Louis Pagillo

Louis Pagillo graduated summa cum laude in May 2021 with a bachelor's degree in journalism and a minor in digital arts. He's worked as an esports journalist covering competitive video game leagues and events, and as a writer, content producer, and graphic designer on various other projects, including Stony Brook Transformed and Scenes from a Pandemic.

Supercomputers Map the Coronavirus

In a video interview with Stony Brook University more than a year ago, Carlos Simmerling, Ph.D., presented a 3D printed model of a spike found on the surface of the coronavirus. The chemistry professor’s excitement was obvious as he explained that the colorful parts of the red, blue and yellow model represented the “fingers” of the virus, which it uses to attach itself to human cells. He showed another model that demonstrated what those fingers look like when they open. Since then, nearly all of Simmerling’s research has been devoted to these models. 

Working in his eponymous lab in the Laufer Center for Physical and Quantitative Biology at Stony Brook University, Simmerling and his team of researchers and graduate students have been creating 3D computer models of the coronavirus. Unlike most models, which are static and don’t show important molecular movement, his team is using supercomputers to create models that simulate the movement of these viruses in order to gain a deeper understanding of exactly how they attach to cells. 

“It’s the same thing as taking a picture with a camera,” said Simmerling, who is the Marsha Laufer Endowed Professor of Physical and Quantitative Biology. “If you’re sitting still it’s going to be fine, but if you’re running, the photos are going to be blurry. We take in data from these experiments, and then simulate the parts that are fuzzy.”

A depiction of the protein spike found on the coronavirus. Provided by the Laufer Center

By focusing on the specific interaction virus spikes have when connecting to ACE2 receptors – proteins found on the surface of many common cells – Simmerling’s team found a pocket that opens on the coronavirus during this process. This opening could potentially allow small-molecule drugs to enter and effectively target the virus itself before a person is infected – unlike drugs such as remdesivir that aim to stop the virus from replicating after it has infected someone. This treatment could one day be more effective than vaccines, especially if new mutations of the virus make them ineffective. But such potential treatments are still far away. 

“We are still working on this, trying to understand how the spike mediates membrane fusion to allow the virus to get inside the cell,” Simmerling explained. “There is very little experimental detail on this process, but a better understanding could lead to treatments that are effective against all coronaviruses”

Simmerling has a way of making his complex research understandable. “Imagine you teach someone to recognize a car – if you teach them color or shape, that won’t work for different cars, but if you teach them that it has four wheels and doors it is much more general.”

Carlos Simmerling. Photo provided by Stony Brook University

The research has received funding from various grants and organizations, including the Research Corporation for Science Advancement – a private Arizona-based foundation that funds innovative research in the physical sciences – as well as seed money from Stony Brook and the State University of New York, and a pending National Science Foundation proposal for approximately $200,000. 

In addition, Simmerling’s team has been authorized to use supercomputers through the COVID-19 HPC Consortium – a national collaboration between the White House Office of Science and Technology Policy, the U.S. Department of Energy and IBM, which offers use of supercomputers across the country to various researchers. He says time on the supercomputers is “worth far more than the dollars.”

Simmerling was part of a national research team that used a supercomputer named Summit to simulate the coronavirus spike protein and viral envelope using 305 million atoms. Summit resides at the Department of Energy’s Oak Ridge National Laboratory in Tennessee, where it takes up the space of two tennis courts, weighs more than a commercial aircraft, is connected by 185 miles of fiber optic cable and can do 200,000 trillion calculations per second. 

The Stony Brook professor and his human colleagues won the 2020 Gordon Bell Special Prize for High Performance Computing-Based COVID-19 Research. The Gordon Bell Prize is known as the “Nobel Prize for Supercomputing” and comes with a $10,000 award.

Searching Sewage for the Coronavirus

Cheng-Shiaun Lee sat in his office at Stony Brook University’s Center for Clean Water Technology, resting his elbows on the only clear spot on his desk. His neatly parted hair, thick-rimmed glasses and plain gray sweater complimented by a red lanyard around his neck didn’t match the cluttered surroundings. Papers detailing nitrogen levels in wastewater were strewn about his desk, with two empty coffee mugs for paperweights. 

