Understand and Fight

Notre Dame researchers and the COVID-19 pandemic

The hero in Mary Shelley’s “The Last Man,” her second sweeping political science fiction after “Frankenstein,” is left alone in Rome, in a post-apocalyptic world. A global plague apparently took the lives of everyone else, yet he discerns a duty to forge ahead, no matter what.

In this Story Type of Research
Brian Baker Biophysics and Structural Biology
Cindy Bergeman Developmental Psychology
Kyle Bibby Environmental Engineering and Microbiology
Eileen Hunt Botting Political Theory
Paul Brenner Computational Infrastructure for Scientific Discovery
Matthew Champion Microbial Proteomics and Metagenomics
Hsueh-Chia Chang Micro/Nanofluidics
Ying “Alison” Cheng Quantitative Psychology
Kirsten Cornelson Labor Economics
Norman Dovichi Analytical Chemistry
Jeff Harden American Politics and Methodology
Cheng Liu Computational Modeling
Thomas Merluzzi Clinical Psychology
Alex Perkins Infectious Disease Epidemiology and Population Biology
Gina Svarovsky Engineering Education

Published in 1826, the novel mirrored Shelley’s life as she despaired at the loss of several of her loved ones. Her sister Fanny died by suicide. Her husband, the poet Percy Bysshe Shelley, drowned after a sailing accident. She lost another friend, the poet Lord Byron, to infection. Two of her toddlers died — one of malaria, and another from a fever. She kept a kind of plague journal, according to Eileen Hunt Botting, a professor in the department of political science, “in order to fight fatalism.”

“She found the courage to persist by writing about the reasons why she had an obligation to continue in this world, and serve in this world, despite the tragedy,” says Botting, whose book, “Artificial Life after Frankenstein,” will be published later this year. “At the end of Shelley’s novel, we find this powerful image of the seemingly last surviving human looking for other survivors, even as he sometimes doubts he will find them.”

As Notre Dame’s laboratories went into hibernation in March, many researchers from various fields — chemistry, engineering, political science, psychology, education — looked for ways to pivot their own work toward furthering knowledge into how COVID-19, the disease caused by the SARS-CoV-2 virus, works, how it’s transmitted, and how our country and world can cope with the unexpected pandemic crisis. They decided to jump into the research at different times, but for the same reason: They knew they could help.

COVID-19 crept onto the radar of epidemiologist Alex Perkins, the Eck Family Assistant Professor in the Department of Biology, in January. By February, the father of three children began personally preparing, loading up his cart at Costco with soap, sanitizer and toilet paper for the storm he knew could come. He models the trajectory and spread of other diseases — dengue, malaria, Zika — and learned some lessons from those epidemics.

Alex Perkins sits with a man at a computer.
One of Alex Perkins’ studies shows that social distance measures at April levels would have needed to be maintained until the summer to avoid a new spike in cases later.
An animated chart showing the trajectory and spread of other diseases.
Perkins’ model shows that as more emphasis is placed on relaxing control measures, a resurgence becomes more likely and more difficult to bring under control later in the year.

“It was good preparation for this,” the expert in population biology and Eck Institute for Global Health and Environmental Change Initiative affiliate said about his decision to pivot to research on the spread of COVID-19.

One of his studies related to the pandemic was published April 23. It shows that social distancing measures at April levels would have needed to be maintained until the summer to avoid a new spike in cases later. He added a model to a hub of other forecast models — one that includes the frequently cited University of Washington COVID-19 model that at first predicted 60,000 deaths and adjusted it much higher after states began reopening.

The virus has created such massive problems in so many areas of our lives, Perkins noted, that he’s thankful he can assist. “I’m happy with the way we’re targeting the work.”

The way states respond to the pandemic — rather than the population epidemiology — interested Jeff Harden, the Andrew J. McKenna Family Associate Professor in the Department of Political Science. He chose to expand his research agenda on what is known as policy diffusion. The concept describes how and why states adopt similar policies over time. With the clear tension between health risks and economic risks, Harden knew that a focus on policies because of COVID-19 would reap important findings. Which states are leaders? Which are followers? And how does the relationship occur?

To delve into policy diffusion, Harden and his team are “scraping” government websites and social media accounts by writing code that quickly scans the sources. He and his collaborators recently received a RAPID grant from the National Science Foundation (NSF) to continue the work through the summer, at which point he will be able to evaluate his findings.

“I hope that the research will be especially useful for understanding which policies are most effective,” Harden said. “There’s such a clear tension between health risks versus economic risks.”

