Putting Artificial Intelligence on the COVID Case

Computer science and bioinformatics researchers at Stony Brook University are trying to expand doctors’ understanding of COVID-19 with a little help from artificial intelligence.

Prateek Prasanna, an assistant professor in the biomedical informatics department, is one of many researchers across the globe who are focused on putting machine-learning algorithms to work in the fight against the coronavirus. He is a doctor of biomedical engineering who came to Stony Brook in January 2020, and has previously used AI to study and analyze lung cancers. Prasanna arrived on the cusp of the coronavirus outbreak, and just four months later, he and his team were selected to receive seed grants from the university’s COVID-19 research program, a fund created to accelerate projects that study the virus.

They have spent the months since shaping computer brains to recognize and label certain features on COVID-positive lungs from X-ray images. Once these brains are properly trained, they will be able to detect COVID-19, and even offer a prognosis for the potential severity of each case.

“We saw that there might be these subtle differences in imaging signatures between, let’s say, a patient who is COVID-positive and does not required mechanical ventilation and another COVID-positive patient who needs mechanical ventilation,” Prasanna said on a Zoom call, his face superimposed on an image of Stony Brook University Hospital.

He spoke with a careful, measured cadence, but his excitement resonated as he discussed his findings. “So we hypothesize that there might still be imaging differences between these cases, and using machine learning and AI techniques, we would be able to tease out what these differences are.”

This infographic from Prasanna’s team demonstrates how their artificially intelligent algorithms identify lungs in an X-ray through “segmentation,” and predict particular outcomes based on their features. This is accomplished using two types of artificial intelligence algorithms known as convolutional neural networks (CNN) and random forest (RF). Photo courtesy of Prateek Prassana

Prasanna’s team includes two researchers from Stony Brook, four from Newark Beth Israel Medical Center in New Jersey and one from the Indian Institute of Technology in Bombay, India. Their expertise also varies, from bioinformatics — the analysis of biomedical data — to electrical engineering and radiology. They began their study with 514 chest X-ray images gathered from Stony Brook and Newark Beth Israel Hospitals. Some showed the lungs of COVID-positive patients and some showed those of COVID-negative patients. 

Each image included demographic data about its subject: age, the severity of the disease and underlying medical conditions, among other data points. That data, collected by medical institutions and prepped by the researchers, became what is known in the world of AI as the “ground truth” on which an artificially intelligent computer formed its own understanding of each set of lungs. After processing a number of human-sorted positive and negative cases, the algorithm was able to begin classifying them by itself, generating the probability of sickness for each image.

Machine learning, the basis for Prasanna’s study and thousands of others like it, relies on a computer processor’s ability to observe patterns and by recognizing them, to refine itself — in other words, to learn. In this case, minute features in COVID-positive X-rays — one is called “ground-glass opacity” or GGO — began to emerge as distinct characteristics that the trained algorithm, when tested blind, can use to predict the presence and severity of COVID.

The flexibility of the resulting algorithms allows the team’s research goals to shift with ease. For example, they began to examine the experimental practice known as “proning,” or having certain COVID patients lie on their stomachs instead of their backs during hospital care. Their existing machine-learning model reviewed X-ray scans from patients who were placed in prone positions and those who were not, demonstrating the benefits of the practice.

In May 2020, their research was recognized among 17 research studies to receive seed grant funding from the university’s Office of Research. “In very short order, I think in just a matter of a week, we redirected some funds that we would have used for other seed funding, and we created a seed funding program,” said Richard Reeder, Stony Brook’s senior vice president for research. “We got the funding to them right away … and the idea was that they would carry out research [and] position themselves to be able to put together a proposal for federal funding.” 

Prasanna’s team has been using that time and funding to develop algorithms and submit papers to national organizations. So far, their work has been accepted by the 2021 Society of Photo-optical Instrumentation Engineers (SPIE) Medical Imaging Conference, the Journal of Clinical Medicine, the 2021 Medical Imaging with Deep Learning Conference (MIDL) and the Medical Image Computing and Computer Assisted Intervention Society (MICCAI). An additional manuscript is still in revision. “The initial results are quite promising,” Prasanna said. “Still, there’s still a lot of research to be done … before we can even start thinking about, let’s say using some of these studies as a triage mechanism to decide … which patients we need to pay more attention to.”

That research is expected to come as national institutes such as the American College of Radiology and the Radiological Society of North America release larger sets of images and data. These will allow researchers like Prasanna to further sharpen their algorithms, delineating positive diagnoses from negative ones and severe COVID cases from minor ones.

“God forbid, if there’s another sort of wave where you might not have enough testing… can we use imaging to diagnose and predict the trajectory of COVID?”

– Prateek Prasanna, assistant professor in Stony Brook’s Bioinformatics department

Of the first 514 chest X-rays Prasanna’s team used, 463 came from Stony Brook University Hospital’s own COVID-19 database. Known as the Data Commons and Analytic Environment, it was created to enable fast research that could result in medical use.

Dr. Kenneth Kaushansky, the former dean of Stony Brook’s Renaissance School of Medicine and senior vice president of Health Sciences, explained the need for such a database. 

“Early on in the pandemic, I felt like we ought to have a single site with highly reliable scrubbed data on every patient we see. I think it took something like 40 people in the Department of Biomedical Informatics — graduate students, volunteers, students, medical students, staff and faculty — to set this up. And now people in radiology or image analysis or computer sciences can get into that database and extract the images, and all the other clinical history that goes with that particular image, and now use deep learning algorithms, AI as well, to sort out ways to better diagnose and prognosticate from images.”

