Beyond the Peak: New Antibody Analysis Predicts Serious Outcomes for COVID-19

PITTSBURGH, June 27, 2022 — Most research on SARS-CoV-2 virus immunity and COVID-19 vaccine development has focused on antibody responses to the spike protein and other viral surface proteins. But antibodies that recognize internal proteins of the virus could also be important for immunity and disease outcomes, according to a new study led by researchers from the University of Pittsburgh, the Georgia Institute of Technology and the University Emory.

In the study, online now in Cell reports, the team performed the most comprehensive analysis to date of COVID-19 antibodies in a small group of patients with severe disease. They found that antibody profiles of internal viral proteins, including those conserved across coronaviruses, predicted which patients survived or died just as well as corresponding profiles for surface proteins, suggesting that targeting other parts of the virus beyond the spike protein could be important for improving COVID -19 vaccines and therapies.

“The novel aspect of this study is that we did a very thorough profiling of SARS-CoV-2 antibodies and looked at many different aspects of these antibodies,” said co-lead author Jishnu Das, Ph.D. , Assistant Professor of Immunology and Computational and Systems Biology at Pitt Medicine School. “The whole world has focused on the spike protein and the receptor binding domain, but this study is the first concrete evidence that specific antibodies against internal proteins are also positively associated with survival in severe COVID-19. .”

When the immune system encounters a virus, it produces antibodies that help neutralize and eliminate the infection. Each antibody specifically recognizes a single antigen, often a viral protein. Most research into COVID-19 immunity has focused on the spike and other surface proteins, which form the outer envelope of the virus, but beyond these so-called “canonical antigens”, the SARS-CoV-2 has about 25 other internal proteins.

To see if immune responses to these non-canonical antigens could predict survival outcomes in patients with severe COVID-19, Das teamed up with co-lead authors Aniruddh Sarkar, Ph.D., assistant professor at Wallace H. Coulter Department of Biomedical Engineering at Georgia Technology and Emory Universityand Harinder Singh, Ph.D., professor of immunology and director of Systems Immunology Center to Pitt.

The researchers analyzed blood samples that had been taken from 21 patients hospitalized with severe COVID-19 in 2020 – before the vaccines were approved. Seven of these patients died of the disease and the other 14 survived. Using a microscale antibody profiling platform developed by Sarkar, the team extensively analyzed antibodies to three canonical antigens and four non-canonical antigens.

According to Sarkar, the platform analyzes three key characteristics of antibodies. One is the specificity of the antigen, or what the antibody binds to. The second is effector function, which relates to the role of the antibody in the immune response. The third feature is glycosylation, or the addition of carbohydrate molecules to the antibody, which dramatically impacts antibody function.

“By profiling these three characteristics simultaneously, we can gain a much deeper understanding of a given antibody than just looking at antibody titers,” Sarkar explained.

The researchers found that no single antibody characteristic could differentiate patient survival outcomes. But when they analyzed the overall antibody profiles – canonical or non-canonical – they noticed clear differences between survivors and non-survivors.

“We were surprised to find such compelling evidence that antibodies against canonical and non-canonical antigens were equally predictive of survival outcomes,” Singh said. “Our results suggest that non-canonical antibodies may play a role in recovery from severe disease, although further research is needed to prove causation and identify mechanisms.”

Most COVID-19 vaccines and monoclonal antibodies – the artificial antibodies used to treat COVID-19 – have become less effective with the emergence of the delta and omicron variants because mutations in the spike help the virus avoid detection. Far fewer mutations have accumulated in the virus’s internal proteins, Singh says, suggesting that increasing vaccines or therapies to target these non-canonical antigens could elicit more robust immunity against emerging variants of concern.

When the team limited their analysis to antibodies against noncanonical antigens conserved across coronaviruses — including those that cause the common cold and other respiratory infections — in COVID-19 patients, they could still distinguish between survivors and non-survivors. These antibodies were also found in nine pre-pandemic healthy control subjects, suggesting that exposure to coronaviruses in addition to SARS-CoV-2 may induce antibody responses linked to favorable outcomes in severe cases of COVID- 19.

According to Das, these findings could inform the development of pan-coronavirus vaccines.

In ongoing work, the team is using its platform to look at antibodies in vaccinated people with breakthrough infections compared to unvaccinated people. They also want to understand whether different antibodies play different roles in protecting against COVID-19 over time.

They also plan to expand the platform to understand antibodies in other settings, including organ transplant rejection and other infectious diseases.

Other contributing authors to this study were co-first authors Sai Preetham Peddireddy, Georgia Institute of Technology, and Syed A. Rahman, Ph.D., Pitt, and Anthony R. Cillo, Ph.D. ., Godhev Manakkat Vijay, Ph.D., Ashwin Somasundaram, MD, Creg J. Workman, Ph.D., William Bain, MD, Bryan J. McVerry, MD, Barbara Methe, Ph.D., Janet S. Lee , MD , Prabir Ray, Ph.D., Anuradha Ray, Ph.D., Tullia C. Bruno, Ph.D., Dario AA Vignali, Ph.D., Georgios D. Kitsios, MD, Ph.D., and Alison Morris, MD, all of Pitt.

This research was supported by the National Institutes of Health (DP2AI164325 and U01AI141990) and the UPMC Center for Transplantation and Immune Therapy.