Usually, Lee would be putting his doctorate in chemical and biological oceanography to work by studying the environmental impacts of pollutants and chemicals in wastewater and groundwater. 

But these are not usual times. Since the spring of 2020, he’s been shifting his focus toward a different bad actor lurking in wastewater – the coronavirus.

Lee gets right to the point – and he doesn’t mince words. 

“We do chemistry in water,” Lee said. “If people get COVID, the viruses will stay in their feces and urine samples. So in wastewater, we are able to detect the virus.”

Lee’s work is an integral part of a study led by Chris Gobler – the center’s director and Endowed Chair of Coastal Ecology and Conservation in the School of Marine and Atmospheric Sciences – and Arjun Venkatesan, assistant director for drinking water intiatives. By using wastewater epidemiology – the study of diseases in wastewater – their team has been monitoring treatment plants across Long Island for small traces of the virus and drugs used to treat it, such as hydroxychloroquine and remdesivir. With this technology, they may be able to predict geographic areas where large outbreaks of COVID-19 could take place based on the amount of the virus found in sewage.

“We can predict, maybe this community has a high level of viruses in their wastewater, so maybe there’s a community infection,” Lee said, scratching his chin. “It doesn’t matter if you’re asymptomatic, the virus will shed from their bodies”

The team of researchers split their efforts between testing for the virus and testing for treatment drugs, with Gobler leading the virus team at the university’s Southampton campus and Venkatesan leading the drug team at the main campus. Both teams use the same samples collected from several sites in April 2020. At the time, there weren’t enough resources available to accurately test the dozens of samples, so they were frozen for three months until the team was more confident of its tools and methodology. Team members continued testing samples regularly until January, and also sampled campus wastewater during the fall 2020 semester. 

“When the pandemic hit, none of us knew how to start this kind of analysis,” Deepak Nanjappa, a postdoctoral researcher working with Gobler’s team, said. “Our lab wasn’t so equipped for this kind of study. We had to get the lab certification done, so we started with collecting samples.”

They began sampling from the Stony Brook campus and from any wastewater facility that would collaborate with them. The Town of Riverhead Sewer District was one of them.

“Any way we can play a part in whatever’s going on, whether it be different studies, we try and help out as much as we can for anything,” Michael Reichel, superintendent of Riverhead’s sewer district, said. “We’ll give them samples, we’ll give them information, we just try and work with anybody.”

The Riverhead Sewage Waste Treatment Plant’s sample collector. Photo provided by Michael Reichel

Reichel’s facility was one of two sites – the other is the Patchogue Wastewater Treatment Plant – that worked with the Stony Brook teams last year. But the researchers stopped taking samples because of a lack of funding. During the collaboration, providing samples became part of the Riverhead Sewage Waste Treatment Plant’s regular routine.

Reichel’s job hasn’t changed much in the past year. During the pandemic, all employees were considered essential workers, but that didn’t necessarily change what they did. Members of the small team have focused roles, so they couldn’t shift their schedules to reduce the number of people in the building. And they were already operating at a safe distance from each other. They didn’t have to wear additional personal protective equipment because they already protect themselves from myriad diseases in the sewage. It’s part of the job.

“Between Giardia and cryptosporidium and all the other crap that’s in wastewater, [coronavirus] is probably one of our smallest worries,” Reichel said with a laugh before continuing in a more serious tone. “There’re many other germs in wastewater that you can contract.”

While the research teams stopped collecting samples from the Riverhead facility and most of the other sites, they began a new collaborative program with Suffolk County in January 2021. Under this pilot program, four samples from the Bergen Point Wastewater Facility in West Babylon were collected until the end of April. The study was approved for a six-month extension to include samples from the Selden Wastewater Facility. As of now, the data from this study has not been made public. 