It will likely be months before Prasanna’s algorithm is put to work in a medical setting. Although Prasanna sees his study going in many directions for practical use, one easy application he foresees is as a supplement for existing clinical testing.

“God forbid, if there’s another sort of wave where you might not have enough testing … can we use imaging to diagnose and predict the trajectory of COVID?” Prasanna said. “That, I think, is ripe for transition to clinic.”

In the meantime, Prasanna and his team continue to receive images from Stony Brook as well as medical centers in Newark, India and other areas, feeding the data through their algorithm — and honing its accuracy as it keeps learning.

How Will We Remember the Pandemic?

Psychologists at Stony Brook University are studying how different groups of people will remember the COVID-19 pandemic.

Lauren Richmond, Ph.D., an assistant professor of cognitive science and co-principal investigator of the study, is exploring how a person’s role and experiences during the pandemic will impact memory. 

She explained that a tragic event like the 9/11 terrorist attacks would likely create a vivid and emotional memory, often called a flashbulb memory. But the pandemic is unique in how people remember it because it is taking place over a long period of time and affects everybody differently. 

“We’re all experiencing this in a really idiosyncratic way,” Richmond said. “And social distancing makes us really have to experience this on an individual or a really small network level. … Understanding the different varieties of experiences that different groups in different geographic locations is really important for understanding how people will remember this event later.”

Richmond said she believes the biggest difference in memory perception will be between two groups: people who are working from home and have been static through the pandemic, and people who are working and are more actively involved in the pandemic, like essential workers.

“For better or for worse, 2020 was a year that had a lot of stuff happening. So I think we have the ability to look at a few interesting facets of how we, as a nation, collectively think about some of the things that happened during that period.”

– Lauren Richmond, Ph.D., assistant professor of cognitive science at Stony Brook University

To collect data, Richmond surveys participants and examines their self-reported autobiographical memories, which are based on their own perception of the world around them. She said that there is no way to know if what’s being reported is true or not.

“But we can look at – since we are doing this longitudinal data collection – whether or not what people are reporting on changes over time,” she said. She is also looking at whether any changes  on a group level can be predicted by differences in the social support someone has or what news a person consumes, among other factors.“We can look at whether any of those factors seem to predict changes and stability in these memories over time.”

The surveys are also asking respondents questions about their memories of nationally and personally significant events in 2020, such as the presidential election and the Black Lives Matter protests. 

“For better or for worse, 2020 was a year that had a lot of stuff happening,” Richmond said. “So I think we have the ability to look at a few interesting facets of how we, as a nation, collectively think about some of the things that happened during that period.”

Richmond said preliminary data suggests that older people have more positive memories than younger people.

The study will last as long as the pandemic lasts, she said, because “we are trying to understand how people’s experiences and memories are unfolding as the event is still unfolding.”

Richmond is tapping into the Stony Brook University community for participants, including undergraduates, affiliates at Stony Brook Medicine and older people in the Osher Lifelong Learning Institute, known on campus as OLLI. The team is also using Amazon’s Mechanical Turk, or mTurk, a crowdsourcing website, to obtain nationally representative data. The study is being funded collaboratively by Richmond’s lab and the lab of Suparna Rajaram, Ph.D., a distinguished professor of cognitive science.

Political Partisanship and the Pandemic

Researchers in Stony Brook University’s political science department have been keeping tabs on the coronavirus. They aren’t tracking the number of new COVID-19 cases or deaths or how many people have been vaccinated or where the next outbreak will occur. Instead, these social scientists are looking at the relationship between the pandemic and political partisanship.

Professors John Barry Ryan and Yanna Krupnikov – in collaboration with researchers from the University of Pennsylvania, Northwestern University and the University of Arizona – were originally analyzing how Americans viewed their political opposites. But when the pandemic hit, the researchers began to trace respondents’ reactions to the coronavirus as an indicator of their political biases. 

“What was great about this survey is we already had their attitude towards the parties,” Ryan said. “And so we can see if they changed in response to COVID, but we can also see how their previous attitudes towards the parties shaped how they responded to COVID.”

Graph provided by John Barry Ryan and Yanna Krupnikov

The researchers defined political partisans as people who strongly support their political parties to the point that they are unwilling to compromise with the opposition party and actually hold it in contempt. 

Ryan said the pandemic was a good lens for studying partisanship. Case counts and death rates were clear indicators of how the pandemic was being handled as opposed to other issues such as the state of the economy, where multiple complex factors are at play and room exists for broad subjective analysis and competing philosophies.

The most telling results of the survey came in the beginning of the pandemic, when states began to lock down. “In areas where there’s not a lot of cases, you see greater partisan splits,” he said. “And as the cases go up, you see the partisans coming together, responding in sort of similar ways.” 

This is because partisans in COVID-19 hot spots had similar experiences. Republicans had to be “hit over the head,” as Ryan put it, with the danger that the pandemic could cause in their communities to favor lockdowns and more restrictive policies. 

In areas with low COVID case counts, Republicans displayed some form of denial about the pandemic’s severity, while Democrats exhibited what Ryan called an “obsession” with safety precautions, vaccines and news surrounding the pandemic.

The research also focused on how partisans reacted to former President Donald Trump through his response to COVID-19. One method the researchers used involved how they phrased questions on the survey. In one version of the survey, participants were asked if Trump handled the pandemic well, while in another they were asked if the country was handling the pandemic well. 

“In areas where there’s not a lot of cases, you see greater partisan splits. And as the cases go up, you see the partisans coming together, responding in sort of similar ways.” 