“There’s such a clear tension between health risks versus economic risks.” –Jeff Harden

Kirsten Cornelson, Assistant Professor in the Department of Economics, wasn’t as interested in states’ policies as she was in how they align with residents’ politics, and wanted to quantify the polarization that people on both sides of the political aisle are feeling — even with a health pandemic. She and her co-author, Boriana Miloucheva of the University of Toronto, surveyed 1,000 people across 12 states where elections were barely won by one of the parties. Their research discovered that people were less willing to cooperate with certain measures (social distancing or handwashing) when their governors’ political party didn’t align with the respondents’.

Overall, this type of social fragmentation can limit economic growth, she said, because much of what a society accomplishes depends on people’s willingness to cooperate and contribute to the public good.

“The pandemic was not a political thing, and really did not seem like it would be something that should be controversial,” Cornelson said.

Her research usually focuses on the role of social environments and how they lead to racial and gender inequality, but this work fit in well, she said, noting that she felt like she was doing something proactive while embarking upon it.

“Social scientists aren’t developing vaccines, but this is one big area where social scientists can show the public what type of work we do and how it’s useful to them, rather than why it’s just important to us,” Harden said. “It wouldn’t have been possible to get started on this quickly if I had not already been doing related work, and this speaks to the importance of funding academic research in general — because you don’t always know what comes next out of a research project.”

Brian Baker, chair of the Department of Chemistry and Biochemistry and the John A. Zahm Professor of Structural Biology, had been doing fundamental research into immunology as it relates to cancer therapies with the Harper Cancer Research Institute. He studies T-cell responses in cancer, but so much in this field originated with work on viruses: It was really only after researchers had learned so much about viral immunology and T-cell responses to them that they were even able to pivot to cancer, he said.

Two people in lab coats in a research lab.
Professor Brian Baker and a graduate student in the X-ray facility, Stepan Chemistry.

So he pivoted back. Members of his team began electronically looking in the SARS-CoV-2 genome for parts of the virus T-cells might recognize, then modeling these to determine how well they might do at initiating anti-viral immune responses as components of prophylactic or even therapeutic T-cell vaccines. Baker is thankful that much of the work right now can be done on the computer, although his team is now ready to begin testing immune responses in the laboratory.

“At the start, there’s an awful lot of computational work to be done, examining and comparing genomes, structural modeling and network training,” he said. “The laboratory is waiting and ready to validate our predictions.” For further development, Baker has leveraged existing collaborations and developed new ones, including investigators at Texas Biomedical Research Institute, who are already working with live SARS-CoV-2 in animal models in secure facilities.

During lab hibernation, other scientists were mostly doing computational work, but Hsueh-Chia Chang, the Bayer Professor in the Department of Chemical and Biomolecular Engineering, was given permission by the University to have one graduate student in his lab at a time to work on developing a new diagnostic test that is more sensitive to a small number of SARS-CoV-2 in a sample. Early testing nationwide at the beginning of the pandemic returned false negative results between 40 percent to 70 percent of the time. Even now, the false negatives for the most advanced tests can be as high as 30 percent, Chang, an affiliate with NDnano and Advanced Diagnostics and Therapeutics, said.

A white plastic box with a yellow and red square and a green button. Cords come out of it. ChangLab ND is imprinted on it. Two men in lab coats and face masks walk down a hallway carrying a white box, the testing device. A man in a labcoat works on a COVID-19 test device.
Doctoral candidate Chenguang Zhang and postdoc Ceming Wang carry a testing device built by the Chang lab. The device allows a higher extraction efficiency from COVID-19 tests to hopefully reduce false negatives.

Like Baker, Chang had been using the technology for cancer research. He realized that his micro/nanofluid testing device could easily be used to work with viruses the size of SARS-CoV-2.

“Two major factors made us want to do this,” Chang said. “We thought there was a need for such a technology for this virus, and we wanted to contribute to this research.”

Chang had hoped to work with the SARS-CoV-2 virus itself, and reached out to colleagues at other institutions to collaborate, but none of the other institutions was open for collaboration. Meanwhile, he’s developed collaborations with other colleagues on the Notre Dame campus, including David Go, professor of aerospace and mechanical engineering, who is helping him build better instrumentation for his technology, and Jun Li, associate professor in the Department of Applied and Computational Mathematics and Statistics, who is helping to develop an optimum sample pooling strategy to reduce the number of tests based on medical records. He is also working with David Leighton, professor of chemical and biomolecular engineering, to develop the best pooling strategy for the Notre Dame students in particular.