“At this point, we’re not ready to share the information publicly, but we will be soon,” said Michael Jensen, associate public health sanitarian at the Suffolk County Department of Health Services. Jensen also said that should a coming outbreak be detected, the department would inform the public and notify area hospitals to prepare for a potential influx of patients.

Once the samples arrive at the Southampton campus, they’re tested the same day to avoid deterioration. The testing process begins by extracting RNA from the coronavirus and re-synthesizing it into more stable DNA. Then, a process called polymerase chain reaction (PCR) is used to copy the DNA at an exponential rate. As these copies are made, researchers look for fluorescent signals in the DNA to determine the concentration of the virus in each sample, and use PCR to create copies of that DNA. The researchers are more concerned with the concentration and frequency of the virus, rather than its inevitable presence during a pandemic. 

“We need to analyze multiple samples, and then we can arrive at a decent conclusion,” Nanjappa said. While he wasn’t able to give many details, he confirmed that the team found trends from the sampling that indicated increases and decreases in the virus that lined up with COVID infection data. 

The PCR machine the team uses to test each of their wastewater samples.
Photo provided by Deepak Nanjappa

Widespread usage of wastewater epidemiology as a form of pathogen surveillance has been around for decades, especially when monitoring for the poliovirus. The Global Polio Eradication Initiative tests wastewater in countries with poor infrastructure and a high likelihood of outbreaks for traces of the virus as soon as people show symptoms of acute flaccid paralysis, a neurologic condition that causes weakening of the muscles and reflexes and is a common indicator of polio. 

Researchers in Russia have also been performing regular, standardized wastewater tests for polio since 1996 as part of their National Poliomyelitis Eradication Program. The World Health Organization even has guidelines for using wastewater epidemiology for polio testing.

Now, in the midst of a pandemic, dozens of other studies using wastewater epidemiology have been taking place across the globe. One such study in Sweden began as early as mid-February 2020.

And in Syracuse, researchers are implementing an entire wastewater surveillance system across various counties. Led by David Larsen, an environmental epidemiologist at the Falk College of Sport and Human Dynamics, the project receives samples from several treatment plants, all of which have their own funding. Larsen, who hopes to create a statewide wastewater surveillance system, thinks one of the greatest challenges will be educating health workers to operate on a large, collaborative scale as well as connecting to different county and privately owned wastewater treatment plants. 

“Health workers are clinicians, they’re not epidemiologists,” Larsen said. “Some of them have Ph.D.s, some don’t. I look at this as a challenge of the pandemic in general. Our public health field is controlled by clinicians, people who deal with health on an individual level.”

While systems are being established and the field of wastewater epidemiology is expanding rapidly, there’s still much to learn about testing for the coronavirus. Methods for testing for polio and commonly abused drugs are well established, but for a novel virus, much of the research is entirely new. 

“This science is kind of new for this virus,” said Stony Brook’s Lee. “We can certainly have room to improve the recovery, for example, if there’s 100 viruses in the water, we can maybe recover 10 percent of them. There must be a way to improve the sensitivity of this method.”

To complicate matters, the wastewater they work with isn’t just human waste. While they collect both effluent and influent, the wastewater is still exposed to other, unexpected materials that make testing each sample more difficult. 

“In terms of viruses, whether or not we’re doing it ongoing as a regular practice, I doubt that would happen,” Meliker said. “But having the techniques available … you could use it in the flu season to see how the flu is spreading.”

That could change as more technology becomes available. The sampling process could be streamlined or automated, and testing methods could potentially become cheaper – making it a more viable method of environmental surveillance.

“The value for this approach has been understood and realized by all researchers and health agencies around the world,” Venkatesan said. “Researchers are also focused on developing real-time sensors to get data quickly using this approach. Currently, samples are collected and transported to the lab for analysis, and this will change in the future with targeted sensors.”

For now, the county is still funding the pilot study, but the health department has shown interest in continuing and expanding the research. 

“Everything is contingent on funding,” Jensen said. “There is value in it. We all agree. We have routine calls with state health departments on it, and we all agree this type of surveillance is worthy and efficient… even during non-pandemic times.”