– John Barry Ryan, Ph.D., associate professor of political science at Stony Brook University

“These are the same questions. There is no difference between Donald Trump and the United States, Donald Trump is the United States,” Ryan said – or he was because he was still president when the survey was conducted. “And for Democrats, that means everything that the U.S. does is terrible. For Republicans everything the U.S. does is great. Regardless of what the reality is.”

How the question is framed affects the ferocity of the partisan response, the researchers noted. “So you get this sort of thing where you say Donald Trump and it activates the partisan response in people,” Ryan explained. “But when you just say the United States, they all kind of say, ‘Eh, it’s not great, not terrible, we’re sort of in the middle.’” 

Ryan said the research can help policymakers craft their messages to target different groups. If policymakers understand their audiences, including partisans, they could better communicate about policy pertaining to the virus, even as the pandemic winds down. 

Ryan and his colleagues have published three academic articles on their surveys and plan to compile the results in a book. 

Listen to more of Alek Lewis’ report:

Read about their research in the Journal of Experimental Political Science and in Nature Human Behavior.

Their Labs Shut Down But Their Research Kept Going

In 2013, the Stony Brook Foundation — the nonprofit arm of the university that receives and manages private donations — established the Discovery Prize, a contest to fund original research with private money at a time when federal support was receding. Each year the prize has been awarded — 2013, 2017 and 2019 — four finalists were selected, and one winner received a $200,000 grant to continue and expand their research team’s work. Previous winners pioneered new methods of cancer research, electron analysis and mapping the unconscious brain. “Our goal is to encourage our faculty to ask the big questions and pursue the unknown,” actor and Stony Brook University donor Alan Alda said in a 2020 promotional film.

This was an unusual year to give a Discovery Prize. In March of 2020, all but the most essential in-person research at Stony Brook paused as COVID-19 began moving across the United States. At the time, all four finalists and their research groups left their labs, preparing for a break that became a year of social distancing and mask wearing. Some were able to transition to a virtual approach, and others lost whole months of research. All of them were affected by the pandemic, as the very nature of life was reshaped by the coronavirus, and none of their labs have yet to return to business as usual.

And yet all four made immense strides in their respective fields, pushing the boundaries of their disciplines and by extension, the horizons of human knowledge. 

One was awarded the $200,000 prize. And even though the winner has already been officially announced and the congratulations and accolades are no doubt still pouring in, it’s worth taking a look at the final four and the work they continue to do. 

Greg Henkes – Rock Star

In his office on the third floor of the Earth and Space Sciences building, Professor Greg Henkes caught a brief break from the social distancing and mask wearing that his research mandates. He sat at his desk, but behind him signs of his work in progress were visible — a binder filled with creased, typed pages, and an expansive whiteboard marked with calculations and figures. 

As a geoscientist, Henkes’ work involves vaporizing rocks into atom-sized particles, searching for clues to the climate conditions on planet Earth millenia in the past. The project made him a finalist for the Discovery Prize.

“This idea of reconstructing — or reanimating — environments in the past is kind of interesting, all over the surface of the Earth if you can find the right rocks,” he said. The metal zipper of his red puffer vest dangled as he gestured enthusiastically.

Last March, as COVID-19 began to spread across the country, Henkes was informed that his lab would have to shut down, pausing his research immediately with no return date in sight. He would return once a week to monitor the lab’s state-of-the-art mass spectrometers — the rock vaporizers. 

“These mass spectrometers are, you know, some of them are as expensive as a Ferrari,” he said. “You don’t just sort of pull your Ferrari over to the side of the road, get out of it and walk away, right? You got to go find a garage, and … maybe you put a sheet over the car, so that when you walk away from the car for, you know, two months, you come back to it, and there’s not a ton of dust.” 

That maintenance involved regularly checking the machines, monitoring the health of sensitive chemical mixtures known as reagents, and performing updates to the lab’s electronic systems. 

Returning from the initial closure was a gradual, meticulous process, governed by Stony Brook’s administration in accordance with multiple levels of regulations. In June, as the first wave of the pandemic began to die down, the Office of Research began a staged return-to-work plan as part of the university’s “Coming Back Safe and Strong” initiative.  

“We brought research, faculty, students and staff back, so as to gradually increase the density in labs,” Richard Reeder, Stony Brook’s vice president for research, said. “And we did that with appropriate safeguards too” — all provided by an alphabet soup of agencies: the Centers for Disease Control and Prevention (CDC), the State University of New York (SUNY) and the New York State Department of Health (NYSDOH), among others.

The university administration required researchers like Henkes to develop their own plans for return following those guidelines. His plan involved slowly bringing back his fellow researchers. It also involved a lot of red tape. And other colors as well.

“We would only have no more than two people in our 1,400-square-foot lab space at a time,” Henkes said. “This was, in hindsight, probably unnecessary, but I did run into the lab when it was just me here, and started taping off six-foot … markers with lab tape.” Soon the floor was a rainbow of social-distancing strips. 

“We’re making do, but if it weren’t for COVID, a student might be sorting through a cord shed in Alberta, Canada right now. Or if it weren’t for COVID, you know, we might have been just getting back from the field in Kenya.”

– Greg Henkes, Stony Brook Geology professor and Discovery Prize finalist

Henkes works with a team of eight undergraduate, graduate and doctoral students, all of whom focus on their own projects — and the mass spectrometer is an integral part of everyone’s research. Although some of them were deemed essential workers and allowed to re-enter the lab over the course of the break, all of their lab procedures were stalled as they focused on maintaining the machinery for future use.

One such student, Ella Holme, uses the machines in Henkes’ lab to compare rocks from the surfaces of Earth and Mars. Her work analyzing rocks similar to those found on Mars was incorporated into geochemistry equipment onboard NASA’s Perseverance rover, which landed on the surface of the Red Planet last February. When the lab shuttered, plans to continue her research were dashed. 

