People with long COVID are likely to have immune cells showing signs of chronic inflammation and other unusual characteristics, according to a new study by scientists at the Gladstone Institutes and the University of California San Francisco (UCSF). Their findings, which appear in Nature Immunology, support the hypothesis that long COVID may involve a low-level viral persistence.

“Not every person with long COVID had these pro-inflammatory cells, but we only saw them in the long COVID group,” said Kailin Yin, PhD, postdoctoral fellow in the Roan lab and co-first author of the study. “It underscores the idea that there isn’t just one uniform thing that characterizes all individuals with long COVID.”

The team analyzed immune cells from the blood of 43 people with and without long COVID, focusing particularly on T cells. They used omic assays and serology to “deeply characterize the global and SARS-CoV-2-specific immunity in the blood of individuals with clear LC and non-LC clinical trajectories, eight months post infection.”

“Our results are an essential first step to understanding what’s going on with T cells in long COVID,” said senior author Nadia Roan, PhD, a senior investigator at Gladstone and a professor at UCSF. “This paves a path toward answering ongoing questions about the different types of long COVID, the mechanisms that cause it, and how to treat and prevent it.”

Long COVID, also known as “post-acute sequelae of COVID” (PASC), is broadly defined as symptoms that continue or emerge after an initial infection with the SARS-CoV-2 virus. The symptoms and trajectory of this condition can vary between individuals. In addition, vaccination status and subsequent infections can impact a person’s long COVID risk and disease progression.

“This is a very heterogeneous condition,” Roan says. “There’s a diverse mix of long COVID cases, which makes it difficult to work out what’s really going on. That’s why it was so important to eliminate some of this variability. We analyzed and compared a set of pristine samples not complicated by the effects of vaccination or re-infection, which can affect T-cell and other immune responses.”

Roan’s group worked with researchers at UCSF who are part of a multidisciplinary team running an observational COVID study called LIINC, or Long-term Impact of Infection With Novel Coronavirus, which follows a cohort of people who were infected one time with COVID. For this study, patients were classified as having long COVID if they consistently had symptoms during the entire study period. Those who had no symptoms following their initial infection were in the control group.

In this study, Roan and her team used six different technologies, including CyTOF (Cytometry by Time-of-Flight), serology, RNA sequencing, single‐cell RNA-seq, and plasma proteomics. CyTOF can measure levels of specific molecules on or within T cells. 

Notably, they found CD4 T cells were in a more inflammatory state in people with long COVID. Meanwhile, CD8 T cells, which normally kill cells infected by viruses or bacteria, showed signs of exhaustion preferentially in people with long COVID. These signs were observed only in T cells that recognize the SARS-CoV-2 virus, not in the broader population of CD8 T cells.

“Such exhaustion is typically seen in chronic viral infections such as HIV, and means the T cell branch of the immune system stops responding to a virus and no longer kills infected cells,” said Micheal Peluso, MD, assistant professor in the UCSF Department of Medicine and co-first author of this study.

In their conclusion, the researchers write, “Our analysis suggested an improper crosstalk between the cellular and humoral adaptive immunity in LC [long COVID], which can lead to immune dysregulation, inflammation and clinical symptoms associated with this debilitating condition.”