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Research roundup: EPI's COVID-19 projects

June 28, 2021: A look back at the contributions of UF’s Emerging Pathogens Institute to campus-wide COVID-19 research.

Research roundup: EPI's COVID-19 projects

The University of Florida’s Emerging Pathogens Institute has played a supporting role in many different research efforts focused on the COVID-19 pandemic since early 2020.

“We were keeping eyes on this new disease as soon as we learned about it back in December 2019,” says EPI Director J. Glenn Morris, Jr., M.D., M.P.H. & T.M.

But UF investigators weren’t just watching to see what would happen next. In February 2020, a team began surveying for SARS-CoV-2, the virus that causes COVID-19, by quickly adjusting an existing flu survey project to include the new virus. A full month before the first COVID-19 infection was confirmed in Florida, UF and EPI investigators found it on swabs taken from a door handle of a public building.

But that was just the beginning. More than a year later, researchers affiliated with the EPI are still studying SARS-CoV-2 and the global pandemic it spawned.

A look back at EPI and COVID-19

Spillovers. Dr. Morris’ longtime interest in public health in Haiti helped found a program to survey and monitor school children for emerging infectious diseases. When a child at a participating school developed a fever with no known cause, and if the child and their parents consented, a blood sample was taken and studied for uncommon or unknown viruses. Recently, in light of the pandemic, Morris’ team ran a new analysis on samples taken several years ago and they discovered the first instances of two different porcine deltacoronaviruses known in people. 

“What we’ve shown is that there is likely some movement back and forth with coronaviruses between animals and people,” Dr. Morris says. “It’s simply not detected because we don’t look for it.” Luckily, most spillovers also don’t result in person-to-person transmission, he added.

The team involved in this study included John Lednicky, a research professor, microbiologist and molecular biologist in UF’s College of Public Health and Health Professions and the EPI where he studies an array of disease-causing microorganisms. Even before the pandemic emerged, Lednicky had studied coronaviruses and had sampled the feces of wild Brazilian free-tailed bats in Florida to see what kinds of coronaviruses they may be carrying.

Diagnostics. In January and February 2020, Lednicky used some of his past samples of alphacoronaviruses from the bat project and developed a diagnostic test for SARS-CoV-2. His test would become the basis of seven different studies that sought to assess how the virus was spreading in vulnerable populations.

 UF researcher Rhoel Dinglasan also developed a test for the SARS-CoV-2 virus. Dinglasan is a professor of infectious diseases in UF’s College of Veterinary Medicine, who took knowledge gleaned from developing a saliva-based malaria test and applied it to developing a rapid test for COVID-19. The idea propelled him and two colleagues to a second-place prize in the National Institutes of Health Technology Accelerator Challenge.

Aerovirology. Lednicky and Morris were also involved in cross-disciplinary work that sampled viable, or active, SARS-CoV-2 particles from the air of a car driven by someone confirmed to be infected. (The driver was not wearing a mask while in the car.) And Lednicky’s longtime partnership with UF engineering researcher Chang Yu-Wu to develop better machines for sampling air for viable viruses, contributed to a stream of early research that demonstrated the airborne nature of COVID-19.

Druggable targets. A different team of researchers coalesced around the idea of using gene editing techniques to search for genes that either help or hinder the infectiousness of SARS-CoV-2. The interdisciplinary team included Christopher Vulpe M.D., a professor in UF’s College of Veterinary Medicine, in collaboration with Stephanie Karst, a professor in UF’s College of Medicine, and Mike Norris, a professor in UF’s College of Liberal Arts and Sciences. The team used CRISPR genome editing techniques to screen human cell lines in labs within EPI’s facility. Their work was made possible by seed funding from UF’s Clinical and Translational Science Institute

Biostatistics and modeling. Outside of the laboratory, other researchers affiliated with the EPI applied their skills in biostatistics and modeling. Mathematician Burton Singer worked with researchers from Brazil and Harvard University’s School of Public Health to model how COVID-19 spread in Brazil. He also collaborated with researchers from Yale University’s School of Public Health to model how to shorten COVID-19 quarantine times by testing upon exit from quarantine and how vaccination efforts might affect the pandemic’s trajectory.

