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Unraveling long COVID: Here's what scientists who study the illness want to find out

Researchers looking for root causes of long COVID work in the autopsy suite inside the Clinical Center at the National Institute of Health in Bethesda, Maryland.
Valerie Plesch/Bloomberg via Getty Images
Researchers looking for root causes of long COVID work in the autopsy suite inside the Clinical Center at the National Institute of Health in Bethesda, Maryland.

For people suffering from long COVID's often disabling symptoms, including intense fatigue, breathing troubles, cognitive issues and heart palpitations, the list of scientific unknowns may sound defeating. There's still no validated treatment or diagnostic test specifically for the condition, although there are many candidates.

Clinicians who treat long COVID are acutely aware of the unsettled nature of the field. "You do sort of feel like you're out in the wilderness," says Dr. Rasika Karnik, medical director of UChicago Medicine's post-COVID clinic.

Karnik first began seeing long COVID patients in the fall of 2020. There's more information to work with now, she says, but doctors' approach still comes down to treating individual symptoms, rather than the underlying cause of the illness. "It's hard to look a patient in the eyes and say 'we're not quite sure yet' and to keep repeating that," she says.

But researchers are making progress in the field, and they presented their recent findings at one of the first major gatherings dedicated to sharing emerging evidence about the possible root cause of long COVID and implications for treatment.

"I know there's been a lot of frustration that there haven't been faster answers," says Dr. Catherine Blish, a professor of medicine at Stanford University and one of the organizers of the conference, held by the nonprofit Keystone Symposia in Santa Fe, N.M., in late August.

"But in all honesty, we are so much further ahead at this relative point than for any other major disease in my lifetime as an infectious disease specialist," she says.

The meeting underscored that scientists have made headway in developing evidence of a clear biological basis for what patients have been reporting for years.

"I've never doubted it — people are suffering," says Harlan Krumholz, a cardiologist at Yale University who's involved in long COVID research. "But we're now seeing imaging evidence, biopsy evidence, physiologic testing evidence of derangements in people who have long COVID."

Here are some of the new findings and promising lines of research highlighted during the three-day gathering.

Narrowing in on some key suspects behind the disease

If long COVID were a crime scene, authorities would have no shortage of leads.

They've pinpointed a handful of possible reasons why patients suffer from an array of chronic symptoms. The tricky thing is disentangling which mechanisms are bystanders and which are actually doing the damage.

"At this point, we have hints and correlative data," says Blish. "We can say we see this finding in a subset of people, but that doesn't mean it's the cause of their problems."

Take the theory of viral persistence: There's now strong evidence that protein and genetic material from SARS-CoV-2 persist in the blood and tissue of some long COVID patients well after their initial illness. Scientists believe these "viral reservoirs" could be driving many of the problems in long COVID patients, although it isn't yet clear exactly how this is happening — and whether the virus itself is replicating.

Dr. Michael Peluso, an infectious disease specialist at the University of California, San Francisco, told conference attendees that his team is now confident in their data showing pieces of viral antigen in the blood of people anywhere from six months to more than a year after they've had COVID-19.

They compared these blood samples to ones collected years before the pandemic to verify their conclusions. "That's a very, very important finding, showing that this is indeed real," he says.

But the story gets more messy from there because these viral reservoirs may not be the primary culprit.

While they are more likely to find viral persistence in the most symptomatic long COVID patients, not everyone with long COVID has it, Peluso notes, "And then really importantly, we're also seeing this in some people who feel totally fine — and we don't know what that means."

Finding activated T cells where they shouldn't be

Other leads have come from imaging technology that traces the activity of T cells, a type of white blood cell, which are part of the body's main antiviral immune response.

"We saw some very unexpected findings," says Dr. Timothy Henrich, an associate professor of medicine at the University of California, San Francisco.

His lab has found activated T cells in the gut wall, lung tissue, certain lymph nodes, the bone marrow, the spinal cord and the brainstem, long after someone's initial infection.

"You really shouldn't have activated T cells in the spinal cord or the brainstem," he says. "We are seeing evidence of this immune response in areas we don't typically see in the setting of an acute viral infection."

Here too the immunological detective work opens up even more questions: This T cell activity is also present in people who've recovered from an infection and have no long COVID symptoms, although Henrich notes the levels appear to be higher in certain tissues of people with long COVID.

So what does this immune response actually indicate about the underlying cause of the disease?

Henrich says T cell activity could be evidence that the immune system is trying to purge the viral reservoirs, or that the immune response has gone awry, possibly in the form of an autoimmune response, and is "doing damage to people, even if the virus has been cleared or is not replicating in those tissues," he says.

Patients and advocates for people suffering from long COVID and myalgic encephalomyelitis/chronic fatigue syndrome hosted an installation of 300 cots in front of the Washington Monument on the National Mall in Washington, D.C., in May, to represent the millions of people suffering from post-infectious disease.
Andrew Harnik / AP
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AP
Patients and advocates for people suffering from long COVID and myalgic encephalomyelitis/chronic fatigue syndrome hosted an installation of 300 cots in front of the Washington Monument on the National Mall in Washington, D.C., in May, to represent the millions of people suffering from post-infectious disease.

Similar questions bedevil researchers pursuing another theory.

Research shows that people with long COVID have high levels of Epstein-Barr antibodies and that an acute COVID infection can trigger reactivation of the virus.

Akiko Iwasaki, a professor of immunobiology at Yale University, says it's well known that this herpesvirus can lead to a "long COVID-like syndrome," but whether or not the reactivation is driving long COVID symptoms — or just an indication of a dysregulated immune system — remains to be seen.

