The last year has revealed numerous signs and symptoms of SARS-CoV-2 infection, including some unruly immune responses. COVID-19 sometimes overwhelms the immune response to the point of confusion, convincing it that its own cells are the enemy. This autoimmune response may continue long after the virus runs its course, and it may be partially responsible for some of the odd side effects that patients experience months after initial infection, such as dementia and kidney problems. 

Nadine Rouphael, a clinician scientist from Emory University, spearheads the IMPACC study analyzing the immune response of COVID-19 patients.

Credit: Rouphael

To figure out how this autoimmune response originates, Nadine Rouphael, an infectious disease researcher at the Emory Vaccine Center, is spearheading a prospective, long-term clinical trial dubbed the Immunotyping Assessment in a COVID-19 Cohort (IMPACC) that will track the immune responses of nearly 2,000 individual patients from across the United States for one year past their first positive test. 

“We’re trying to target the virus. We’re trying to target the immune response of the person affected by the virus. But we don’t exactly understand how the virus and the host interact,” Rouphael said.

The strangest part of short-term and long-term COVID-19 immune responses is the variability between patients. For some, COVID-19 is deadly, but others just get the sniffles. Some patients experience no long-term effects, while others never fully recover. They endure symptoms ranging from memory loss to gingivitis in a phenomenon known as long COVID-19. By deepening scientists’ understanding of the underlying causes of long COVID-19, IMPACC will inform the development of personalized treatments for patients in the future.

“The IMPACC group is doing phenomenally important work that I think is about the only way we're going to be able to figure this out,” said P.J. Utz, an immunologist from Stanford University who is not involved in the IMPACC study. 

COVID-19 may trigger an autoimmune response 

When the COVID-19 pandemic struck, honing in on the new virus was a no-brainer for Ignacio Sanz, an immunologist from Emory University who is not involved in the IMPACC study. But he didn’t expect the extensive similarities in the immune cell and antibody profiles of COVID-19 infected patients and those of the disease he normally studies: systemic lupus erythematosus.

B-cells produce antibodies against foreign molecules. They activate when they bind to an antigen, such as a viral protein. Activated B-cells proliferate, resulting in a pool of mature B-cells that produce antibodies against the encountered antigen, neutralizing a pathogen.

Sanz found that patients with severe COVID-19 infections had overactive activation and expansion of a subpopulation of activated B-cells known as follicular B-cells, which is similar to the response seen in patients with systemic lupus erythematosus (1). This overzealous immune response could result in the production of antibodies against native proteins by autoreactive B-cells.

“The extrafollicular pathway probably doesn’t get good regulation in terms of avoiding autoreactive B-cells,” said Sanz. 

Patients with severe COVID-19 infection have more than just an overactive immune response; their B-cells seem to produce autoantibodies (2). Sanz screened patients with severe COVID-19 for a panel of autoantibodies he regularly uses to characterize patients with systemic lupus erythematosus. The patients carried a long list of biomarkers commonly found in autoimmune disease. Patients even had antibodies against the viral response molecule type-1-interferons, suggesting that the immune response was tempering itself. 

Sanz’s results build on growing evidence that COVID-19’s effect on the immune system is more complex than scientists imagined. Other groups found autoantibodies in patients targeted towards cytokines, chemokines, phospholipids, and carbohydrates (3-6). Some researchers even detected these autoantibodies months after the initial infection.

“The degree to which autoimmunity contributes to either acute, severe, or long COVID-19 is still not fully understood,” Sanz emphasized.

In a separate study, Utz showed that patients produced autoantibodies in response to COVID-19 (7). 50% of hospitalized COVID-19 patients had autoantibodies, compared to 15% of healthy patients. Many of these autoantibodies were not present in the early phases of infection, suggesting that increasing severity of COVID-19 infection induced their production. 

Unfortunately, no one has determined exactly how COVID-19 promotes a lasting autoimmune response. But one popular hypothesis amongst immunologists is molecular mimicry, where part of the virus looks so similar to a molecule we possess that antibodies meant to target the virus end up targeting our own cells or proteins.

“With these hypotheses in mind, we’re hoping to try and unravel what causes these persistent symptoms in patients,” said Esther Melamed, a neuro-immunologist from the University of Texas at Austin.

Unraveling the mystery 

Melamed sees patients in the clinic with autoimmune diseases and symptoms of long COVID-19. She joined IMPACC to get answers for these patients. 

