 through several large wastewater treatment plants that served more than 1 million people in the state.

Those samples closely traced the ebb and flow of the virus within many of the state’s most populated communities, including Bridgeport, Stamford, Norwich, Hartford, Waterbury, Danbury and New London.

But the state contract under which that work was performed ended in October 2021, and when it did, the public health data that was being collected was cut off in many locations.

Yale was able to find private donations to continue the wastewater sampling at one of its sites in New Haven for the first half of 2022. But that testing will also cease to exist this summer without additional financial support.

Max Reiss, a spokesman for Gov. Ned Lamont, said the data that Yale was able to publish between August 2020 and October 2021 proved to be an "effective tool" in monitoring the spread of the virus in Connecticut. But the state chose not to renew the $768,045 testing contract last fall, he said, because the numbers Yale was publishing each week were seen as a secondary source of information that only reinforced the data the state was already compiling from individual COVID tests.

In other parts of the country, however, epidemiologists and public health officials are now looking to sewage treatment plants as a more efficient and long-term solution for monitoring the persistent spread of the deadly virus.

There have been a large number of researchers -- many of them centered at universities throughout the country -- who have performed lab testing on fecal samples taken from wastewater treatment plants to track the virus's pace.

The testing those groups conducted repeatedly showed that samples taken from human waste can quickly and accurately detect spikes in coronavirus cases at the community level, even before people start showing symptoms or begin to seek out testing for the virus.

As a result, there is a growing effort at the federal level to expand the network of wastewater treatment plants that are screening for the genetic markers of COVID-19, which are found more frequently in sewage as the number of infections in a community rise.

The U.S. Centers for Disease Control is now encouraging additional testing at sewage treatment plants throughout the country, and the agency is in the process of setting up a new website where the data collected from those plants can be shared and analyzed. That effort is being referred to as a National Wastewater Surveillance System.

In response, states like New York are dramatically expanding the number of treatment plants they have partnered with.

Jordan Peccia, a professor of environmental engineering at Yale University who helped lead the wastewater testing in Connecticut, said the samples collected from treatment plants during the early stages of the pandemic were largely used as a backup source of data to confirm what the state's testing numbers were showing.

Since then, the science surrounding wastewater testing "rapidly matured," Peccia said, and the techniques that are used have proven to be a reliable indicator of how prevalent coronavirus is in a given town or city.

At this point, Peccia said, the samples being collected at wastewater plants likely provide a more accurate representation of the pandemic than the individual test results that are compiled by state health departments.

"I see an increased need for it now," he said.

Pulling samples from wastewater, Peccia said, is better than nasal swabs and saliva testing when it comes to understanding community-wide trends. It detects upticks in community spread faster than testing at drive-up sites or sampling in hospitals.

It also captures a picture of everyone within a geographic region, not just the people who are choosing to get tested because they are symptomatic or are required to be screened for their work. That's important at this point in the pandemic, when some people may not show any symptoms from the virus or are performing at-home tests that are not reported in daily testing numbers.

"I'm not being critical, but the information that you get from the compiled tests is getting worse and worse and worse," Peccia said. "And that's because the systems are stressed, and we are all doing these at-home tests now. We don't report that to anybody."

"The data stream that is going into governments that are tracking whether outbreaks are going up or going down is getting weaker and weaker, because the testing efforts are less and less controlled."

That doesn't mean that individual COVID tests don't have a role to play in the public health response. Individual nasal swabs and at-home testing kits are essential tools for telling an individual whether they are infected, Peccia said. Those tests inform people whether they need to isolate and take other precautions to stop the spread of the virus.

They just aren't the most efficient way to monitor whether a town, a county or a state is experiencing a spike in COVID cases, Peccia argued.

"We can't ever replace home testing kits or the testing apparatus that we have completely," Peccia added. "But wastewater is probably a much better way to look at trends in a community. It's a good thing to have, whether cases are high or cases are low."

Labs like the one at Yale are also able to run sequencing on the sewage samples to track which variants of the coronavirus are most common in a community at any given moment.

Take the wastewater sampling in New Haven. Over the past month, Peccia and his team were able to closely track the replacement of the delta variant with the omicron variant, which hit the state in late December and January. Omicron overtook delta by Dec. 23, the data show.

Relying on samples from centralized sewage treatment plants could also be a more cost-effective way to monitor the virus long into the future, Peccia said. Instead of paying for thousands of individual tests, public health officials could pay for a single sample each day that tracks the spread of the disease among hundreds of thousands of people.

"We really shouldn't be testing in order to track cases," Peccia argued. "That's a really expensive proposition."

When Yale's lab tests the wastewater sample from New Haven each day, they are effectively testing more than 200,000 people for COVID-19 at once, Peccia said. It captures everyone. Between the reagents needed to run the tests and the workers staffing the lab, it can cost as little as $50 per sample, he estimated.

Under its contract with the state, Peccia said the biggest cost was paying couriers to get the samples to their lab. In total, the state spent $768,045 in federal funding on Yale's testing efforts.

The investments in that type of work are still ongoing just across the border in New York, where officials are now attempting to set up a statewide "wastewater surveillance system."

The New York Department of Health is currently working with researchers at Syracuse University and the State University of New York to solidify a testing network that includes at least one treatment plant in each of the state's 62 counties.

David Larsen, an environmental epidemiologist at Syracuse, said he expects the statewide testing push for treatment plants in New York will enable local and state health officials to respond to the pandemic with more precision.

The data being collected from the plants could allow officials in New York to identify which communities have limited spread so local officials can safely end mask mandates and other precautionary measures, like social distancing.

It could also enable state health officials to quickly stand up more testing sites in areas where the virus is spreading rapidly or target vaccine drives in communities that are at the most risk.

"If we have a good understanding of what locations have high risk of transmission and what locations don't, then we can tailor our interventions to those locations," Larsen said.

All of those things could be important with the virus continuing to surge throughout most of the country.

"The virus isn't going away," Larsen said. "The virus will still be around. It will still be a threat. So if we are in this for the long haul, we need to build systems that support that."

Andrew joined CT Mirror as an investigative reporter in July 2021. Prior to moving to Connecticut, Andrew was a reporter at newspapers in North Dakota, West Virginia and most recently South Carolina. He’s covered business, utilities, environmental issues, the opioid crisis, local government and two state legislatures. Do you have a story tip? Reach Andrew at 843-592-9958