“I was not doing research in person” — for example, running samples on the mass spectrometer — “from about this time last year until mid-June, and it was a big setback,” she said. 

As a fifth-year doctoral student in geochemistry, Holme, who lives in Smithtown, had to defend her dissertation over Zoom while maintaining her research, which was largely incomplete. 

“I did a lot of writing, or trying to, but my research at the point that quarantine hit was really at a pivotal point where I needed more data before I could really write,” she said. “So I did as much as I could, but it was fairly limited.”

Other members of Henkes’ team were more fortunate. Yang Gao and David Burtt, second- and fourth-year Ph.D. students respectively, were able to work from data they collected before the shutdown. Still, their experiences were shaped by the isolation of working virtually.

“There are definitely pros to being able to write alone in your own house,” Burtt, who analyzes rocks from ancient meteorite impacts, said in the spring. “But you also miss out on easy access to other people for conversations, for editing … just those random conversations where you’re like, ‘You know what, I was thinking about this interpretation of our results. What do you think of that? Am I just blowing smoke right now, or have I actually jumped on something?’”

When the lab was back in operation, some students resumed their two-week sessions on the mass spectrometers, persevering through the layers of lab tape on the floor. Others worked from existing data. Still, a question hangs in the air — what could have been if the pandemic hadn’t hit?

“I could name half a dozen specific cases where like, we’re making do but if it weren’t for COVID, a student might be sorting through a cord shed in Alberta, Canada right now. Or if it weren’t for COVID, you know, we might have been just getting back from the field in Kenya,” Henkes said. “If it weren’t for COVID, we might have more students working on one of the mass spectrometers.”

Mae Saslaw is one of those students, part of a team studying the conditions that may have brought about the evolutionary split between apes and chimpanzees 15 million years ago in East Africa. She hoped to return to Kenya to collect samples over the summer, but the continuation of the pandemic has made her plan tentative.

“That uncertainty is a bit of an issue,” she said in March. “If I don’t go this summer, I will be in a pretty bad situation data-wise — like, I kind of won’t really have anything to work on… I can start writing my dissertation around the data that I don’t have… but at that point, I would be looking at probably extending my timeline overall” — pushing her graduation past 2024.

Saslaw was eventually able to travel with a small group of vaccinated researchers, and anticipates a return to the field in summer 2022.

Scattered on and off campus, the Henkes Lab team, as it’s known, is still recovering from their months in the dark — but their rock-busting Ferrari is roaring back to life. 

Kevin Reed – Hurricanes in the Age of Climate Change

When Climatology Professor Kevin Reed joined a Zoom meeting on Feb. 19, 2021, he quickly switched from a view of his darkened kitchen to an almost blindingly saturated virtual background. He superimposed himself at the intersection of Nicholls Road and Shirley Kenny Drive — a sunny view of the sign at Stony Brook’s main entrance, the same image he’d used three months prior when he was featured on PBS NewsHour to describe his team’s research. 

Through mathematical climate models, Reed and his team have developed a kind of alternate universe of weather forecasts, showing how much more devastating hurricanes have become due to climate change.

“We change the question that the public and journalists are asking, which isn’t, ‘Was Hurricane Laura due to climate change?’ but, ‘How has Laura changed because of climate change?’” Reed said. “How [have] the different characteristics of that storm … changed over the last 150 years due to human-induced warming?”

On NewsHour, he presented a view of Laura without any of the effects of climate change — still a swirling mass on the map, but smaller and less dangerous.

When the Stony Brook campus was locked down in mid-March 2020, Reed’s sunny Zoom background became his permanent virtual residence. His tight-knit team of graduate students transitioned quickly to online meetings, running their simulations remotely through supercomputers at the National Center for Atmospheric Research, stationed in Tennessee and California. 

“I still think that we all struggle individually with, you know, the human interaction — even if you’re a numerical modeler, that human interaction of discussing results, right? Over a coffee, or randomly in the hall, when we see each other or in our one-on-one meetings, you know, that’s gone away.”

– Kevin Reed, Stony Brook Climatology professor and Discovery Prize finalist

Alyssa Stansfield, one member of Reed’s team, is a fourth-year doctoral student. Her research into the impact of climate change on rainfall during extreme weather events easily transitioned to a new virtual setting. 

“I was able to continue with my work pretty much unimpeded,” she said. “I consider myself very lucky. I know a lot of people in our department who do use actual labs more — they’re more on the marine science side — but they have definitely been impacted by the pause in research work. Even now, I honestly don’t go onto campus much, because I just don’t have to, and I felt like, you know, if I don’t have to risk being on campus, why add another person?”

Still, Reed said they faced some inevitable difficulties. 

“I still think that we all struggle individually with, you know, the human interaction — even if you’re a numerical modeler, that human interaction of discussing results, right?” he said. “Over a coffee, or randomly in the hall, when we see each other or in our one-on-one meetings, you know, that’s gone away.”

Stansfield particularly regretted the loss of community at the tight-knit School of Atmospheric and Marine Sciences, which is composed of 500 students and 90 faculty members, often involved in highly focused in-person research at off-site locations.

“I’ve never even met the new student in our group in person,” she said. “We used to have in-person seminars every week where we would have lunch afterwards together, and now those are virtual. And we used to have some fun events throughout the year within our department, which obviously have not been able to happen. … I’m like, really looking forward to the fall semester where we can hopefully get the in-person stuff going back again.”

