How wastewater testing works to predict COVID-19 spikes

University of Wyoming Professor Bledar Bisha and Laramie City Councilor Sharon Cumbie explain how the testing works, why it’s important and the goals they hope to meet.

A lab at the University of Wyoming is testing Laramie’s wastewater for presence of COVID-19; it’s the only lab in the state doing so.

The goal is to provide Laramie with real-time information about the level of transmission in the community. With better and more timely information, individuals can make more informed decisions about whether to mask up at the grocery store or whether to attend some large event.

Federal funding cuts have threatened the wastewater testing program — but it continues regardless, supported by federal funding, the state Department of Health, a local COVID taskforce and “a lot of goodwill.”

“There is a lot of hard work that goes into this, from a lot of people,” said UW Professor Bledar Bisha, who runs the testing program. “The graduate students and technicians that carry out all of this work. I’m really appreciative of their efforts and I really have appreciated all the collaboration from the WDH and the City of Laramie. Everyone is really interested in advancing public health and there are a lot of good people working towards that goal. I’m happy to be in the company of really good collaborators.” 

The science of wastewater testing

Researchers at Laramie’s water treatment facility collect a composite 50 milliliter sample over the course of 24 hours, twice a week. 

That sample can provide a pretty good snapshot of what’s going on in Laramie, said Laramie City Councilor Sharon Cumbie, who has been involved with the local COVID response taskforce since early in the pandemic.

“80 percent of households in Laramie are served by municipal wastewater collection systems,” she said. 

The sample is then tested by Bisha and his team at the University of Wyoming. 

At the lab, the samples are pasteurized in a water bath to deactivate any bacterial or viral matter that might be present, making them safe for the lab techs to handle. 

The samples are then put through a filtering process. Only viral matter can pass through the filter used, so researchers are left with a substrate that is made up entirely of viral matter. 

“From that moment on, we start the process of concentrating viral nucleic acids,” Bisha said “In this case, we’re talking about COVID-19 virus or SARS-CoV-2.”

The substrate goes through multiple testing phases that can take hours at a time. Polyethylene glycol precipitation is then used to make larger conglomerates of the viruses that might be present. 

The researchers then extract nucleic acids. Polymerase chain reaction (PCR) is used to detect the nucleic acids present in the real-time format, called qualitative real-time PCR. Qualitative real-time PCR is able to provide testing results in the course of hours.

PCR tests might sound familiar because they are similar to the nose-swab tests you’ve probably had to do at some point. 

There are two gene targets that the lab looks for — N1 and N2. Both are nucleocapsid proteins that indicate viral particles within the substrate. Through this process, the virus is either “detected” or “not detected.” 

“If we detect the virus, we can detect it in a more sensitive manner or less sensitive manner, depending on how much virus is present,” Bisha said. “Typically, if there is a lot of virus, you would detect it sooner, it would take two cycles of PCR to detect it. This is an indication of how much virus is already in the wastewater.”

With that information in hand, the lab team is able to extrapolate the amount of virus that was detected from the volume of wastewater that was processed. Knowing the number of people serviced within the sewer shed, the team comes up with a semi-quantitative measurement of how much the infectious trend rate has changed within the population. 

If there is a change greater than or equal to 15%, the level will be reported as green or red. Green would signify that there was at least a 15% drop in the amount of viral matter found with PCR testing. Red would signify that there was at least a 15% increase in the viral matter detected. If there is no change in the levels, it is reported as yellow.

What the results mean, and where the program is headed

Wastewater testing is able to predict a COVID spike before that spike is registered by other metrics, such as the percentage of positive tests or the number of people in the hospital. Wastewater testing can detect that spike by 6-14 days before the population shows these other trends appear.

The goal of the testing is to inform the community about the actual transmission risk by looking at the trends present in our wastewater. 

“This helps answer the question of ‘should our group meet in person or over Zoom?’” Cumbie said. “We are trying to create a system with weekly updates so people can act accordingly to weekly states.”

The lab’s findings are updated on the COVID Act Now website every other Friday. The last report was made July 8; the next report lands on July 22.

The testing will be used as a tool to get information out to the public during peak events and to monitor the impact of social events.

Cumbie and Bisha both said federal funding for the testing was lost in December. Through the help of the city, the testing has been able to continue. Bisha is working with the Wyoming Department of Public Health to regain funding for the project.

Funding for testing was provided by money from the CARES Act, and the state department of health funded the lab work. The lab at UW had not only been testing the wastewater in Laramie but 5 other municipalities. This provided coverage for close to the whole state of Wyoming. Once funding is restored, they hope to start testing in the other 5 municipalities again. 

Without the federal or state funding, the team is not able to detect which strain of COVID-19 is most active in the county. Bisha said they want to start testing for the active strains once funding is restored.

There is a national database that reports the results of wastewater testing. After funding, the state will be reported on the national database for trends throughout the country. Federal funding also requires that the testing is published to the national database, for public access. 

This story is supported by a grant through Wyoming’s Established Program to Stimulate Competitive Research (EPSCoR) and the National Science Foundation.

Correction: An earlier version of this story incorrectly stated that the research was supported by the CARES Foundation. It was not. It was funded, in part, by money from the CARES Act passed by Congress in response to the COVID-19 pandemic.