Esther Melamed is a clinician researcher working with the IMPACC group at the University of Texas at Austin.

Credit: Melamed

“We're very interested in understanding how the immune system evolves from the beginning when patients are infected with COVID-19, and what happens in the long term. Do people develop autoimmune responses? Could this explain the long-lasting symptoms? Or are these transient symptoms that happen in the short term, and they go away over time?” said Melamed.

Melamed teamed up with Lauren Ehrlich, an immunology researcher from the University of Texas at Austin to include the university as one of 15 testing sites recruiting patients for the IMPACC study. 

“We really combined our expertise on the scientific and clinical sides,” said Melamed. “Despite all of the suffering during the pandemic, and despite so many bad things that happened this year, it’s really been so wonderful to come together to try to resolve these questions.”

At each of the IMPACC study sites, researchers enroll patients in the study within 36 hours of their arrival at the hospital. Clinicians collect blood and nasal swabs upon admission and throughout hospital stays. They also collect lower airway secretions from patients on ventilators. After discharge, patients come in every three months for a year so that clinicians can collect follow-up samples that provide snapshots of the patient’s immune system during recovery.

Researchers perform several techniques on these samples to determine which immune cells are most prevalent and what those immune cells are doing. By understanding the immune cell profile, the IMPACC team hopes to understand how intense a patient’s immune response is and if it is autoreactive.

Each type of immune cell expresses a unique set of genes and proteins, so researchers sequence DNA and RNA to infer how many cells are in the sample. They also measure the expression of inflammatory molecules like type I interferons or cytokines to see how the active immune cells respond to COVID-19. 

Lauren Ehrlich is a clinician researcher working with the IMPACC group at the University of Texas at Austin.

Credit: Ehrlich

The team complements this sequencing data with flow and mass cytometry, which rely on proteins expressed on the surface of cells to distinguish subpopulations of cells. Sequencing determines how many mature B-cells a patient has, but flow cytometry counts the number of follicular B-cells.

The researchers plan to use their resulting massive dataset to correlate immune profiles with COVID-19 severity, long COVID symptoms, and much more. They will make the dataset publicly available so that in the future, clinicians can look at a patient’s immune cell profile and personalize treatments based on how each patient responds to infection. 

“I like the fact that we can use big data to personalize treatment. It’s not one size fits all. We’ve seen that with this disease. Some people don’t feel a thing when they have it, while others lose their life,” Rouphael said. “There must be a better way to tailor treatments, and that’s what we’re trying to do.”

This dataset should also help answer many basic questions about COVID-19: How long does immunity last? What prevents repeat infection? Why do some patients have long-term symptoms?

Teasing apart how the immune system contributes to the variability of the disease is exciting, but identifying a common signature amongst patients could be tricky, especially in long-haulers. Long-COVID symptoms and severity vary as much as the initial infection itself, and grouping patients by symptoms such as brain fog, depression, or lethargy is challenging. 

“There are all these basic science concepts that can be so helpful clinically, but [clinicians and researchers] also need to talk to each other, and really listen to each other, and understand where the clinical needs are, what we’re learning in basic science, and how we can bring these together and move that forward to treating patients,” said Ehrlich. “This is the ultimate goal, especially in a crisis like this one.”

References

1. Woodruff, M.C. et al. Extrafollicular B cell responses correlate with neutralizing antibodies and morbidity in COVID-19. Nat Immuno.  21, 1506–1516 (2020).
2. Woodruff, M.C. et al. Clinically identifiable autoreactivity is common in severe SARS-CoV-2 Infection. medRxiv (2020).
3. Butler, D.L. et al. Abnormal antibodies to self-carbohydrates in SARS-CoV-2 infected patients. bioRxiv (2020).
4. Zuo, Y. et al. Prothrombotic autoantibodies in serum from patients hospitalized with COVID-19. Sci Transl Med  12 (570) (2020).
5. Wang, E.Y. et al. Diverse Functional Autoantibodies in Patients with COVID-19. medRxiv (2020).
6. Bastard, P. et al. Autoantibodies against type I IFNs in patients with life-threatening COVID-19. Science  370 (6515) (2020).
7. Chang, S.E. et al. New-Onset IgG Autoantibodies in Hospitalized Patients with COVID-19. medRxiv (2021).