Reed’s group proves that, even when research means manipulating code and examining maps, the pandemic can destabilize the process and deeply affect each person involved. As Stansfield and her fellow team members await a return to the pre-pandemic norm, Reed visits the lab a few times a week, maintaining his presence amid his scattered surroundings.

Eszter Boros – Turning on a Radioactive Light Switch to Find Cancer 

In her video for the Discovery Prize finalists’ webpage, Chemistry Professor Eszter Boros wore lab goggles and a white lab coat. Behind her, clear tubes and funnels wove a structure of flowing chemicals. 

Her work involves the development of what she calls a “radioactive light switch” — certain metal ions that, when injected into the body, can emit a flash of blue light upon contact with a cancerous tumor. Those compounds then work in conjunction with a novel light-activated form of therapeutic drugs, allowing for hyper-targeted cancer treatments — “a sort of more broadly applicable, more clinically relevant chemotherapy,” as Boros put it.

Before implementing their treatments on a broader scale, Boros and her team test on mice to ensure efficacy and safety. That process had to stop entirely when the shutdown occurred.

“We had this mouse population that we purchased, looking forward to doing a lot of experiments, maybe in March and April,” Boros said. “And then of course, we couldn’t do any of it because everybody was at home. It was good for the mice, because they were just hanging out at the animal facility, getting old and chubby, basically eating and having a good time. But we weren’t able to do our experiments.”

In the meantime, the Division of Laboratory Animal Resources, staffed by essential lab workers, cared for the mice at Boros’ expense. 

“It came at a financial cost, but at the end of the day, it kept people safe in my lab,” she said. “I wasn’t raging in my living room that we couldn’t do these animal experiments, because in the grand scheme of things, it was much more important that we were able to keep our trainees safe, our lab members safe and ourselves safe.”

For Boros’ research team — two postdoctoral researchers, seven graduate students and one undergraduate student — the pause was a time to reflect, and even to learn new skills. Angus Koller, a graduate researcher in his second year, delved into computational chemistry at home, bringing a new field into the scope of the lab’s study.

“In my case, I kind of had a unique opportunity,” Koller said. “For a long time, Eszter wanted someone in the lab group to do things involving computational chemistry, like chemical modeling and things like that. So that was one kind of project I had, was teaching myself how to do that through the quarantine since it was something I didn’t need to be in the lab to do.”

“We’re expected to keep working as if, you know, we just got sent home, we’re in detention or something, but everything else should keep going — but we tend to forget that we are in a global pandemic.”

– Eszter Boros, Stony Brook Chemistry professor and Discovery Prize finalist

Additionally, the transition to virtual research was complicated by a personal matter — Boros was nearly four months pregnant when the shutdown began, and her son was born in the middle of the pandemic. She split her time between the lab and caring for her newborn, allowing her team to work more independently. 

Like the other groups spread far and wide by the shutdown, Boros’ team faced difficulties supporting each other and communicating their ideas. To better assist their efforts at home, Boros transformed the team’s once weekly in-person meetings into a series of Zoom sessions over the course of each week. On Mondays, the group would share findings from literature, on Wednesdays, they held a midweek check-in, and on Fridays, Boros met individually with each team member, ensuring any problems with their progress were addressed. She said that the meetings also helped ease personal stressors.

“Trying to just keep morale up somehow, I tried to get them to talk about what kind of movies they’re watching on Netflix and things like that, and who’s watching Tiger King and whatnot,” she said. “As an advisor, you’re trying to just kind of make up on the fly what helps keep the lab afloat the best way you can.”

“We were having Wednesday check-ins to be able to communicate with everyone,” Kirsten Martin, a third-year graduate researcher, said. “It was also just like an update on, ‘What am I having issues with? What do I need some help with?’ So that was really helpful for facilitating that communication.”

Although Zoom calls limited some of the in-person connection that made the lab flow, it also enabled an entirely different form of collaboration, knocking down borders of distance and time. Guest speakers and colleagues from universities across the country shared insights and information with Boros and her team virtually.

 “Normally, when you do things like departmental seminars, it would always be an in-person thing — you’d have to fly somebody from wherever, bring them to the department, and then have them give their presentation,” Koller said. “But with the quarantine, it normalized the whole Zoom thing a lot more. So we’ve had seminar speakers who live in different countries even, or different states, and things like that. So it’s kind of nice in that regard. You can kind of get to know some people that you would basically never get to interact with, because of time barrier issues and things like that.”

For Boros and her team, one of the most valuable lessons learned from the pandemic involved managing expectations.

“We’re expected to keep working as if, you know, we just got sent home, we’re in detention or something, but everything else should keep going — but we tend to forget that we are in a global pandemic,” she said. “And this is, for our generation especially, it’s completely unprecedented. … Now we’re experiencing this constant baseline stress and baseline anxiety that we need to take into consideration and maybe not be so hard on ourselves occasionally.”

Eric Brouzes – Plumbing the Depths of a Single Cell

Biomedical Engineering Professor Eric Brouzes and his team are self-described plumbers, but not the kind who unclog toilets or fix broken pipes. They work at a scale smaller than a human hair, using tiny microfluidic tubes to analyze and sequence living tissues on the single-cell level. Unlike other methods of single-cell genomics, which require that tissues be broken down into isolated cells, the project Brouzes proposed for the Discovery Prize allows for sequencing within unbroken tissue.

“Cells don’t live by themselves,” Brouzes said. “They are in the ecosystem, and it’s really important to understand how they communicate, how they coordinate their action. So that’s the question we’re addressing with the Discovery Prize.”

