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Tracking COVID-19

As the COVID-19 pandemic continues, researchers are taking a look at our waste — specifically regional wastewater — to get a better view of outbreaks and trends to help ensure local communities have the information they need when making public health decisions.

“Wastewater surveillance is helpful in looking for trends that can provide insight about what might be going on at the population level,” said Angela Harris, assistant professor in the Department of Civil, Construction, and Environmental Engineering (CCEE).

With support from the North Carolina Department of Health and Human Services (DHHS), the Centers for Disease Control (CDC) and Wake County Public Health, NC State researchers have been testing wastewater to identify trends in COVID-19 outbreaks across Wake County.

This research is led by Harris, with assistance provided early on by Nadine Kotlarz, postdoctoral researcher at NC State’s Center for Human Health and the Environment, and Francis de los Reyes, CCEE Glenn E. and Phyllis J. Futrell Distinguished Professor #2.

A shift to community testing

SARS-CoV-2, the virus that causes COVID-19, is shed in feces, making wastewater surveillance an optimal tool for public health officials to monitor outbreaks, moving testing from an individual to community level.

“We are trying to understand how the level of infection is shifting inside of a community from one variant to another by testing the wastewater instead of each individual,” said Tanvir Pasha, a CCEE Ph.D. student and researcher working under Harris.

In April 2020, NC State and other universities, including Rice University, Howard University and the University of Southern California, began testing wastewater within their respective cities to compare communities across different environmental contexts. This research was funded by a one-year, $200,000 National Science Foundation Rapid Response Research (RAPID) grant.

NC State’s research continued with funding from the North Carolina Policy Collaboratory and North Carolina DHHS, and is now a part of the CDC’s National Wastewater Surveillance Program.

“That was a really important role that universities played in supporting state-level public health efforts,” Harris said. “The data we collect feeds into the state program, which feeds into that national database that the CDC is operating and maintaining.”

Zeroing in on SARS-CoV-2

Harris’ lab gathers wastewater at six sites across Cary and Raleigh, NC, with these facilities serving more than 800,000 people. Two 24-hour composite samples are collected weekly from each location.

Using membrane filtration with a vacuum pump, Harris concentrates 40 milliliters of wastewater using filter paper with a pore size 60 times smaller than a particle of dust. Virus particles are even smaller. But to concentrate the COVID-19 virus particles, they must stick to the filter paper. Harris treats the sample with a magnesium chloride solution that causes the COVID-19 virus particles to stick.

SARS-CoV-2 is an RNA virus, and Harris and her team perform nucleic acid extraction on the filter paper, which allows for molecular detection of the virus using digital droplet polymerase chain reaction (ddPCR). Specifically, they target the N1 and N2 genes of the virus that in combination prove its presence in a sample.

“The idea with an environmental sample is that you want to remove all the compounds that are in wastewater that can impact you doing molecular work,” Harris said. “You just want the nucleic acid.”

We are trying to understand how the level of infection is shifting inside of a community from one variant to another by testing the wastewater instead of each individual.”

Tanvir Pasha

This process involves a digital droplet PCR with primers that consist of short sequences of RNA that identify unique genomic sequences. The sample is broken up into thousands of droplets that signal the detection of the virus through a luminescent molecular tag.

Based on the number of positive droplets, researchers are able to estimate the total quantity of SARS-CoV-2 particles in a sample and compare concentrations in previous specimens to further categorize them within percentiles that range from very low (0-19.9 percent) to very high (80-100 percent) within wastewater.

The testing method is sensitive enough that low concentrations of SARS-CoV-2 can be detected, and when compared to reported cases, the data correlates accurately. Additionally, this form of testing provides results more quickly than individual testing.

Harris’ lab and the CDC program are not able to accurately identify how many people are infected with COVID-19 as variables including weather and behavioral patterns in water usage can influence the concentration of particles within a sample.

Future implications of wastewater surveillance

Harris hopes to expand research to other enteric, or intestinal, pathogens such as rotavirus and norovirus or bacterial pathogens like campylobacter and salmonella.
She also thinks that wastewater can be helpful in understanding disease trend dynamics related to variables such as climate change and mass behavioral changes.

“We can gain insight and predict ahead of time what [public health] messaging would be useful or give hospitals a heads up on when they can expect more patients,” Harris said.

Working with the CDC and the North Carolina DHHS, researchers have also improved at making the data and trends easier to understand.

“When looking at some of the published data, you might not feel comfortable making an individual decision based on this information right now because it’s hard to make sense of it,” Harris said. “I think working with the CDC and the North Carolina DHHS has put a lot more thought into these data visualizations and how to make it accessible to the public.”


This story was originally published by College of Engineering.