UF-EPI biostatistician Ira Longini modeled the limit of travel restrictions on the spread of COVID-19 and contributed along with UF-EPI biostatistician Natalie Dean to an ongoing effort by the GLEAM project to model COVID-19 deaths in the US. Longini, Dean and fellow UF biostatisticians also uncovered trends in the household transmission of SARS-CoV-2. Another researcher affiliated with the EPI, Gregory Glass, a medical geographer, applied ecological theory to modeling how the pandemic is worsened, in the absence of vaccines, without coordination of mitigation strategies.

Vaccine effectiveness. UF-EPI Biologist Derek Cummings participated in research that determined the CoronaVac vaccine was effective against the P.1 variant in healthcare workers in Brazil during the height of their second wave. And back when vaccines were still in development, Ira Longini provided commentary on crucial criteria that should be evaluated in COVID-19 vaccine trials, and the EPI hosted a seminar series on vaccine effectiveness.

Disease dynamics. Cummings also produced a comprehensive literature review of coronaviruses early in the pandemic, which became the seventh most-read paper at Nature Communications in the life and biological sciences category for 2020. His team also used data from 45 different countries to establish death rates for COVID-19, in an early effort to understand the pandemic’s scale even as countries did not report death data in a uniform way.

A partner in early testing efforts

Some of the EPI’s earliest efforts at the start of the pandemic’s arrival in Florida centered on testing. The institute’s 70,000-square-foot building has a large cluster of secure labs that became a hub for COVID-19 testing early in the pandemic. By working with its extensive network of contacts on campus, the institute quickly flipped several laboratories in March 2020 and reconfigured them to process large numbers of COVID-19 tests daily.

COVID-19 tests processed at the EPI were not approved by the US Food and Drug Administration, but they provided a powerful tool for surveying communities and occupational groups at high risk of contracting the novel coronavirus.

“This was really about a series of high-risk populations that we wanted to monitor across time,” Dr. Morris says. “We got the idea for this very early, and the projects kept growing.”

Although the dedicated high-security laboratories are a critical feature of EPI, the institute also serves as a network to link researchers across various fields and nurture projects that fuse disciplines. Between January and summer 2020, the EPI either spearheaded or supported seven COVID-19 testing efforts. In some cases, Dr. Morris played a pivotal role in linking interdisciplinary researchers.

Farmworkers. The EPI supported an idea brought forward by Joan Flocks, a professor in UF’s Levin College of Law, to test farmworkers. Flocks works closely with the Florida Farmworkers Association and she recognized that farmworkers were at high risk due to working closely with each other, lack of access to handwashing facilities, crowded living conditions, and shared transportation to and from work. Flocks is the director of emerging issues at the Southeastern Coastal Center for Agricultural Health and Safety, which is also directed by Morris. 

Working with UF Health, farmworkers in Apopka, Fla. were tested in May 2020 both for active and past infections, using a combination of nasal swab tests that detect the presence of the SARS-CoV-2 virus that causes COVID-19, and serosurveillance tests that detect antibodies made by the immune system and signal a past infection. EPI deputy director Mike Lauzardo, M.D., oversaw the testing and Megan Nodurft-Froman coordinated the field operations; their home department is UF’s College of Medicine, Division of Infectious Diseases & Global Medicine. Funding and support were provided by the National Institute of Occupational Safety and Health.

Flocks, Morris and Lauzardo later coauthored an editorial that cast a spotlight on how occupational conditions of farmworkers could facilitate the spread of COVID-19, based on a case study in northcentral Florida.

