From almost the beginning of the COVID-19 outbreak in early 2020, the world waited anxiously for a vaccine, the safeguard that would enable a return to normal life. Researchers around the world eagerly picked up the challenge.

Penn State scientists have been active among them from the earliest days. Drawing on the knowledge, skills, and technologies they have developed over their careers, and taking advantage of infrastructure built for the purpose, teams of experts around the university moved rapidly to face the crisis. 

“As a university, we’ve put a lot of care and effort into positioning ourselves to be able to respond to pressing global needs,” says Leslie Parent, vice dean for research and graduate studies at the College of Medicine, and a leader of one of those teams. “So, when it became apparent that a COVID-19 vaccine was urgently needed, we already had the people and facilities in place to act very quickly.”

By year’s end, thankfully, the all-out global effort was starting to bear fruit, as three major pharmaceutical companies, Pfizer, Moderna, and Johnson & Johnson, were each granted emergency-use authorization by the FDA for their vaccines. By late March 2021 the United States was administering more than 3 million shots per day, and as of mid-April some 84 million Americans had been fully vaccinated. But the race for a cure is far from over.

“These first-generation vaccines have proven remarkably effective so far,” explained Andrew Read, Evan Pugh Professor of Biology and Entomology and director of the Huck Institutes of the Life Sciences. “No matter how good they turn out to be, however, additional options will likely be needed to achieve the highest possible immunity levels for the greatest number of people across the globe.”

Accordingly, Penn State researchers are still hard at work. Using a variety of approaches, they are pursuing COVID-19 vaccine candidates that aim to complement the first-generation solutions. The hope is to develop options that may be even more efficacious, and better able to reach different segments of the population, such as the young and elderly, in rich and poor countries alike. New mechanisms of action and modes of delivery may also be useful for fighting future coronaviruses and other pathogens.

Penn State’s scientists, Read notes, are particularly well situated to conduct the innovative, cross-disciplinary research that yields novel materials and procedures with the potential to advance vaccines to more sophisticated levels. “Very few universities have the strength we do in bringing people in engineering together with people in life sciences and clinical research to address a complex problem like this,” he says.

From HIV to COVID-19

With previous experience creating a vaccine candidate for HIV, Nikolay Dokholyan, the G. Thomas Passananti Professor in the College of Medicine used that knowledge, along with novel technologies he developed, to pursue a COVID-19 vaccine. 

Dokholyan explained that one of the reasons HIV has been so hard to defeat is because it has such a high mutation rate. “This has made it difficult to target with a vaccine,” he said. “If you create a vaccine for one strain of the virus, it won’t work against other, mutated strains.” But not all parts of the virus mutate, he added. Some of HIV’s genetic material is conserved, meaning it remains constant from generation to generation. “These conserved areas are vulnerable spots on the virus that can be targeted with a vaccine,” he said.

As it turns out, these conserved areas, called epitopes, also occur on SARS-CoV-2, the virus that causes COVID-19. To build a vaccine for COVID-19, Dokholyan and his team adapted software it had previously created, using it to identify the SARS-CoV-2 epitopes.

Next, the team performed what they call molecular transplantology. “We used molecular scissors to cut the epitopes out of SARS-CoV-2 and transplant them all over small protein scaffolds,” explained Dokholyan. “This increases the chances that antibodies will find the epitopes and launch an immune response.”

In collaboration with Neil Christensen, professor of pathology and microbiology and immunology, the team is currently testing its vaccine candidate in mice and rabbits. Already, the team has found that the transplanted epitopes produce a significant immune response in these animals. The researchers have also seen similar responses in antibodies collected from patients who had COVID and developed an immune reaction. If the lab work continues to prove successful, the next step, says Dokholyan, will be to run human clinical trials.

Protection at the site of infection

With prior experience studying intranasal influenza vaccines, Troy Sutton, assistant professor of veterinary and biomedical sciences, recognized the benefit of an intranasal vaccine that targeted the primary site of COVID-19 infections — the nose.

“Other COVID-19 vaccines in development are designed to be delivered intramuscularly,” Sutton explains. “These vaccines can protect the lungs and that may be good enough to keep people out of the intensive care unit, but if you really want a vaccine that both protects you from getting sick and prevents transmission you need to target the site of the infection.”

Sutton teamed up with Scott Lindner, associate biochemistry and molecular biology, who, along with Susan Hafenstein, professor of biochemistry and molecular biology, had previously engineered and patented a self-assembling soccer-ball-shaped scaffold made of proteins that could display up to 60 additional proteins on its surface.

The idea behind the scaffold is to hold proteins that are too tiny and unstable to be seen — even with Penn State’s FEI Titan Krios cryo-electron microscope, a one-of-a-kind instrument that is the gold standard for visualizing small biological molecules. The scaffold makes it possible to study these molecules for the first time. Its size and shape, in this instance, also make it perfect for an intranasal vaccine.

