It’s in our sewage: tracking “low rumble” of COVID-19 cases
For the past two years, a Yale team has conducted weekly analyses of New Haven’s wastewater as a reliable early-warning measure of COVID-19’s trajectory and surges.
In the race to track COVID-19 infection rates, wastewater testing takes the lead in speed, accuracy and cost. The Yale team in charge of wastewater tracking reflected on a week of low COVID-19 levels in New Haven sewage, and the team’s overarching role in the pandemic.
After a toilet is flushed, the waste traverses sewers underground, eventually flowing into a sewage treatment plant to be processed. Cities around the globe have invested in these centralized plants, where a community’s waste is concentrated and mixed together. At New Haven’s wastewater treatment plant, the “sewage sludge” filtered out of water has proven valuable for tracking COVID-19’s trajectory. The Yale team responsible for this effort is led by professor of chemical and environmental engineering Jordan Peccia and PhD student Alessandro Zulli GRD ’26.
“The reason why [wastewater testing] tends to be more representative is the fact that you’re not subject to any biases in testing,” Zulli said. “When you do traditional testing, people have to come in, people have to be sick enough for it to prompt them to get a test and the testing site has to not be overwhelmed — which has happened both recently and in the past. While with wastewater, you’re getting a sample from every individual that is in your wastewater county, without any of those biases.”
“Sewage sludge” refers to the solid waste component separated from the liquid waste in wastewater. The team of researchers first investigated this sludge in March 2020, around the time of the first quarantine restrictions in Connecticut. Zulli had been studying viruses in the environment — one of which was coincidentally a related coronavirus — priming him for this chance to test for COVID-19 in environmental samples.
The team is currently trying to see if there is an outbreak of BA.2 — the novel sub-variant of the Omicron variant — in New Haven. According to Peccia, their wastewater analyses will likely provide the earliest stream of data for predictions about the virus’ trajectory. Weekly updates can be found on Peccia’s twitter feed. His most recent tweet described the past week’s BA.2 levels as “a low rumble” in New Haven wastewater.
While levels as of April 4 are higher than they were in mid-February — which was the lowest point for COVID-19 detection — this increase is relatively small and gradual. Meanwhile, BA.1 caused almost an “exponential growth” in levels, Peccia said. The slight rise in COVID-19 over the last couple of weeks is likely representative of a few local outbreaks “which then died down,” Zulli said.
“The BA.2 keeps going at a low rumble,” Peccia said. “There’s not a huge outbreak, but it’s not zero. There are little pockets of infections here and there, but it’s at least 20 times less than it was at the peak for BA.1.”
Given the current vaccination rates, an increasing number of people with COVID-19 may be asymptomatic. Even if these people do not seek testing, wastewater analyses would still detect their infection. This has allowed the wastewater testing system to track community levels of COVID-19 two to three days ahead of traditional testing data.
During the Omicron outbreak, the team was the first to indicate a peak in New Haven. Wastewater testing allowed detection before testing results did, and well before it could be seen in hospitalization rates. According to Zulli, the Connecticut Department of Health regularly uses this data to monitor outbreaks.
“We’ve worked over the last couple of years to make [the wastewater testing] really quick, efficient and low cost to transform it into something that can be used for public health,” Peccia said. “It is hundreds or thousands of times less expensive than testing programs. And so it’s important for us to make sure that our protocols are easy and accessible.”
Peccia’s lab group had been concerned with viruses in wastewater for years. However, Peccia focused on the afterlife of wastewater. Once processed at the treatment plant, wastewater may be applied as a fertilizer product or flow into rivers and other bodies of water. There has been public health concern about people being exposed to pathogens from drinking or swimming in such water. Fortunately, the team did not find risk of transmission for COVID-19 through wastewater.
Wastewater monitoring itself is nothing new. According to Zulli, this method had been used to detect polio virus in the United States decades earlier, but was less precise. Researchers would first test the polio virus levels in wastewater before a vaccination campaign. Afterwards, when polio virus in wastewater reached undetectable levels, the vaccination campaign could be considered successful.
“We definitely saw [COVID-19] vaccinations have an effect on the wastewater levels, particularly early on,” Zulli said. “As some of the new variants increased in vaccine evasion, we saw a resurgence. With BA.1 we saw much higher levels in wastewater, higher than we’d seen previously.”
Biotechnology advances have allowed researchers to track the number of RNA copies of COVID-19 per milliliter of wastewater. Building on their research, the Peccia group has expanded to endemic viruses — viruses which exist at a constant, predictable level in a community — which generally do not have good community coverage through traditional testing.
“There are a lot of endemic viruses that don’t have good coverage through traditional testing, but that still cause a lot of socioeconomic damage, and sadly, deaths,” Zulli said. “Influenza being a big one. [Testing] is still pretty much only limited to people who go to the hospital for influenza. Wastewater testing could easily give you a heads up on when things are happening and when [levels] are increasing.”
Peccia said that the project has never been that well-funded. While the state had previously funded the project for an entire year, enabling daily monitoring and expansion to seven Connecticut townships, that program ended. Max Weiss, a spokesperson for Gov. Ned Lamont, told the Hartford Courant that the state chose not to renew the contract as they already have data from individual COVID-19 tests.
A donation from Jonathan Rothberg GRD ’91 enabled the project to continue on a weekly basis. However, this funding will be finished by June, which will conclude the wastewater analysis project. According to Peccia, there does not seem to be any funding on the horizon, though he sees advantages of continuing wastewater testing in the fall, when a possible resurgence of COVID-19 may occur.
However, the Connecticut Department of Health continues to use Peccia’s team’s data as a secondary source for tracking the virus’ trajectory.
“The Connecticut Department of Health, I believe, pretty regularly uses our data,” Zulli said. “Before the BA.1 wave we would have weekly meetings with them to update on all seven of the townships [we covered] … so I do think they look at this data, particularly when they first start seeing a few more cases pop up, to see if the levels match up.”
Peccia earned his PhD from the University of Colorado in 2000 while studying the UV inactivation of bioaerosols.