When research at Stony Brook shut down, most of the work at Brouzes’ lab on the second floor of the Bioengineering building ground to a halt. He proposed one possible use of microfluidics as a diagnostic tool for COVID-19, which allowed him a limited presence through the shutdown period. But he was the only one in the lab for that two-month span. He used the time to monitor the team’s instruments and chemical reagents.

“We had a very limited presence, but still a presence during that time,” Brouzes said. “So that mitigated the risks of something going bad.”

Beyond basic maintenance, Brouzes and his team, made up of three graduate students and one undergraduate student, suffered from the lack of physical presence. All the research work that went into their Discovery Prize proposal was created “at the bench” — in-person in his lab. Forced to scatter for two months, their progress languished.

“For us, it was about time,” Brouzes said. “Dynamics in the lab can be complicated and can be fragile. So when you’ve got, for instance, a project that starts working out … you want to basically keep it rolling. And then you have to couple that with the funding of the lab as well. So we are at a point where we needed dynamics to go quickly, to get those data, and then request more funding and so on.”

Evan Lammertse, a fourth-year doctoral student, worked as an independent paid researcher in Brouzes’ lab. His time off campus was complicated by a herniated disc that went untreated through the early months of the pandemic, leaving him in chronic pain as he tried to complete what work he could with the data he had collected before the shutdown.

“I had only completed maybe 40 percent of my experiments that I had scheduled when the university shut down,” he said. “The direct result … was me not being able to collect that extra 60 percent, but the impact on my work was a lot broader than that, because it was kind of intertwined with that physical injury that I had. … I couldn’t even leave the house to walk around the neighborhood and get some fresh air. I was stuck inside for months. … The overbearing sense of powerlessness … certainly had an effect on my mental health.”

“COVID has kind of forced us to institutionalize things that previously were just informally done in lab, talking amongst people, you know, without having to create the structure for it.”

– Evan Lammertse, fourth-year doctoral student, Brouzes Lab

Even after returning to the lab last fall, working on microfluidic instruments proved to be more difficult. Maria Alvarez Amador, a first-year doctoral student, found herself struggling with procedures that she could have resolved had others been in the lab to help her.

“The paper instructions of how to do something don’t tell the whole story of the minutiae of what works and what doesn’t, especially in microfluidics, because you’re working on a small scale — any difference in temperature and the pressure you apply could mean your device has been successfully fabricated or not,” she said. “Once you’re in a roadblock, you really need other people to bounce off from in order to get over those roadblocks and make progress.”

Additionally, as with other research groups, Brouzes’ team began to lose the knowledge they would have gleaned from outside sources like conferences and literature and shared through discussions. When Brouzes set guidelines for his researchers’ outside work, he was met with some pushback.

“He kind of laid out expectations that he had of us as grad students, and a lot of those were more like experiential learning and like reading papers in your field and attending more seminars, and just being more extracurricularly engaged,” Lammertse said. “And my response to that was like, okay, that’s well and good, but it’s really hard to do those kinds of things without a social structure in which to do them. It’s a lot harder to stay engaged and in a dialogue with your colleagues, and learn from your colleagues, when you’re not physically present with them in the lab.”

The team said that the weight of the pandemic has had a significant impact on their ability to work. Small annoyances and adjustments accumulated over the course of the year, infringing on their ability to focus.

“There’s a lot of small things in your everyday that have changed that add up to all the stresses,” Alvarez Amador said. “Not just not seeing people, not just wearing a mask all day, not just being stuck at home, but like, where you can eat actually … tiny things that add up and affect your psyche.”

Additionally, the potential for the lab to close for two weeks after a COVID-19 exposure, in accordance with university protocol at the time, loomed over the researchers’ heads, as Alvarez Amador explained. “Every time you get a sore throat, you’re like, ‘Oh, if I test positive, I am halting my work for two weeks, I’m halting everybody’s work for two weeks,’” she said. “So there was that mental component of always being stressed out — if you hear somebody had COVID, you’re like, ‘Oh, do I have it? Do we have to get shut down for two weeks and [will I] be the reason that nobody’s making progress on the lab?’” 

In order to manage these additional stressors, the team began meeting over Zoom on Wednesday mornings last January. They also maintained a journal club, which meets on Thursdays, in which one group member picks a piece of literature for the entire group to discuss. 

“COVID has kind of forced us to institutionalize things that previously were just informally done in lab, talking amongst people, you know, without having to create the structure for it,” Lammertse said. “But when you don’t have everyone in the lab every day, you kind of need to do the work to create the spaces for these discussions to happen.”

The Brouzes lab anticipates a return to greater normalcy in the fall, but until then, they continue to deal with the underlying stresses of the pandemic world as they plumb the depths of single-cell genomics.

And the Winner Is . . .

Eszter Boros. 

“I’m very much humbled and incredibly grateful,” Boros said as she accepted the award at a virtual event on April 28 that included the finalists, judges and President Maurie McInnis. “This enables really exciting science for my research group and my students, who are super excited.” 

With the $200,000 prize, Boros and her team will further develop their light-activated cancer treatments, seeking publication in medical journals and hopefully a contribution to clinical implementation down the line.

“Although much has changed over the last year of the pandemic, the passionate, committed pursuit of knowledge, research and discovery at Stony Brook University has not,” McInnis said. 

Through their perseverance and adaptability, Boros, Brouzes, Henkes, Reed and their teams proved her right.

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.

Bats’ Best Friend

Bats have long been the subjects of mystery. Much of the stage has been taken up by vampire bats – technically, a species of the subfamily Desmodontinae – as blood-sucking manifestations of fear and fantasy horror. They inhabit our literature and our nightmares and fly across our movie screens with the power to shape shift into Dracula and a penchant for Halloween hangouts with witches and black cats.