As Lindner explains, “The scaffold is roughly the size of a coronavirus and with coronavirus proteins attached to it, it looks a lot like SARS-CoV-2. Yet it cannot replicate, so you don’t have the safety concerns that come with a live attenuated virus.”

A virus-like particle that mimics SARS-CoV-2

At the College of Medicine, a team led by Nick Buchkovich, associate professor of microbiology and immunology, and Leslie Parent, is also developing a virus-like particle (VLP), a non-infectious particle that resembles a virus — another way of tricking the immune system into eliciting a response. In this case, the VLP expresses the SARS-CoV-2 surface proteins. Buchkovich, a virologist who studies human cytomegalovirus, a type of herpes virus that causes congenital birth defects, said the team hopes their vaccine will provide longer-term immune protection than many others in development.

A problem with some of the current vaccines being developed, he said, is that they use only the S protein, and studies suggest the structure of the S may vary depending on whether it is expressed alone or in segments. Using the S protein in the context of a VLP will allow for it to maintain the interactions with other viral proteins and have a structure similar to what is seen by the immune system.

The researchers are currently working to optimize and scale up the production of their VLPs and are starting to test them in mice. 

“In mice, we know we get a robust antibody response, which is good, but we’re still working on analyzing the T-cell and B-cell responses, which we know will be critical for getting longer-term protection,” said Parent, an expert on retroviruses. “If we get good data in animals, we will begin to look for industry partners to help us take the vaccine to clinical trial.” 

An “aerogel” to deliver nucleic-acid-based vaccines

Of the various vaccine types in clinical use, vaccines based on nucleic acid, including DNA and RNA, are among the easiest to develop and produce, and they induce a wide range of immune response types, thereby providing robust protection.

“Unfortunately,” said Scott Medina, assistant professor of biomedical engineering, “nucleic-acid-based vaccines have, until recently, not been widely adopted because they are rapidly degraded by enzymes in the body and they are not readily taken up by host cells.”

Medina, whose pre-COVID research focuses on developing a universal flu vaccine, has found a way around these obstacles by developing a gel-like nanoparticle aerosol, or "aerogel," that protects the vaccine from degradation and promotes its uptake into cells. His vaccine is intended to be delivered to the lungs through inhalation.

“We’ve designed the aerogel to mimic human lung tissue,” Medina explained. “Immune cells in the lungs are really sensitive to these types of materials because they look like pieces of lung tissue that have been degraded or destroyed by a bacterial or viral infection. These immune cells in the lungs [called macrophages] basically eat and digest them to remove them.”

He explains that the aerogel encapsulates DNA that encodes for a protein on the surface of SARS-CoV-2. “When macrophages clean up what they detect as pieces of damaged lung tissue, they internalize the DNA and express a viral protein, which stimulates an immune response to the virus.”

The team is currently testing its vaccine in mice in collaboration with Girish Kirimanjeswara.

A vaccine built from a non-human adenovirus 

Adenoviruses are responsible for human illnesses including the common cold and pink eye and, in principle, because they are so good at infecting humans, adenoviruses make good candidates for vaccine vectors. With a $3.8 million grant from the National Institutes of Health, Suresh Kuchipudi, clinical professor of veterinary and biomedical sciences, and his colleagues are developing a novel vaccine that uses an adenovirus as a delivery vehicle. 

“Unfortunately, because many of us have already been exposed to these adenoviruses, our bodies could be immune to an adenovirus-based SARS-CoV-2 vaccine,” he said. To get around that and make the vaccine more effective, the group is using a harmless form of a common cold-like adenovirus found in cattle as a vaccine platform. “Using a non-human adenovirus as a vector for delivering the vaccine is important because it means that the human population will have no preexisting immunity to it,” said Kuchipudi.

Working in mice, the team is assessing the quality and durability of the immune response that their vaccine creates. So far, Kuchipudi said, the work suggests that their novel adenovirus vector system could serve as an excellent delivery vehicle, both for the development of recombinant vaccines against SARS-CoV-2, and for future emerging pathogens.

“An effective vaccine is the best hope to finally end this pandemic,” Kuchipudi added. “But it will take more than just one vaccine to solve the problem. We will likely need to deploy multiple vaccines with different mechanisms of action. A key focus of our technology is to develop a COVID-19 vaccine that is also effective in older people with weakened immune systems who are at a higher risk of developing severe disease. We will also need effective therapeutics to treat the virus after infection and to treat the symptoms of the virus.

“Finally, and it can’t be said enough, if we all strictly follow recommendations for social distancing, mask wearing and handwashing, we can go a long way toward protecting ourselves and each other from this virus.”

Editor's note: This story appears in the Spring 2021 issue of Research/Penn State magazine.