Much like Chang is collaborating with others on campus, Kyle Bibby, associate professor of engineering and the Wanzek Collegiate Chair in the Department of Civil and Environmental Engineering and Earth Sciences, has begun work with others on different projects that may help track this and future diseases. Bibby, who graduated from Notre Dame in 2008, is an environmental engineer and applied microbiologist affiliated with the Environmental Change Initiative. He started on two projects related to finding SARS-CoV-2 in municipal water samples, and both have been funded by the National Science Foundation.

With Perkins, Bibby has begun connecting measurements from wastewater samples to epidemiological models, with the goal of completing some short-term forecasting and monitoring. Other diseases — from polio to measles to norovirus — have been tracked this way in the past.

Bibby is working with Matthew Champion, associate professor in the Department of Chemistry and Biochemistry, on sequencing the genome. They hope to notice slightly different variations of the genome to decipher from where the majority of a community’s viruses originated.

Every Monday, Wednesday and Friday, Champion drops off sterile, 1-liter bottles at a local wastewater treatment plant to be filled. Champion and his collaborators, including Norman Dovichi, an emeritus professor of chemistry and biochemistry, want to understand if the virus can be detected in the water by sequencing the virus. They also hope to track how the viral content of the wastewater changes during an outbreak.

“Down the road you can use that information to inform community response,” Champion said.

If their hypothesis is correct and wastewater can be monitored for the presence of viruses like SARS-CoV-2, labs can continue to test. Increases of virus, or new viruses, that show up in the wastewater can be used as sentinels of future outbreaks. Champion and Dovichi would like to continue monitoring through the end of the year.

“We want to collect long-term, because then we can tell what a potential surge looks like,” Champion said.

On top of his research satisfaction, Champion said his work picking up the water — it doesn’t look disgusting, but it is gray — has helped him stave off cabin fever. He also feels good about being able to provide information that he will be used to monitor viruses and diseases in the population.

“I feel like I can do something; I’m not in health care, so this is my contribution,” Champion said. “Though last week I gave blood as another way of giving back!”

Being able to work — and even having a feeling of giving back in any way during the pandemic — is one way of staying mentally healthy. But that’s not possible for everyone all the time, and research into people’s mental health is another window into evaluating the effects of the crisis.

It’s scary to live in a pandemic, because it is physically and economically dangerous, Botting, the political science professor, said, describing how Mary Shelley used literature and life-writing to come to terms with the existential crisis she dramatized in her novel “The Last Man.”

“She models a way for us to find a way forward by looking inward at ourselves,” Botting said.

Cindy Bergeman, professor of psychology and an associate vice president for research, as well as Thomas Merluzzi, another psychology professor, are conducting different research projects that report on how people are looking inwardly. Bergeman’s laboratory is in the 13th year of a 15-year longitudinal study with three cohorts of people — young adults, people in midlife and those in later life — to monitor their stress on a variety of different levels.

Two women in lab coats in a research lab.
Cindy Bergeman and a student work in the new psychology lab in Corbett Family Hall.

“In the past few years we have been bringing people into the lab, getting their health history, blood drawn, assessment of functional abilities; we’re interested in blood assays for health-related problems associated with stress,” she said. One aspect of the study is to find out how people deal with adversity. When the COVID-19 pandemic began, her team decided to delve into the daily impact of social quarantines, health concerns, financial strain and other issues by sending out a four-page Qualtrics questionnaire every day throughout April.

“Given that we had previous information about everyone, it will be really valuable to see what people’s state of mind is and how they’re feeling about the situation,” Bergeman said. “I’m really interested in the potential long-term effects.”

Merluzzi, who is affiliated with the Harper Cancer Research Institute, completed a survey study about the relative impact of the pandemic on the mental health and quality of life of cancer patients and survivors, compared with people who do not have cancer. The study consisted of a national sample of 155 people who have cancer or have survived cancer, and 50 non-cancer matched control participants. Merluzzi’s team asked several questions related to mental and physical health, job and food security, as well as virus exposure, in order to find out about distress levels the different groups were experiencing.

He has only preliminary results, but so far data show that 32 percent of non-cancer participants reported an increase in mental health problems, whereas 54 percent of cancer patients and survivors reported an increase in mental health problems since the onset of the pandemic.

Also, isolation because of existing health conditions appears to be significantly greater in the cancer group. For a quarter of that group, the isolation may be contributing to not being able to have enough food in their houses. Also, among the cancer group, there was a substantial number of people who were experiencing increases in other health problems not related to the virus. These issues may account for the higher distress levels in the cancer group compared to the non-cancer group.

“Other research has shown that interim outcomes such as stress, distress and declines in quality of life have been related to adherence to cancer treatment regimens and longevity in those with cancer,” Merluzzi said.