The advent of the coronavirus turned these creatures of the night into real-life monsters – prime suspects, some would say, for spreading a virus that has killed more than 600,000 Americans and 4 million people worldwide.

But there’s a bright side to these nocturnal creatures that just might redeem them. They may also hold the secret to humankind’s salvation – they are immune to the very virus that has been killing us. 

Liliana M. Davalos, a professor in Stony Brook University’s Department of Ecology and Evolution, is one of the world-renowned researchers looking to uncover the mysteries of these winged mammals of the order Chiroptera. She has been working for the past few years to understand how their genomic and molecular evolution has resulted in their immunity to severe acute respiratory syndrome coronavirus, or SARS-CoV-2. 

“One of the problems with the human pathogen is that the virus has such terrible consequences, particularly for the elderly or people under particular kinds of treatment,” Davalos said, referring to those with weakened immune systems such as cancer patients. “But for other kinds of people that are young [or healthier], it doesn’t seem to have as much of an effect. That tells us something about the condition of the organism that the virus interacts with.” 

Even though she doesn’t work with the exact species of bats involved in the spread of COVID-19, Davalos is on a quest for answers to what she sees as fundamental questions: “Does the genome of bats have the same elements as humans? If we created a model of the immune response of the bat, how would it differ to that of a human?”

Davalos’ study on bat genomic adaptations, published last July, was part of the Bat1K Project – an initiative by Nature, the leading international journal of science. It brought together a consortium of researchers like Davalos with biologists, conservationists and plain old bat-lovers to sequence the genomes of all 1,400 living bat species. The project provides one of the most extensive studies of the bat genomes to date.

“Our reference-quality bat genomes provide the resources required to uncover and validate the genomic basis of adaptations of bats,” according to the study, which featured the contributions of more than a dozen scientists.  It also predicted that these genomes will “stimulate new avenues of research that are directly relevant to human health and disease.”

The study revealed that bats have developed anti-inflammatory responses to viruses as well as an expansion of an anti-viral gene, which contributes to their exemplary immunity.

How the virus developed into a human pathogen is still unknown, according to a recent report published by the World Health Organization (WHO). President Joseph R. Biden ordered a deeper look into the origins of COVID-19, including whether the virus may have leaked from a lab in Wuhan, China – the city that was the global ground zero of the pandemic. After a 90-day investigation, United States intelligence agencies issued an inconclusive report, citing the Chinese government’s unwillingness to share essential data. But the review settled one key issue – the virus was not developed as a biological weapon.

While both origin stories remain plausible, the prevailing theory in some circles is that the virus was transmitted from an infected animal. More than a dozen researchers from around the world were involved in the WHO study, which analyzed surveillance data of early cases of COVID-19 and genomic data of the virus. The research found related coronaviruses in bats and pangolins – scaly nocturnal anteaters that live in Asia and sub-Saharan Africa. Bats remain the prime suspect, as they carry two strains of SARS-CoV sharing more than 90 percent similarity to COVID-19. 

Davolos detailed the difficulty of narrowing down the development of the virus. “There is a very large gap, biological gap, that happens when a virus that circulates in wild populations of bats, for it to become a human pathogen. That gap persists. … We still don’t know how the virus evolved, what changes it underwent. … We have … this darkness with regard to this.” 

Davalos began her journey into bat genomic research after finishing her undergraduate studies in biology at the University of Valle in her native Colombia. She continued her education at Columbia University in New York, earning a master’s degree, then a doctorate in ecology, evolution and environmental biology.

Although her focus of study was birds, she ended up accepting a post-graduate position as a research associate at the American Museum of Natural History in Manhattan, where her interest shifted to bat evolution and genomics. Since then, she has worked on several studies relating to the morphology and characteristics of neotropical and frugivorous, or fruit-eating bats.

Now, her research focuses on the evolution of bat noses and the creatures’ immunological adaptations.

“For the longest time, I think roughly since 2014, I have become very interested in the olfactory receptors of bats,” Davalos said. “So by the time the pandemic came around, we had this unique data set that no one else in the world had, that was focused on the genetics, and the morphology of bat noses.” 

Stony Brook researcher, Laurel Yohe, worked alongside Davalos for her dissertation on the genetic evolution of bat noses. “Specifically what we’re looking at is why bats are able to be infected or be potential reservoirs for coronaviruses, but not manifest any symptoms,” Yohe said, discussing the work she did in collaboration with Davalos. “And we’re particularly focusing on the sense of smell per se, or noses, because the nose is actually ground zero for where the SARS-CoV-2 virus enters the cells. So there’s these mucus-producing cells within your nasal cavity that are directly attacked and are expressed with different proteins that allow the virus to enter into the body.”

This research can provide more context for studies of COVID-19 and how it has spread among humans. It may also shed light on other SARS-type diseases – because how bats tolerate coronavirus infections may hold clues for the human species.  

As the report of her study in Nature concluded: “This is of particular global relevance … and ultimately may provide solutions to increase human survivability – thus providing a better outcome for this, and future, pandemics.”

Transforming Spare Parts into a Ventilator

The pandemic hit New York like a tidal wave in March 2020, as the number of coronavirus cases in the United States rose from an estimated 300 to more than 200,000 — and the death toll skyrocketed from one to 3,000. Stony Brook University locked down with virtually all classes going online, and Stony Brook University Hospital quickly found itself facing a dangerous prediction — there would be a shortage of at least 1,000 ventilators if the virus kept spreading at its then-current rate. This could mean hundreds, if not thousands, of preventable deaths. 

Something had to be done. 

