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Wastewater unlocks new possibilities in COVID-19 surveillance

Monitoring data from wastewater allows better tracking of COVID-19 and new variants in communities.


As the initial omicron surge recedes, scientists are using an unexpected source — wastewater — to track COVID-19 infections in North Carolina.

The N.C. Wastewater Monitoring Network tracks trends in the COVID-19 pandemic for the state and the national Centers for Disease Control and Prevention, and the wastewater data is about six days ahead of the clinical testing data, said Rachel Noble, a professor of marine and environmental microbiology whose lab is helping lead the project.

The network began tracking SARS-CoV-2, the virus that causes COVID-19, in January 2021. Along with partners across the state, University of North Carolina researchers and the N.C. Department of Health and Human Services work together to track levels of SARS-CoV-2 in wastewater.

Fecal material can be sampled and provide a picture of the pandemic’s trends even before clinical testing shows an increase or decline in cases.

Five more collection sites were added in Wake County early this year, taking the state’s total to 24, and at least 12 more will be added soon, according to a press release from DHHS in early February.

The results are reported on North Carolina’s COVID-19 dashboard and can be sorted by participating location. In the same release, DHHS announced that North Carolina now participates in the CDC’s COVID Data Tracker, which uses data from the National Wastewater Surveillance System

UNC researchers and DHHS work with local partners to sample the wastewater. That data buys valuable time for hospitals and government leaders to make decisions even before symptomatic cases rise.

In conjunction with clinical data, the information is useful for decision-makers to use as a predictor, Noble said.

“Because a lot of people just kind of look at it and think it’s just what’s going on in the now, but they don’t realize it’s actually reflecting what happened last week,” she said.

The wastewater data captures a broader sample size even before individuals might suspect they are sick, according to Noble. While people might become infected days before they feel ill and seek a test, the viral particles in their fecal matter reveal the illness even earlier.

Some people may not be tested for COVID-19 even if they experience symptoms. Others who are ill but asymptomatic may not even know they are sick but still shed viral particles.

That message from the past is helpful but supplements other data rather than replacing it, according to Noble. Clinical testing is still invaluable.

“So, what the data can help (hospitals) do is to see you’ve got a big surge coming — you should at least maintain your ICU bed availability and potentially even think about increasing it,” Noble said.

“We know that hospitals are looking at data, especially a larger hospital system like the UNC hospital system. They’re not looking at the wastewater data in a vacuum, though. They look at the wastewater data paired with clinical data in order to make those decisions.”

Counties sign on

Wake County was an early participant in the program and started contributing samples to the N.C. Wastewater Monitoring Network in January 2021, according to Leah Holdren, a communications consultant for the county.

On Jan. 27, Wake added another five sites to the program, bringing it to a total of six areas in the county that are participating in the network, according to Holdren. The county plans to ask other towns to join. Collected data is provided to county leadership.

“The data from the wastewater monitoring program is regularly shared with the Wake County Board of Commissioners during COVID-19 reports at their board meetings,” Holdren said via email.

Dr. Nicole Mushonga, associate medical director and epidemiology program director for Wake County, is grateful that the wastewater data provides valuable information even when clinical testing declines.

“The ability to track the COVID virus in wastewater has really been a valuable contribution to overall public health protection,” Mushonga said via email.

“Because a high number of infected people go untested and because of the recent increase and availability of at-home testing (which also aren’t officially reported to us), having this early warning system has been incredible.”

Since that data is an early indicator, it can wave a red flag for health officials and county leadership. The monitoring network also remains steady even if clinical testing levels fluctuate.

“It signals us to begin to scrutinize our other data sets, and the ability to factor them all together helps us make public health decisions more confidently and timely,” Mushonga said.

“Even though (the) number of people utilizing our Wake County Public Health drive-thru PCR testing is decreasing, this data will continue to help us monitor COVID and is a reminder to stay vigilant since the virus is still a threat,” she said, referring to polymerase chain reaction tests.

Mushonga said the data is an important tool.

“Wake County’s leaders have viewed this program as a proactive step in protecting our community, and they have appreciated the municipalities who have agreed to participate with us on this,” Mushonga said.

“They support having a diverse toolkit for our public health team to monitor disease increases in our community.”

According to Mushonga and Holdren, there is about a one-week wait from the time the samples are collected to when the data is received.

Future possibilities

At the moment, North Carolina, like much of the rest of the country, is busy tracking COVID-19. A rise in the next omicron subvariant, BA.2, increases concern about the next wave.

The wastewater monitoring network is working and “more streamlined than ever,” according to Noble. But there are still details to work out.

“So, we’re analyzing samples for variants, but the state is interested in kind of moving to a framework where we’re analyzing all samples for variants all the time and reporting that data along with the general, what we refer to as the total SARS-CoV-2 data, right?” Noble said.

“So, what we’re trying to work to do is to develop our capacity to do the variant work, and what that means is that we’re successfully doing work on omicron and delta right now, but we want to be able to put together a framework where we quantify a specific number of variants in a specific window of time and we do that regularly, right?”

Some variants have largely come and gone, while others continue to pop up. Tracking too many variants unnecessarily will bog down the system and keep it from being as efficient. The network needs to track relevant, active variants.

“We would move forward with delta and omicron and even stealth omicron and other variants of concern for the future, but we might not include something like alpha and beta in all of our analyses because they’ve largely disappeared from the cases with the public,” Noble explained.

Noble doesn’t just want to track COVID-19 variants. She wants to use the same methods to track other illnesses.

“For now, we have been focused primarily on COVID, but I think the day is going to come very soon that COVID just becomes one of many pathogens that we’re reporting on,” Noble said.

The data won’t just provide research but could potentially provide more immediate benefits, according to Noble. The network will have to decide which pathogens to focus on.

“We can’t pick to do influenza in Charlotte and then turn around and do norovirus in Raleigh, and then turn around in Rocky Mount if you get another virus,” Noble said.

“We want to create a system that works consistently, so building that takes a little bit of effort. The way that I look at it is, what’s the value of measuring other viruses as part of a surveillance program? What’s the value to the state? How many lives can we save? Can we save money helping the hospitals operate properly?”

The program is ideal not just in larger cities but also in rural areas that may have fewer resources, Noble said. Including rural areas in the network provides those areas with valuable data and helps the state fill in more blanks across the map.

The program is designed to have a low burden for participating areas. Samples can be sent to Noble’s lab by FedEx. The costs are paid for by the state and the CDC, allowing even smaller areas to collect valuable information for little or no cost.

In the future, expanding the network to track more than COVID-19 could even assist with the opioid crisis.

“We can actually do not just pathogen testing in the wastewater, but we can actually use it to routinely test across the state for opioids and identify locations where there’s really high usage, and so we can have a better way of going into those communities and trying to help people,” Noble said.

Because of the significant amount of wastewater material even in small areas, Noble said, the tracking is intended to be on a large scale.

“Think about it as a stock market,” Noble said. “We’re more interested in wastewater surveillance as a long-term tool and we’re not interested in trying to respond to little blips here and there because you can’t, really. You need to rely on the long-term data and use it to predict what the wastewater surveillance is capable of.”

Not everyone can be so eager about the future of wastewater. But for Noble, the system provides actionable data that can save lives.

“It’s new, it’s exciting,” Noble said. “There are really good possibilities with it.”

Imari Scarbrough is a contributing writer to Carolina Public Press. Email her at imari.scarbrough@gmail.com.

Carolina Public Press is an independent, in-depth and investigative nonprofit news service for North Carolina.

COVID-19, wastewater