UF personnel in PPE performing a nasal swab test

The Villages®. In March 2020, one of the first testing projects the EPI became involved with was community testing at The Villages®. The community comprises Florida’s largest population of retirees and is considered vulnerable due to the heavier mortality toll COVID-19 has wrought in older age groups. Symptomatic individuals, or those with certain travel histories, received an FDA-approved test, while people who did not have symptoms but were concerned about their COVID status, could receive a test developed by John Lednicky, a virologist shared by the College of Public Health and Health Professions and the EPI. Mike Lauzardo, M.D., EPI’s deputy director and a professor in UF’s College of Medicine, Division of Infectious Diseases and Global Medicine, led the project. (Photo credit: UF Health)

UF personnel at GRACE marketplace for covid testing

Grace Marketplace. UF College of Medicine faculty, staff and students teamed up to provide pop-up testing for members of Gainesville’s homeless population at Grace Marketplace on March 30 and April 1, 2020. People without a home of their own often live together in groups where resources are shared and maintaining social distancing can be a challenge. Tests were analyzed at EPI’s facilities. Grant Harrell, M.D., an assistant professor in the UF College of Medicine Department of Community Health and Family Medicine (pictured at left) and a physician at UF Health Family Medicine – Old Town, oversaw the project. (Photo credit: UF Health)

COVID-19 testing team in main street at Cedar Key, group photo

Cedar Key. In April 2020, EPI members helped coordinate a community-wide pop-up event for aquaculture workers in Cedar Key, Fla. Aquaculture workers are vulnerable because, similar to farmworkers, they often work in close proximity to one another in settings where social distancing is not always feasible. More than 80 community members participated, and the tests were analyzed at EPI’s facilities. Andy Kane, director of EPI’s Aquatic Pathology Laboratory, and a professor or toxicology in UF’s College of Public Health and Health Professions Department of Environmental and Global Health coordinated the testing project with Mike Lauzardo, M.D., EPI’s deputy director and a professor in UF’s College of Medicine, Division of Infectious Diseases and Global Medicine. (Photo credit: Andy Kane)

COVID-19 testing in Durkeville, UF personnel triaging citizen

Jacksonville. Testing was offered in April to people age 65 and older within underserved populations with the goal of finding people who were infected but either presymptomatic or asymptomatic. At the time this study was conducted, little information was available about the role of so-called silent spread, which was later found to be a significant driver of COVID-19 transmission. This effort was led by Ross Jones, M.D., an assistant professor and medical director of UF Health and Family Medicine at UF’s College of Medicine-Jacksonville. (Photo taken at the Durkeville testing site operated by UF Health-Jax, credit: UF Health Jacksonville Communications and Marketing)

Tent in a parking lot for walk-up COVID-19 testing for first responders

First Responders. In May, when COVID-19 tests were still scarce in much of the country, UF Health expanded research-based testing to City of Gainesville employees and first responders with occupations spanning emergency medicine, police officers, firefighters, pre-hospital emergency medical services and front-line health workers. UF Health News first reported the effort, which was led by Lisa H. Merck, M.D., M.P.H., who is the vice-chair of research in UF’s College of Medicine Department of Emergency Medicine. Tests were analyzed at EPI’s facilities, and tests were offered on an ongoing basis. The effort formed the basis for an NIH grant application seeking to investigate the long-term effects of the pandemic on first responders. (Photo credit: UF Health)

Medical professionals in PPE outside PK Yonge Developmental Research School

P.K. Yonge Developmental Research School. Several professors from UF’s College of Public Health and Health Professions Department of Environmental and Global Health and the College of Medicine brainstormed a project to examine how school-aged children and households were affected by the pandemic over time. This long-term cohort study began in April 2020 and participants are tested every six months for active or past infections. The study also uses a social science-based questionnaire to assess mental health outcomes. The researchers want to identify if knowledge, attitudes and behaviors change health outcomes for children or their families, and also if children play a role in household transmission chains. Funding for this study came from the UF Clinical and Translational Science Institute, the UF College of Medicine Department of Pediatrics, and the UF College of Public Health and Health Professions. (Photo courtesy of the study authors.)


Acknowledgments

EPI thanks the following entities for their partnership and support during the pandemic:


The EPI at UF

The EPI was established in 2006 to foster research into new and reemerging pathogens that cut across academic disciplines. The institute is housed directly under UF’s Office of Research and connects projects and academics that span between UF Health, UF’s Institute of Food and Agricultural Sciences, the UF College of Liberal Arts and Sciences, and other campus entities and colleges.


Written by DeLene Beeland