Virginia expands sewage surveillance for COVID

Virginia Department of Health’s (VDH) statewide wastewater surveillance testing program to monitor trends in COVID-19 infection rates kicks off Sept. 13.

Because virus particles are detectable in sewage before case are reported, according to the Centers for Disease Control and Prevention, strategic sampling of wastewater can provide information on infection trends at the community level, said Rekha Singh, wastewater surveillance manager at VDH.

“It can be used as an independent tool even without access to clinical testing, so it can be very useful in places where there is lack of access to health care facilities,” Singh said.

The department has not conducted this type of analysis before and learned of it through work at the CDC as well as the Hampton Roads, Va., Sanitation District (HRSD) and the Chesapeake, Va., Health Department, which were among the first localities to perform such studies when the pandemic began. So far, VDH has received data from those two entities, which sample sewage on their own, but now it will start receiving data weekly from 25 sites selected based on geographical location and population-testing rates.

Each participating sewage treatment plant will receive sampling kits, collect samples each week and send them to the state lab, which will coordinate the analysis and send the data back to VDH. The department and the local entities can use the results to better target testing and vaccination outreach efforts. VDH will also join other states in submitting the data to a new CDC database stood up through the National Wastewater Sewage Surveillance Program to create a nationwide view.

“This is the first time that [CDC has] done this. There is no database for any other type of sewage surveillance, but they’re looking at this potentially as a model that could be used for other types of infections,” said Marcia Degen, a technical program manager at VDH’s Office of Environmental Health Services who is overseeing the project for the wastewater division. “When we’re monitoring this virus in the wastewater, the virus is not active. As it passes through the gut, it breaks down. There has been no reported infections from somebody coming in contact with wastewater or sewage.”

HRSD’s pathogen lab has experience quantifying viruses in wastewater for research purposes, said Kyle Curtis, an environmental scientist at the district’s Water Quality Department. It has been collecting samples of untreated sewage weekly since the first week of March 2020 from nine large regional wastewater facilities. The lab runs a PCR, or polymerase chain reaction, assay on them to amplify small segments of DNA. In this case, the RNA present in COVID-19.

“It’s very similar to the assays that they would be running if you had a nasal swab – a PCR test – but obviously we’ve had to adapt them for monitoring for those same genetic targets in sewage,” Curtis said. “We can quantify the RNA target, which tells us specifically that this virus is there. We get that in terms of copies of that target per volume of sewage.”

Trends in copies of that target going up or down indicates increases or decreases in infection in the community that the wastewater plant services.

“Two other things that make it really important: One, the assays are really specific and so you won’t be shedding anything like these targets into sewage if you’re not infected,” Curtis said. “If we see the presence of it, particularly early on in something like this pandemic, we know there are infections in this community,” he said. “Secondly, whether you have a symptomatic or an asymptomatic infection, you’ll shed the virus.”

Curtis wrote code to generate dashboards that help other Hampton Roads region officials visualize the results. One shows a time series view of how things change, while another provides a spatial view by plotting concentrations normalized by population on a map of where HRSD’s catchments are in Virginia.

“The data comes out of the PCR instrument, it gets [quality controlled] by a molecular biologist … and then I would get it and create some of those plots on the dashboard and then also share it with our collaborators” at VDH and Chesapeake, a city within the region, Curtis said.

Comparing those dashboards to VDH-level data showing infection rates in the city got the attention of Cynthia Jackson, Chesapeake Health Department environmental health manager.

“It was interesting to me how they mirrored each other,” Jackson said. “We can see detection [in the wastewater] a little bit earlier than our spikes. That’s what stimulated our local interest.”

She decided to do testing at some of the 280 sewer pump stations in Chesapeake and brought in David Jurgens, the city’s director of public utilities, to determine the best places for testing based on a list of things they would like to know: if they could pinpoint vaccination rates by census tract and how the city’s numbers on the Virginia Health Opportunity Index can pinpoint where health care is not as accessible or affordable.

“What it’s allowed us to do is to develop some actionable strategies to help prevent and control [COVID] within our community levels,” Jackson said. For instance, they have set up vaccination and testing outreach efforts in neighborhoods where they see infection rates increasing before they can spike.

What’s more, the department partnered with professors at Old Dominion University to create prediction models that indicate where infections are most likely to increase.

Applicable now, the work is also a proof of concept, Jurgens said. “Because the markers show up in wastewater before somebody has symptoms, this is not simply a COVID thing, but this is a potential future science and life thing,” he said. “It’s been a really cool opportunity to get some incredibly meaningful and actionable data from a source that most people would never even think to look.”