Under the guidance of New York State Assemblyman Steve Englebright (D-Setauket), an interdisciplinary team was established to take on the task of creating an easily produced ventilator that could supplement the hospital’s reserves. Ventilators – commonly known as breathing machines or respirators – enable patients to breathe if they are unable to do so on their own. A typical hospital-grade ventilator can cost between $25,000 and $50,000 — and estimates showed that Stony Brook University Hospital might need an additional 25,000 machines. 

This project would come to be named CoreVent 2020.

The team leader was Jon Longtin, then associate dean of research and entrepreneurship in Stony Brook’s College of Engineering and Applied Sciences as well as a professor of mechanical engineering. Now interim dean, Longtin had experience in other high-profile collaborative COVID-related projects such as the design of the Clear-Vu Medical Face Shield, thousands of which are now in use at the university’s hospital as well as other area hospitals.

John Britelli – a clinical professor in the respiratory care program in the School of Health Technology and Management – was brought in by Englebright. With more than 30 years of experience, he has a host of certifications, including as a registered pulmonary function technologist and a specialist in neonatal and pediatric respiratory care.

Dimitris Assanis, an assistant professor of mechanical engineering, had just started at Stony Brook two months before. His research focuses on vehicles – specifically their engines and how to make them more environmentally friendly. He came to Stony Brook in 2020 after completing all his degrees in mechanical engineering – bachelor’s, master’s and doctorate – at the University of Michigan and spending 12 years working for his mother’s Ann Arbor-based information technology consulting company.

Together, these three formed the core of the CoreVent team, which also included Dr. Brian Margolis, a pulmonary disease specialist at St. Catherine of Siena Medical Center in Smithtown; Dr. Gerald Smaldone, chief of pulmonary medicine at Stony Brook’s Renaissance School of Medicine and Dr. Christopher Page, chief of the acute pain division of the medical school’s Department of Anesthesiology.

“It was quite a project, we worked 10 days straight, day and night,” Britelli says. Ten days was all it took for them to create a device that ended up never being needed – but that remains a one-of-a-kind model of teamwork.

The team created the fully functioning ventilator in 10 days.

It all started with a late-night phone call between Britelli and Longtin on March 27, 2020.  The next day – a Saturday – they were face to face in Britelli’s office at Stony Brook. “We talked for five, maybe six minutes,” Britelli recalls, “and then we went into my laboratory. And we just started writing on the board, figuring things out. All of a sudden two hours went by – I had no concept of time – and we had a ventilator that was easy to build and easy to reproduce.”

The team quickly took advantage of Assanis’s engineering skills to help create the first prototype. That first night they worked in Longtin’s Port Jefferson garage. Then the project moved to Britelli’s respiratory therapy teaching lab in the Renaissance School, where they tested it and developed a second prototype. As they worked, the team took “an abundance of care” with safety procedures, Assanis explains, spending what felt like “16 to 20 hours a day” just a few floors below the hospital emergency department.

“We would get daily reports of how many people were on vents,” Assanis recalls. “You’re on day four, five, six and you’re trying to perfect a design and you realize that perfection is the enemy of good. The longer it takes to perfect it, it’s safe and reliable – but upstairs there are people dying from COVID. You ask yourself, ‘Can I get this done 10 hours sooner?’ because it needs to go on a patient and save someone.” 

The ventilator was designed to be easily replicated for mass manufacturing, being created from what Assanis described as “spare parts.” Britell noted that a spigot from a garden hose was used to control oxygen flow at one point. “We had to use parts that were available in Home Depot, Lowe’s, mail-order, eBay,” he says. “The parts couldn’t be specialized.” And all the parts were available from multiple vendors to eliminate delivery delays in case replacements were needed.

On April 6, the project was finished. And the team unveiled what was officially announced as a “computer-controlled, pressure-cycled, time-limited ventilator” – complete with “assisted-breathing mode, visual status indicators and low- and high-pressure alarms.”

The computer-controlled ventilator was made of spare parts.

Fully functioning as an emergency ventilator, it was tested on an advanced lung simulator provided by Smaldone, the medical school’s chief pulmonologist, as well as lab mice. It was ready to be used on human COVID patients.

As it turned out, the hospital managed to get through the peak of coronavirus cases without running out of ventilators, thanks to donated machines and other financial contributions. As Britelli put it, they “just squeezed it.” 

Today, the CoreVent 2020 remains in storage, never used – and likely to never be mass-produced while professional ventilators are available. The trio of scientists are working on a new project to design a self-powered mask that filters air to the wearer. The goal is a mask that leaves the wearer’s face completely visible and doesn’t need to be connected to an external power source. 

“The problem is, it’s very scary for the patient,” Britelli says of face masks. The design he and his team are working on has benefits for medical workers and patients. “It’s comfortable,” he explains. “You can see the whole health care worker, you can see their eyes, their mouth, their facial expressions. One of the big complaints that we got from the patients was that they felt so isolated because they weren’t seeing their loved ones, because they weren’t allowed to. And the people they were seeing were all gowned and gloved — they were hidden. They weren’t seeing their faces. And people have a need to see faces.” 

Other projects the team has worked on or plan to work on include ventilators that don’t require respiratory therapy training to use and infant incubators for emergency use.

“You make these great things and nothing happens to them,” Britelli says. “You just have to accept that. But with the CoreVent we were tickled pink that it wasn’t used. … It was scary knowing that human beings could go on this and that their breath would depend on this ventilator. So, it’s not a feeling of discouragement, it’s not a feeling of emptiness – it’s a feeling of relief. It’s a good feeling. We were looking for the vent to collect dust and never get used.” 

Additional photos provided by Jon Longtin

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.”