Instruction during the closures of schools, and the institution of e-learning, has been a challenge, and a few Notre Dame researchers saw clearly the need to tackle these issues as part of their research. Quantitative psychologist Ying “Alison” Cheng, associate professor in the Department of Psychology, has been working to understand the link between student engagement and learning among students taking advanced placement (AP) statistics. She had been collecting data from students who were learning through an online assessment and feedback platforms, AP-CAT, with the goal of helping students in under-resourced schools. The platforms provide adaptive assignments and analysis to show them what they needed to review and study more.

With reduced interaction between students and teachers, Cheng knew that students would have to become more reliant on the system she and her collaborators created.

“We predict their utilization and feedback will increase, and want to see if that’s true,” Cheng said. “We’re looking at both the student and teacher ends, and seeing how COVID-19 changes the way they interact with these systems.”

The work hits home for Cheng, who is teaching a graduate-level course this semester. She feels firsthand the inability to have in-person interactions. But she feels grateful that she has a baseline from her previous research to compare with the research she’d now doing during the pandemic. The research should discover what online systems could provide that in-person instruction cannot, and uncover gaps.

“We may be able to do more research in terms of the benefits of in-person instruction,” she said. In the meantime, in an effort to help teachers and students make a transition to online learning assessment, Cheng has worked with collaborators on the Notre Dame campus, including Cheng Liu, lead data scientist in the Center for Social Science Research, and Paul Brenner, senior associate director of the Center for Research Computing, to address the software and hardware challenges in making a publicly available version of the AP-CAT platform available to students nationwide.

On the other end of the teaching spectrum, Gina Svarovsky, associate professor of the practice at Notre Dame’s Center for STEM Education, is conducting the Home-Based Learning Needs Assessment study to understand what resources will be most helpful to teachers, parents and caregivers during this transition to learning outside of the classroom.

Svarovsky, who works both with teachers in the classroom as well as educators from “informal” learning contexts like museums and libraries, was motivated to quickly launch the study after talking with educational partners across the country who shared how overwhelmed they were by the sheer volume of online resources coming at them from every direction.

Her study began by distributing a survey to pre-K to 12th-grade teachers and parents, and then conducting a set of follow-up interviews with both groups to understand the challenges and realities they are facing. Svarovsky also presented the undergraduate students in her spring 2020 course with the opportunity to join the project as research assistants as an innovative option for their coursework after the University moved to remote learning in March.

Preliminary analyses suggest that both teachers and parents are looking to trusted sources for high-quality recommendations and that there are differences in the perceptions and realities of the lived experiences of educators and families during the rapid transition to home-based learning.

“If we can equip people with engineering ways of thinking at an early age, you can come to learn that you solve many different types of problems, and take productive and meaningful action on your world.” –Gina Svarovsky

Svarovsky, who graduated from Notre Dame in 1999, has long thought about the intersection of different learning environments across a person’s life, from the classroom to the museum to the home. She currently co-directs the NSF-funded Head Start on Engineering study, which seeks to better understand how to design and implement activities for young children, their families and their teachers that can lead to the development of early engineering interest and understanding. In one of the project’s activity kits, families start by reading a storybook about a fox and a hen, and then they are asked to build a structure with small foam blocks that protects the hen and her nest from the fox. Afterward, the instructions add narrative constraints, like asking the children to imagine the fox can jump, and also asking if they can build the protective wall with fewer pieces.

Svarovsky and her team believe that supporting and empowering not only the young learners but also their parents and families during STEM activities is key. “We’re not just focusing on what the kids are doing, but also on bolstering parents’ confidence,” she said.

“We want people to know that engineering isn’t just for workforce development,” she said. “If we can equip people with engineering ways of thinking at an early age, you can come to learn that you solve many different types of problems, and take productive and meaningful action on your world.”

Those may even include joining forces with independent and varying areas of research, to someday resolve the current pandemic.

Throughout the crisis, Notre Dame professors are working toward a common good — developing a body of knowledge that will answer serious questions and bring comfort to people with a pillar of understanding, no matter where the research leads.

“Science is built on the shoulders of giants,” Champion said. “I am collaborating with many people, and have good University support, and that makes the work even more worthwhile.”

And though Mary Shelley may have invented a pandemic in her book after feeling like the plague herself when so many around her died, her lessons from 1826 stand true today.

“She feels she has the obligation to save the world, and that each one of us has to step up to the plate to foster life,” Botting said. “She was remarkably stoic, philosophically speaking, as she used the terrifying image of a global plague to explore how people ought to rationally and emotionally react to times of crisis — this makes her a really interesting figure for our current political crisis, as we develop the knowledge we need to weather it, because COVID-19 will not be the last of the pandemics.”