Analysis of Huntsville wastewater can indicate rising COVID-19 infections

single-meta-cal April 18, 2022

A collaboration between the City of Huntsville and one of the nation’s top scientific research institutes is going down the tubes, but it’s a good thing.

Through the simple act of flushing a toilet, scientists at the HudsonAlpha Institute for Biotechnology have learned about the spread of COVID-19 through wastewater analysis. Their findings are designed to help local health care providers better understand current infection rates while also detecting potential surges.

Their research was made possible through a grant from the Alabama Department of Public Health (ADPH), which allowed HudsonAlpha to purchase new scientific equipment. The City provided the specimens, in the form of biweekly deliveries of untreated wastewater.

“Gauging our community infection rate helps our health care providers prepare for a potential surge,” Mayor Tommy Battle said. “Anything we can do to help our science and health care leaders learn more about this virus is something we’re proud to be a part of because it truly benefits us all.”

Some might turn their nose up at this type of science, but Huntsville Hospital CEO Jeff Samz isn’t one of them. Before learning about HudsonAlpha’s efforts, he read about wastewater testing in other parts of the U.S. and was curious about it.

“It may be a little gross, but it makes sense,” he said.

Growing concern

Since the start of the pandemic, scientists and health care professionals have pored over historical and real-time data to not only track the virus and its subvariants, but also predict how it would evolve.

During peak infection periods, in-person test sites overflowed. Drive-thru sites were just as busy. In-person testing has been a key factor in determining current positivity rates, but it doesn’t tell the whole story.

“When it comes to waves of new infections, we wonder what we would we do differently to prepare,” Samz said. “What we’ve seen consistently is that wastewater reacts a couple of weeks before it starts showing up in hospitals. It’s a very interesting early warning.”

Fact: Untreated wastewater is full of pathogens that could tell scientists any number of things about our population. RNA, a close cousin of DNA, is present in fecal matter. Those infected with COVID-19 shed the SARS-CoV2 virus RNA in feces.

Testing fecal matter for COVID-19 wasn’t something that immediately appealed to Dr. Rick Myers, HudsonAlpha’s President, Science Director and Faculty Investigator. Myers had seen a couple of papers on the subject early in the pandemic, but his team had plenty of other projects in the works.

“While we knew about other groups doing testing for infectious agents, we just didn’t have plans to do it,” Myers said. “(HudsonAlpha researchers) are working on cancer, neurodegenerative diseases and other things and have very busy work schedules.”

As wastewater testing research and results became more widely known, interest in the endeavor intensified. Postdoctoral researcher Dr. Benjamin Henderson and Senior Scientist Brian Roberts, both of the Myers Lab, showed particular interest in the subject.

A scientist measures COVID-19 levels in wastewater in a droplet digital machine. He's wearing glasses and a dark T-shirt.

Dr. Ben Henderson measures SARS-CoV-2 levels in the Huntsville wastewater on a Droplet Digital PCR system in the Myers Lab at the HudsonAlpha Institute for Biotechnology.

Data dump

After reading European reports about successful SARS-CoV-2 detection in wastewater, HudsonAlpha submitted a proposal to Mayor Battle’s office. The proposal recommended testing wastewater from three collection sites: Big Cove, which services the Hampton Cove and Big Cove areas; Spring Branch, which services downtown and North Huntsville; and Aldridge Creek, which services South Huntsville.

On a bi-weekly basis, Huntsville Wastewater delivers an untreated 24-hour composite sample to HudsonAlpha. The size is 100 milliliters, which is approximately one-quarter cup.

Once the samples are delivered, they are filtered in a vacuum, which produces concentrated viral nucleic acids on a membrane, or essentially, a sheet of paper. The RNA is then removed from the membrane using RNA extraction techniques.

Because scientists are dealing with untreated wastewater, it’s handled in a biosafety cabinet. Henderson said the risk of lab workers being infected by the virus is low.

“Theoretically, you could be exposed to it, but the nasty stuff would be bacterial,” he said.

Using the ADPH grant, HudsonAlpha procured a Droplet Digital Polymerase Chain Reaction (PCR) system, which allows scientists to set up a reaction using RNA extracted during the filtration process.

“A typical PCR is one reaction per each sample, which would be like a nose swab,” Henderson said. “The technology we employ runs thousands of mini-reactions per sample, which accurately gives us an absolute quantification of SARS-CoV-2 in the wastewater.”

Roberts then takes the data and plots it for a realistic view of COVID-19 infections over the initial test period of October 2020 through mid-May 2021. Testing started again in January 2022 at the height of the Omicron wave.

Impressive findings

Samz said he is impressed by HudsonAlpha’s findings and believes wastewater testing could become routine within the next 5-10 years. He’s skeptical, however, that it could replace individual PCR tests, the primary tool health care providers rely on to predict surges.

“The first thing we typically see is a demand for testing at the Fever & Flu Clinic,” Samz said. “Wastewater (infections) increase a week or two before that, so it’s definitely an indicator.”

Wastewater testing also captures a larger community sample, including those who have the virus but haven’t been tested.

“I do think that’s part of the benefit – the reliability of the data,” Samz said.

Another benefit is greater public awareness about genetic testing of individuals for infections, even though it’s been routinely performed in hospitals for years.

“If you had a respiratory illness, it was used to tailor the antibiotic that would be used to treat it,” he said. “Without question, the pandemic rapidly accelerated genetic testing, even with home tests. Before the pandemic, I don’t think a random citizen would have thought about taking these tests at home.”

What’s next

By spring 2022, COVID-19 positivity rates had decreased to a level not seen since May 2021. However, a new subvariant, BA.2, accounts for 72% of all new cases, according to the Centers for Disease Control and Prevention.

“I expect we’ll have another surge, but right now, we’re in a really good place,” Samz said.

Myers said as national cases rise, wastewater testing could help health care providers prepare.

“Now might be the best time to do it,” he said.

There’s a whole field of wastewater-based epidemiology that has grown from this. It existed before, but it’s become heightened.” – Dr. Ben Henderson

While the value wastewater testing might not be apparent to everyone, many in the science community – like Henderson – believe this could be the tip of the wastewater testing iceberg.

“There’s a whole field of wastewater-based epidemiology that has grown from this,” he said. “It existed before, but it’s become heightened.”

Myers said he’s also curious to see how technology and testing will advance. He believes that within the next five years, more entities will be actively testing wastewater. The state of Colorado, for example, is eyeing statewide testing at all its wastewater utilities.

“I think they’ll be able to take less than a quarter of a cup and screen for dozens or more pathogens, and we’d like to see that happen,” he said. “We might be able to test for two or three different things with the current technology.”

He said it’s also not out of the realm of possibility that technology could one day immediately detect dangerous pathogens in wastewater.

“I don’t think it’s crazy that every site might have a small device that tells you in real time what’s there,” Myers said. “It might be that it’s coming out of certain buildings like hospitals or dormitories. We’re heading in that direction, and hopefully it will happen.”