COVID-19: the state of the science

In 2002, Mark Denison, M.D., who has devoted his more than 30-year career to the study of coronaviruses, was sitting on a beach with his wife in the Florida Panhandle, explaining to her that he might need to look for a new focus for his research due to difficulty obtaining funding.

The two were interrupted by a phone call from a colleague, telling Denison of a coronavirus outbreak in Hong Kong, later identified to be caused by SARS, or severe acute respiratory syndrome. Since then, two more coronaviruses have crossed to humans, including MERS and, of course, SARS-CoV-2, the virus that causes COVID-19, putting Denison’s research in the spotlight.

In April, Denison gave the keynote address at the South Carolina Clinical & Translational Research (SCTR) Institute’s retreat titled “COVID-19: The State of the Science.” SCTR retreats are hosted by SCTR’s Pilot Project Program, which is directed by SCTR associate principal investigators Perry Halushka, M.D., Ph.D., and Kevin Gray, M.D., and co-directed by Dayan Ranwala, Ph.D. The retreats provide researchers across the state a chance to share their work and plan new collaborative projects that will be eligible for SCTR pilot funding. SCTR is now accepting applications for  High Innovation-High Reward and Team Science pilot project grants.

"I'd argue that coronavirus is maybe entering into humans on a very regular basis. My colleagues and I have worried about this for 20 years and felt a little bit like we were crying wolf. But I didn't expect it in this kind of time frame. It's like predicting that a category-five hurricane is already coming to Charleston. There's some probability that it will happen at some point, but you don't expect it in your lifetime, and you hope it won't occur."  -- Dr. Mark Denison

In his keynote, Denison, director of the Division of Pediatric Infectious Diseases at Vanderbilt University Medical Center, described a unique characteristic of coronaviruses that makes them particularly worrisome. Most other RNA viruses are vulnerable to mutations because they have small genomes and lack proofreading capacity. In contrast, coronaviruses have a relatively large genome and can identify and correct mutations. As a result, they can remain stable and viable as they mutate. That could explain why they have been able to spill into humans three times in the past 20 years and why they could do so again. Developing effective antiviral agents, Denison explained, is therefore urgent.

 

“I'd argue that coronavirus is maybe entering into humans on a very regular basis,” said Denison. “My colleagues and I have worried about this for 20 years and felt a little bit like we were crying wolf. But I didn't expect it in this kind of time frame. It's like predicting that a category-five hurricane is already coming to Charleston. There's some probability that it will happen at some point, but you don't expect it in your lifetime, and you hope it won't occur. But I think we need to be thinking about it in those terms as we think about countermeasures.”

Denison’s research has been essential in identifying effective antiviral treatments. His laboratory found that knocking out the proofreading capacity of coronaviruses dramatically decreased their ability to replicate. Denison’s group also identified and tested two compounds in preclinical studies, showing that they were very highly effective early in the disease course at targeting the enzyme responsible for proofreading. One of those compounds, remdesivir (Veklury; Gilead Sciences), was one of the first antiviral agents authorized for COVID-19. The other, EIDD-2801 (molnupiravir; Merck, Ridgeback Biotherapeutics), is currently in clinical trials.

 

With these compounds, timing is everything. Both agents are more likely to be effective early in the disease course, when the virus is still actively replicating. Thus far, they have been used or tested primarily in hospitalized patients, explaining why their effects have been modest. To facilitate early use, Gilead is developing an oral form of remdesivir, and molnupiravir is already in pill form and being tested in patients at earlier stages of the disease. Merck has now licensed it to several pharmaceutical firms in India to address the humanitarian crisis caused by COVID-19.

Ultimately, Denison believes that an effective strategy against COVID-19 will likely involve combination therapy –two or more drugs that target both early- and late-stage disease.

The retreat provided investigators from across the state an opportunity to present their teams’ innovative research on COVID-19 countermeasures. These included developing new therapeutics, understanding who is at higher risk and why, keeping health care workers safe, sequencing and tracking variants, optimizing vaccine strategy, and improving testing. Among the researchers presenting were the seven awardees of MUSC’s COVID-19 pilot project grants supported by SCTR, totaling more than $300,000. These grants were made possible by the generous support of the offices of the president, provost and vice-president for Research.

Developing new therapeutic approaches

Three recipients of pilot project funding discussed preclinical research that is setting the stage for novel COVID-19 therapeutics. 

Chris Davies, Ph.D., who recently moved from MUSC to the University of South Alabama, and graduate student Caleb Stratton developed a high-throughput screening assay to determine whether any of the 120,000 novel compounds in SC3, a unique library at MUSC of over 120,000 chemical agents with drug-like properties, inhibits a protein that is essential for the replication of the SARS-CoV-2 virus.

MUSC biochemist Philip Howe, Ph.D., looked at how SARS-CoV-2 interacts with host cells, finding that a certain SARS-CoV-2 protein could potentially disrupt protein translation by interacting with nine host proteins. Ultimately, Howe’s goal is to find an inhibitor against that SARS-CoV-2 protein.

