Researchers Unlock Mystery Components of Serious COVID-19 Illness

A molecular analysis of deep airway samples from critically ill and ventilated COVID-19 patients has helped researchers identify components that reveal why some patients have an extreme reaction to COVID-19. These components can also be used to identify viruses with pandemic potential. 

At the height of the COVID-19 pandemic in 2020, researchers were scrambling to identify funding sources that would allow them to conduct immediate experiments and analyses of SARS-CoV-2—the virus that is responsible for the COVID-19 disease. 

Researchers strived to develop a vaccine to help people fend off the virus. They aimed to understand why some people have an extreme and prolonged reaction to the virus when others do not. Moreover, they sought to locate signatures in the virus that could be used to prevent future pandemics from occurring. 

The latter two proved to be extremely difficult given the complexity of the virus and how it interacts with a host’s immune system. Unlike other coronavirus strains, such as those typical of the common cold, patients with SARS-CoV-2 can suffer from lingering symptoms well after they no longer test positive for the virus. 

Thanks to CARES Act funding allocated through a Limited Scope proposal at the Environmental Molecular Sciences Laboratory (EMSL), University of North Carolina (UNC) researchers Matthew Wolfgang, Robert Hagan, Jonathan Schisler, and Lance Thurlow teamed up with scientists at Pacific Northwest National Laboratory (PNNL) to analyze samples taken from the lower airways of critically ill, ventilated patients, an uncommon approach at the time. The team successfully analyzed these samples using mass spectrometry at EMSL. 

This effort, combined with research conducted by Gerard Wong at the University of California Los Angeles (UCLA) and at other institutions, helped the team identify specific fragments from the COVID-19 virus that mimic peptides found in the host’s immune system. Peptides are short chains of amino acids that help carry out important processes in the body, such as certain immune responses. In the case of COVID-19, these peptides can reassemble with other components to form new complexes, disrupting the host’s immune system and causing extreme inflammatory responses in some patients. 

Other strains of coronavirus, such as those found in common colds, do not do this, said Wong, a professor of bioengineering, chemistry, microbiology, immunology, and molecular genetics at UCLA. 

“Essentially, we found a way to discriminate between common cold coronaviruses and the coronaviruses that have significant potential for killing you,” he said. 

The team’s results were recently published in a study led by Wong in the Proceedings of the National Academy of Sciences. 

A different approach 

Compared to most other studies that examined the blood of severely affected COVID patients, the team’s project funded through an EMSL Limited Scope proposal homed in on tiny molecules from deep lung samples of patients. This approach helped them understand the environmental factors at play. For one component of their research, UNC scientists studied samples of lung secretions collected though the endotracheal tubes of patients on mechanical ventilators. 

“What was unique about our approach was studying the context of where it happens,” said Wolfgang, an associate professor specializing in bacterial infections via lung diseases at the UNC School of Medicine. “Understanding what’s happening at the site of infection tells us a lot about what is driving disease, so we applied that same principle to COVID. It turns out very few people have taken that approach.” 

This approach helped them identify points of interest, from when a person is exposed to the virus, to their stages of illness and what instruments were used in their health journey, to what their recovery looks like afterward and why it looks different from person to person. 

“There are multiple underlying syndromes happening here that are going to ultimately require different therapeutic paradigms,” Wolfgang said. “You have to think back to early 2020. We had no therapies at the time. The direct result of the funding that made this possible resulted in some great results. We now have an incredibly robust dataset that seems to be unmatched currently in the literature, that we’re aware of.” 

Wolfgang said the data resulting from the project has helped support multiple studies and enabled numerous collaborations. He said they are thrilled that their data could help support Wong’s study. The study ended with the team successfully identifying the peptides in question that they can now use as markers in severe COVID patients and to identify viruses with pandemic potential. 

“This data helped provide evidence that the protein fragments described in the study can be detected in the lung during infection,” Wolfgang said. 

Advanced techniques and expertise spur new insights 

Wong’s team used a range of advanced scientific techniques and sought help from researchers across the country to fully analyze the components of the virus and how it interacts with a host. 

In addition to data generated on lung and tracheal samples in both humans and mice, the team also used artificial intelligence and state-of-the-art synchrotron X-ray structural techniques to analyze entire collections of proteins produced by the virus to identify molecular patterns and reveal other key information. 

The team analyzed samples using proteomics, lipidomics, and metabolomics capabilities and expertise at EMSL and PNNL. These techniques allowed them to explore tiny components ranging from proteins, to lipids, to metabolites within samples that allow a living system to function and thrive. They also accessed computational tools and expertise at EMSL to process their data. 

In identifying pieces of the virus that remain after it is broken down by the immune system and that mimic peptides in the host, researchers also demonstrated that these pieces reassemble with double-stranded RNA, which is a key activator of the host’s innate immune response against viral infections. This form of the virus can strongly amplify the activation of the human immune system, causing extreme inflammatory responses in the body. Effects stemming from this extreme activation in the body can linger post-destruction of the virus in the system. 

“If you look at current textbooks, the usual description is that after a virus is broken down, pieces of the virus are used to train the adaptive immune system so that it recognizes the virus in the future,” Wong said. “In that case, the host becomes progressively less vulnerable to the virus. However, this coronavirus has shown that it is much more complicated than that.” 

Similar to how the digestive system can break down some types of food into molecular components that are harmful for cardiovascular health, the immune system can likewise break down a virus into pieces that are harmful with COVID-19, Wong said. 

“Some of these pieces can mimic parts of our immune amplification machinery that are partly responsible for autoimmune diseases, such as lupus, rheumatoid arthritis, and psoriasis,” Wong said. 

Quick partnerships result in major wins 

Thanks to the team’s research, scientists have a new way of identifying viruses with future pandemic potential. Additionally, researchers are now examining new therapeutic strategies to limit the propagation of these virus fragments, such as protease inhibitors that can block certain enzymes from being able to break down viral proteins into harmful components. 

Wolfgang said the CARES Act funding available through EMSL’s Limited Scope proposal was a major component that made their findings possible. 

“It provided a spectacular opportunity,” he said. “Thinking back to those early days of spring 2020, it was insanity. Everyone was scrambling and doing spectacular science, but no one knew how to get this work funded. EMSL provided a significant resource and a fast-track way to get it done.” 

Wolfgang said after applying through the Limited Scope proposal at EMSL, their project was selected within weeks, and the team was on the phone with researchers at EMSL and PNNL to figure out how to send infectious material. At the time, the Centers for Disease Control had not released guidelines on how to treat the samples. 

“It really accelerated our efforts and put us in touch with some extremely bright people,” Wolfgang said. 

The project featured expertise and capabilities at a range of institutions, some of which include UCLA, UNC at Chapel Hill, University of California San Diego, Harvard University, SLAC National Accelerator Laboratory at Stanford, EMSL, and PNNL.