The immune system readies an arsenal of antibodies the moment it encounters a virus. These antibodies often target the first thing vigilant surveilling immune cells touch. In the case of SARS-CoV-2, that’s often proteins that decorate the virus’ exterior, such as the spike protein, which allows the virus to enter cells. But the SARS-CoV-2 genome also encodes approximately 25 proteins that are likely found inside the virus (1).
In a study recently published in Cell Reports, researchers found antibodies against these viral proteins in blood taken from 21 people with severe COVID-19 (2, 3). They could even predict who lived and died amongst people with severe COVID-19 based on the patient’s noncanonical antibody profile.
“Other studies have looked at antibody characteristics such as this, including antibodies to the spike [protein] with respect to COVID outcomes. Where the study goes further is that they also evaluate targets you wouldn’t normally think about,” said David Martinez, an immunologist from Yale School of Medicine who was not involved in this study. “The author’s take a step further and begin to turn over stones that people haven’t necessarily turned before.”
The researchers searched for antibodies in blood taken 24 hours after a patient was admitted to the intensive care unit with a confirmed case of COVID-19. These patients were part of the first wave of COVID-19 before new variants emerged or vaccines were available to the public. Although all of the patients had the same increase in antibodies against canonical external targets of SARS-CoV-2 compared to healthy patients, seven of the 21 patients died.
Aniruddh Sarkar, a bioengineer from the Georgia Institute of Technology and Emory University and coauthor of the paper, used an antibody profiling platform he developed to do a deep dive into the antibodies floating in the COVID-19 patients’ blood.
“Our flavor of engineering is more like micro- or nano-scale devices and assays. That's basically our way of generating large amounts of data from very small amounts of samples. These precious samples that we get from the patients can give us as much data as can be extracted from them,” said Sarkar.
The researchers exposed the antibody-rich blood from patients with severe COVID-19 to three canonical antigens, such as the spike protein, and four noncanonical antigens, including nonstructural protein 13 (NSP13), a helicase protein conserved across coronaviruses that is required for SARS-CoV-2 to replicate. This protein is now a target for COVID-19 therapeutics in development.
With this massive set of data in hand, Sarkar turned to Jishnu Das, an immunologist and computational biologist from the University of Pittsburg Medical Center. “This is where Jishnu and his computational magic of sorts comes in,” said Sarkar.
Das expected COVID-19 survivors to have higher levels of canonical antibodies targeting the outside of the virus than the seven patients who died, but he was surprised to find that noncanonical antigens were just as high in survivors. Levels of noncanonical antibodies predicted life or death in patients with severe COVID-19 equally as well as canonical antibody levels did.
Das believes that the key to finding the predictive power of noncanonical antibodies was analyzing blood taken only from individuals with severe cases of COVID-19.
“It is possible that in a mild case, the host immune system has minimal encounters with internal protein antigens. But in severe cases, presumably there are a lot of dead cells. There's a lot of lysis so there are these internal proteins floating around in the blood,” said Das.
These noncanonical targets, particularly NSP13, could be important for developing a pancoronavirus therapeutic since Sarkar and Das found the same noncanonical antibody profiles in nine healthy patient samples collected before the pandemic began, likely developed in response to other coronaviruses that cause the common cold.
“The most logical thing to evaluate moving forward following this study would be to try to incorporate some of these noncanonical sites potentially into next generation vaccines. Should we consider including NSP13, a highly conserved protein on these types of coronaviruses, into vaccination strategies that could potentially target parts of the immune system to essentially direct the immune response at these highly conserved epitopes? I think it offers an additional layer of considerations that we might want to think about in the face of what appears to be a bevy of ever evolving variants,” said Martinez.
For now, Sarkar and Das are focusing on repeating their findings in other patient cohorts to convince researchers that considering noncanonical targets such as NSP13 for next-generation COVID-19 treatments is the logical thing to do.
References
- Gordon, D.E. et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583, 459-468 (2020).
- White, M.A. et al. Discovery of COVID-19 inhibitors targeting the SARS-CoV2 Nsp13 helicase. bioRxiv (2020).
- Peddireddy, S.P. et al. Antibodies targeting conserved non-canonical antigens and endemic coronaviruses associate with favorable outcomes in severe COVID-19. Cell Reports 39, 111020 (2022).