MUSC immunologist Shikhar Mehrotra, Ph.D., is exploring T-cell immunity against the virus. T-cells offer another layer of defense beyond antibodies. He is exploring a strategy of isolating T-cells that have learned to recognize and attack SARS-COV-2, expanding them in the laboratory and then reinfusing them to fight the virus more effectively.

Understanding risk

Three pilot project recipients are exploring why some patients with COVID-19 become sicker than others.

MUSC immunogeneticist Janardan Pandey, Ph.D., is studying whether differences in COVID-19 susceptibility could be linked to the expression of three genes known to be important to immunity against infectious disease.

MUSC medical oncologist John Wrangle, M.D., is studying whether past infection with a coronavirus other than SARS-COV-2 leads to more severe cases of COVID-19.  

Finally, Alexander Alekseyenko, Ph.D., is comparing the microbiome profiles of people with and without COVID to explore how their profile might affect their risks for developing severe COVID-19. To do so, he is using the Living μBiome Bank, which provides just-in-time access to specimens and microbiome analysis. Data from the profiles are integrated with rich clinical data in a COVID-19 data mart being developed by Stephane Meystre, M.D., Ph.D.

 Keeping health care workers safe

Pilot project recipient Walter Renne, D.M.D., discussed his innovative design and promising preliminary findings for a dental device that reduces splatter and aerosols that could transmit the virus. The device could help to keep both dental professionals and patients safe.

MUSC infectious disease specialist Scott Curry, M.D., reported that of the 126 vaccinated MUSC care team members who went on to develop COVID-19, most had infections that were incubating prior to vaccination. Curry’s findings show, he said, why it is important to respect public health measures even after being vaccinated.

MUSC Health hospital epidemiologist Cassandra Salgado, M.D., reported results of a survey of COVID-19-positive MUSC care team members, suggesting that most were exposed in the community, not at work. Although respondents report using personal protective gear properly on the job, more than 25% admitted they did not use a mask outside of work. Many COVID-19-positive care team members reported attending large gatherings, eating in restaurants or visiting with friends indoors shortly before falling ill. This research suggests that efforts to reduce transmission among health care workers should focus on behaviors outside of work.

 Sequencing variants and optimizing vaccines

MUSC molecular pathologist Julie Hirschhorn, Ph.D., developed next-generation sequencing for SARS-CoV-2. By April 2021, Hirschhorn’s team has sequenced almost 1,000 positive samples and found that 88% of COVID cases are caused by variants of concern and interest, with the most common variant being the B.1.1.7 lineage (a.k.a. the UK strain).

Carolyn Banister, Ph.D., of the University of South Carolina (UofSC) College of Pharmacy, developed a direct saliva test that was used to test UofSC faculty, students and staff during the pandemic. The sequencing of seventeen of those samples revealed that many of them contained multiple variants. Banister’s team also showed that a person infected with multiple variant strains could pass those same variants on to other people, suggesting, she explained, he need for a new form of “molecular” contact tracing. 

Sharon Bewick, Ph.D., of Clemson University reported findings that could be important to future vaccine design. According to Bewick, it is almost always a better idea to target vaccines against the most highly transmissible variants, even if they aren’t the most frequent strains of  the virus. However, for variants that are less than 50% more transmissible than the original strain, she reports that surprisingly good control can be gained by vaccinating half of the population against the original strain and half against the variant.

Improving testing

As more and more of us return to work and school, better testing will be required to prevent spikes in COVID-19 infections.

MUSC biomedical informatics researchers Stephane Meystre, M.D., Ph.D., and  Jihad Obeid, M.D., reported that natural language processing and artificial intelligence could be used to make pooled testing more practical. Pooled testing is quicker and more cost effective because dozens of specimens can be tested at once, but only if the test turns out to be negative. If the test comes back positive, everyone providing a sample will have to be tested individually. The algorithm developed by Meystre and team analyzes electronic health and other data about patients seeking testing to identify those most likely to test negative and so most appropriate for pooled testing.

An artificial intelligence algorithm has been developed by Obeid and John Del Gaizo that analyzes clinical notes obtained during patient visits to the Emergency Department to improve surveillance for COVID-19 symptoms. Long-term surveillance for new cases in outpatient and emergency visit settings will be necessary to identify future new cases and potential vaccine breakthrough cases.

Clemson chemist Jeffrey Anker, Ph.D., is developing a simple, inexpensive and scalable test for on-site testing that is based on buoyancy and magnetism (BAM). Antibody-enhanced magnetic and buoyant beads seek out and bind to SARS-COV2 in saliva samples. A magnet then pulls these BAM complexes to the bottom of the centrifuge tube. The magnet is then removed, and the buoyant beads are counted as they float back up, enabling SARS-CoV-2 titers to be assessed.