All of those involved in research stress that they don't expect just one answer to long COVID. It's likely that many of these theories about its underlying cause are interrelated. And certain mechanisms may only be causing symptoms in some patients and not others.

Microclots could point the way to treatment

Early in the pandemic, it was recognized that COVID-19 can wreak havoc on the vascular system, in particular causing inflammation and damage to the inner lining of blood vessels, known as endothelial cells.

Resia Pretorius, a medical researcher at Stellenbosch University in South Africa, says the clotting and hyperactivation of platelets in long COVID is essentially a "persistent continuation" of what happens during an acute infection within the blood vessels.

Her research has focused on the role of tiny, harmful blood clots she's seeing in the blood of long COVID patients that appear to have "trapped inflammatory molecules that you might expect inside the blood if you have inflamed [or] damaged endothelial layers."

"It's not unique to long COVID, but long COVID has so much more of these inflammatory molecules in circulation," says Pretorius. "And what makes it so interesting is that the spike protein drives these microclots to form."

As the clots accumulate, they may choke off blood flow, preventing oxygen from reaching tissue.

In Santa Fe, Pretorius shared preliminary data from her team showing that so-called "triple therapy" — a combination of three medications — targeting clotting and platelet hyperactivation could benefit some long COVID patients. The preprint showed that this regime resolved symptoms in the majority of the 91 patients who were followed, although the results are not yet peer-reviewed and the study was not a clinical trial.

The approach is not without risk; many patients reported bruising, some had nosebleeds and one reported a gastrointestinal bleed.

Pretorius says microclots are not necessarily the root cause of long COVID, though.

It could be that viral reservoirs are actually helping trigger this vascular mayhem in the first place. These microclots, if left untreated, could also tie into other problems seen in long COVID patients, perhaps leading some to develop autoimmunity, says Pretorius. "That is a problem to solve because we know autoimmune diseases are notorious for being so, so difficult to treat."

Sex differences may play a role in long COVID risk

In general, males tend to do worse during an acute bout of COVID-19, but studies show that long COVID appears to be more prevalent among females. Yale's Iwasaki says this is also the case for other "post-acute infection syndromes."

This background led Iwasaki's lab to look into sex differences in the immune profiles of long COVID patients, in hopes of finding another path to understanding what could be driving the illness. She says they've found that reactivation of Epstein-Barr virus and the activation of T cells are more prevalent among females, whereas males have different "immune signatures."

"We're already starting to see sex differences in long COVID symptoms, as well as potentially the autoimmunity more associated with female patients," she says. "This insight is critical going forward because now we can separate out long COVID into different clusters. And depending on the driver of the disease, we can start targeting it with proper medicine."

Iwasaki's lab has also zeroed in on the role of hormones.

At the conference, she shared evidence of reduced cortisol levels in long COVID patients and shared a separate, unpublished finding that female long COVID patients tend to have reduced testosterone levels and that males have reduced estradiol levels.

Those who had lower testosterone (compared to the controls who don't have long COVID symptoms) also have higher activation of T cells, whether they're males or females, says Julio Silva, a graduate student in Iwasaki's lab who presented the new findings on testosterone. And this was "associated with higher neurological symptoms and overall higher symptom burden," says Silva.

The impetus to look at testosterone was, in part, because of "anecdotes from trans individuals who were informing us that while on testosterone therapy, their symptoms had improved dramatically," says Silva. While the results are preliminary and need to be replicated, he says they at least raise the question "could hormonal therapy help?"

Taken together, Iwasaki says their data strongly suggest there could be problems in the area of the brain that's responsible for regulating these hormones.

Viral persistence offers one possible target for treating long COVID

In the absence of a clear roadmap for treating long COVID, doctors and patients have taken to trying all kinds of therapies — from antivirals to drugs approved for treating addiction.

"All of this research is so critical to understanding the underlying mechanisms of long COVID," says Lisa McCorkell, co-founder of the advocacy group Patient-Led Research Collaborative. "We need to pair that with focusing on clinical trials. We have enough evidence right now to at least try some things."

In Santa Fe, UCSF's Peluso outlined how his team had just launched a small trial using monoclonal antibodies to target the coronavirus spike protein in long COVID patients — one vehicle for testing whether viral persistence is the underlying cause of at least some patients' symptoms. Meanwhile, Iwasaki and Krumholz, both at Yale, have started a clinical trial testing whether a 15-day course of Paxlovid can help alleviate symptoms.

Stanford's Blish points out that as more clinical trials start up, their success will hinge on being deliberate about which patients should be enrolled, since long COVID is a catch-all term for what may be multiple different illnesses.

"We need to understand in detail who's most likely to benefit from those trials, because if we just take everyone, that trial will fail," she says.

Many other trials are in the works, too, but Dr. Jennifer Curtin says those will inevitably take time to produce evidence that trickles down to patient care.

"It's that tough sort of in-between status right now," says Curtin, co-founder of the telehealth clinic RTHM that treats long COVID and other overlapping conditions like myalgic encephalomyelitis/chronic fatigue syndrome, or ME/CFS for short. "So what do you do for the people who are sick and suffering now until we get that data?"

Curtin, who has lived with ME/CFS herself, says their clinic's approach is to perform intensive workups, draw lots of blood and try to identify which symptoms they can treat.

"Treatment is very much individually tailored," she says. "Right now it's a journey that you take with your patients. You're going through this together. You're both learning on this road and it can be tough."

Always in the backdrop at the Santa Fe gathering was the question of whether there would be enough funding — be it from the U.S. Congress or the pharmaceutical industry — to advance the research agenda toward treatments.

"What we really need here is industry engagement. We need funding for clinical trials. And that, to me, is something that's missing," says McCorkell.

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