Testing what we flush to track COVID-19 in Western Pennsylvania

This article was written by Emily Emullin and published in the Pittsburgh Post-Gazette on February 13, 2022 at 12:04 PM.

https://www.post-gazette.com/news/health/2022/02/13/COVID-19-tracking-wastewater-sewage-indiana-borough/stories/202202130054

Alexandra Wimley/Post-Gazette

Roland Francis saw a wave of omicron cases coming in Indiana Borough before anyone else did.

He was tracking signs of the virus that infected individuals were unknowingly sending out into the wastewater stream from the privacy of their own bathrooms.

Since the early days of the pandemic, Mr. Francis has been overseeing the collection of sewage samples to test for the coronavirus at the Indiana Borough Regional Wastewater Treatment Facility, where he works as the pretreatment coordinator.

Three times a week, a refrigerated sampling machine about the size of a dishwater collects a small amount of water every five minutes over a 24-hour period. At the end of the day, the machine mixes those samples together to form a composite sample — a snapshot of what’s in the wastewater at the moment.

Every week, he mails the collected wastewater to a Massachusetts company called Biobot Analytics, which analyzes it for the presence of SARS-CoV-2, the virus that causes COVID-19. A few days later, the company sends him back a report of the amount of virus in the water, known as the viral load.

In early December, Mr. Francis was alarmed when he received the latest report. The viral load found in the wastewater was the highest it had ever been.

“We were a little scared about what was to come,” he said.

The data foretold a surge in COVID-19 cases hitting in the next few weeks, and that’s exactly what happened as the highly transmissible omicron variant swept through Western Pennsylvania.

Tracking community spread

The idea behind wastewater monitoring involves a smelly truth: Everybody poops. And our poop reveals valuable information about our health. Viruses, such as SARS-CoV-2, can show up in our stool even before outward symptoms of infection do. When we flush the toilet, our fecal matter travels through a series of pipes to a wastewater treatment plant.

In the past, scientists have used wastewater to track evidence of drug use or markers of disease in a community, and realized that testing water for levels of the coronavirus could provide an early indicator of disease spread. The Centers for Disease Control and Prevention launched the National Wastewater Surveillance Program in September 2020.

Nearly two years into the pandemic, lab testing of patients doesn’t capture all COVID-19 cases. Health records don’t include the results of home tests, or cases of people who have the virus but never get tested. Wastewater testing can fill in the gaps, helping health officials better estimate how widespread the virus is in the community.

Wastewater samples are analyzed for copies of the virus per liter using PCR, or polymerase chain reaction, the same test used to detect the presence of the virus in patient nasal swabs. PCR detects RNA specific to the coronavirus. RNA is the virus’s genetic material, so if there’s a lot of coronavirus RNA in a wastewater sample, it means there’s a lot of virus within the population.

“The wastewater surveillance is a good predictor of what’s going to be seen in the clinical cases within the area,” Mr. Francis said. “Generally, if you see a spike in the concentration of viral load in the waste stream, that’s followed by a spike in the number of cases in the local hospitals.”

The weekly wastewater surveillance reports are shared with the public on the treatment plant’s website, as well as on social media.

Forecasting tool

Indiana Borough began sampling wastewater for the coronavirus in April 2020, after Yongtao Cao, an associate professor of statistics at Indiana University of Pennsylvania, heard about a pilot program that Biobot Analytics was launching. The company was looking to partner with cities and municipalities interested in having their wastewater tested for the virus.

Using viral concentration levels and weekly case-count data, Mr. Cao built a forecasting model and web app to predict the number of COVID-19 cases within Indiana Borough and on the IUP campus for up to three weeks in the future. His research was published in the journal Science of the Total Environment in September 2021.

Mr. Cao’s data was one of the factors that IUP officials took into consideration last year when deciding whether to reopen to in-person learning in the fall.

The data also informs Indiana Regional Medical Center on what to expect as far as inpatient volumes due to COVID-19 cases. Mr. Cao has found that there’s a relationship between the viral load in the wastewater and the number of patients hospitalized with COVID-19. He’s working on building a new model to predict hospitalizations.

In other parts of the country, wastewater data has been used to determine whether schools should go remote and where mobile testing units should be placed in cities.

“There are a lot of use cases for how this can be deployed in municipalities,” Jennings Heussner, business development manager at Biobot Analytics, said.

Omicron’s arrival

With a population of only 14,000, Indiana might seem an unlikely place to be ahead of the curve in science. But its wastewater efforts caught the attention of the health department in much larger Allegheny County, which began collaborating with the borough at the end of 2021.

When the highly transmissible omicron variant was first detected in South Africa in November and then in the United States at the beginning of December, county health authorities thought wastewater data might be able to uncover the variant even before it showed up in patient testing.

They were right. Small amounts of omicron started to appear in Allegheny County’s wastewater around Dec. 10. The first case of omicron in the county, in an adult male, wasn’t confirmed until Dec. 22.

“There was some uncertainty as to when it was going to get here,” county epidemiologist LuAnn Brink said.

The wastewater data gave the county a heads up.

“We knew that we were going to hit a big surge,” said Ms. Brink, who has a doctorate in infectious diseases and microbiology from the University of Pittsburgh.

The health department is working with wastewater plants across the county to collect sewage samples three times a week. Currently, the county’s Public Health Laboratory is mailing weekly samples to an outside company, LuminUltra, which provides a breakdown of the variants found in the water in addition to the viral concentration.

At the same time, the county is building up capacity to do its testing on site. It’s running its own wastewater tests and comparing those results to the reports it receives from LuminUltra.

“Going through an external lab doesn’t really give us the predictive power that we would like, so we’re hopeful that we’ll get that in house and we’ll get our results a little bit more quickly,” Ms. Brink said.

It’s taking time because doing a PCR test on wastewater samples is trickier than on patient nasal swabs, explained Robert Wadowsky, director of the county’s Public Health Laboratory. There’s a lot of extra material in a sewage sample that can interfere with testing, and the process is more manual. A nasal swab PCR test takes about four hours for the lab to run, while a wastewater sample takes around eight hours.

The county plans to start publicly reporting its wastewater data by the end of March, Mr. Wadowsky said. The data will also be shared with the Pennsylvania Department of Health, which will submit it to the CDC. Meanwhile, a team at Carnegie Mellon University is developing predictive models and a wastewater monitoring dashboard for the county.

Beyond omicron

As cases of COVID-19 drop sharply, the concentration of virus in the county wastewater is also falling.

At the height of the omicron wave in Allegheny County, viral concentrations were more than 100,000 virus copies per liter. That indicates a rapid increase in the number of infected individuals. Now, the public health lab is recording viral loads in the range of thousands to ten thousands, a sign that omicron is receding.

“We’re seeing viral loads come down, but it’s still there,” Mr. Wadowsky said.

Beyond omicron, wastewater testing could be useful in detecting future coronavirus variants before they show up in patients.

Mr. Wadowsky said the county also plans to use wastewater testing to monitor for enterovirus D68, a virus found in infants and children that can cause a polio-like illness called acute flaccid myelitis. The virus is rare but has been increasing in frequency since an outbreak in Colorado in 2014.

“This virus comes and goes,” Mr. Wadowksy said.

But if it suddenly turns up in wastewater, that could alert health officials to be on the lookout for infections.

“After coronavirus, we’d like to shift to these other types of applications,” he said.