See Lindsey’s Top 3 Takeaways

With the wind brushing my face and wilderness surrounding me, I’m overwhelmed with a sense of gratitude for how far I’ve come. I feel capable and strong as my legs work against the pedals in a comforting rhythm. I’m at peace within my body despite all it’s been through.

Not long ago, I couldn’t imagine showering without taking a rest, much less riding a bike. For 13 years, I lived with a disease no doctor could name. This unknown condition made me weak, sent pain down my legs, and induced muscle twitching throughout my body. Without an explanation, I believed I’d live undiagnosed and struggle with a slowly worsening illness forever.

The turning point came in 2017, when a neurologist discovered inflammation in my nervous system. After 13 long years, I finally had an answer: multiple sclerosis (MS).

This diagnosis was far from easy to receive, but it allowed me to begin a treatment program that changed my life for the better. For the first time in years, I was hopeful for my future.

Long Road to A Diagnosis

I was only 21 when I started experiencing mysterious, debilitating symptoms, including stiffness in my legs and involuntary muscle twitching throughout my body. I couldn’t fathom why my once-healthy body was now struggling. Weeks before the symptoms began, I had been barhopping around New York City to celebrate my birthday.

An MRI of my brain revealed nonspecific lesions, which one doctor suggested might be related to MS. But the first neurologist I saw discounted the possibility.

My condition remained undiagnosed despite my efforts to find an answer. Meanwhile, my symptoms continued, varying like the seasons, and affected every day of my life.

I graduated from college, but the years following that milestone weren’t what I’d imagined they would be. Doctors’ appointments consumed every spare moment, and lab draws were part of my new weekly routine.

Some of the doctors insinuated that I was exaggerating because my disease remained invisible. Many wouldn’t think outside the box or listen deeply to my concerns.

I exhausted every branch of medicine without receiving a diagnosis. Some of the doctors insinuated that I was exaggerating because my disease remained invisible (a growing number of patients are sharing online personal stories of medical providers dismissing their symptoms as unimportant, psychosomatic, or the manifestations of hypochondria. “What Is Medical Gaslighting” for more.) Many wouldn’t think outside the box or listen deeply to my concerns. One physician ­advised me to go home and have a martini, as if a drink could cure what ailed me. I felt hopeless every time I left another unproductive appointment.

It was like I was trapped in a nightmare, unable to wake up. I felt disconnected from my body and unheard by professionals who were supposed to be helping me. I vacillated between worrying that my life was over and trying to control my fear and anger.

I tried to maintain a normal life while managing my symptoms and doctors’ visits. I earned a master’s degree in speech-language pathology, met and married my husband, and started a family in the suburbs of Philadelphia, where we still live today. My symptoms remained stable through the first three years of marriage and motherhood, but I began having flares after weaning my second son from breastfeeding.

I was soon so weak that I struggled to get around my home. Even sitting up in a chair was challenging — I’d find myself hunched over from the effort after only a few minutes.

My symptoms made it difficult to fulfill my role as a stay-at-home mother. I was unable to attend many family outings. Some days I could successfully food shop, though my legs would be shaky and weak by the end. A nanny helped care for our children because those duties were too much for my body to handle.

Finally, I was referred to a neurologist who listened and made sense of the nonspecific lesions on my MRI. He ordered a lumbar puncture, the results of which were consistent with MS.

When I received the diagnosis, I was flooded with concern and relief simultaneously. I cried at the thought of never regaining the abilities I’d lost, but the neurologist reassured me that my life was not over. As hard as it was to digest the news, I felt some semblance of hope.

The Right Direction

My doctor recommended an infusion of an immunosuppressant every six months to kill the cells responsible for MS. He believed the treatment could improve my symptoms but warned that it might take time for the effects to take hold.

The first few years of treatment were tough. Every symptom flared for a few months following an infusion. Weakness, profuse muscle twitching, and debilitating fatigue consumed me. I’d eventually find my way back to baseline only to be knocked back again by another infusion. My neurologist remained hopeful: “Give it some time,” he advised.

After three years of treatment, I started to notice small improvements. I could prepare dinner without my legs aching afterward. While volunteering at my children’s school, I could walk across the parking lot and through the hallways and still be able to stand in my son’s classroom.

After three years of treatment, I started to notice small improvements.

I carried chairs and bags across the field to my son’s soccer game with minimal difficulty. I was having more good days than bad, and that was a change in the right direction.

As my body regained some strength, I was inspired to start using an exercise bicycle. I knew from physical therapy in the early days of my diagnostic journey that biking was easier than walking. When I walked, my legs fatigued quickly, but on the bike, my strength lasted ­longer.

I hadn’t had a consistent exercise routine before I became chronically ill, and I had no intention of making it a daily practice now. But I was determined to take advantage of everything my body was now capable of doing.

In the beginning, I biked about 10 miles per hour on level-one resistance. Some days were manageable. Other days, I had to stop soon after starting because my legs were too weak.

It was hard to stick with the routine: My muscle stamina was low. But I noticed an increase in energy after exercising, which encouraged me to continue. So each day I got on my bike, and I pedaled until I needed a break.

Over weeks and months, I increased my speed, the resistance, and the length of my workouts. I built up to biking 11.5 miles daily and kept this up for a couple of years. Then one day I pushed myself a little harder and noticed I could bike farther than I realized. I was overcome with a sense of awe for how far my body had come. It was an immense improvement from where I’d been before my diagnosis.

New Trails Ahead

My husband is an avid hiker and has passed his love of the outdoors to our boys. Our vacations often revolve around new terrain they’re excited to tackle.

Although I can’t hike mountains with my family, biking rail trails enables me to be outdoors with them. We’ve biked the Ashokan Rail Trail in the Catskills; the Delaware and Hudson Rail Trail in Vermont and New York; and a trail to Bordner Cabin in Pennsylvania’s Swatara State Park — the list goes on, and it’s only just begun.

Today, my symptoms wax and wane, but I’m capable of much more than I was before. I pedal for more than an hour daily, totaling about 17 miles on a level-three resistance. Biking helps my legs build the strength and endurance they need to maintain my walking ability. It also provides cardiovascular exercise that helps keep my heart and lungs healthy.

Most importantly, biking has become my meditation and a source of stress relief. It’s boosted my self-confidence and allows me to feel strong, in control, and capable — feelings I thought I’d never experience again.

I hope to continue biking at home and outdoors with my family. Perhaps one day I’ll be strong enough to bike on hills or even up mountains. But for now, I couldn’t be more excited to live the life I have lying in front of me.

Lindsey’s Top 3 Takeaways

1. Find a doctor you can trust. Their personality should mesh with yours in a way that allows for a healthy doctor–patient relationship.
2. Design an exercise program that meets you where you are. The type of exercise you choose should be most compatible with your ability level.
3. Focus on the better days during difficult times. Living with a chronic disease means symptoms will fluctuate. When symptoms worsen, rest and focus on the better days that lie ahead.

Tell Us Your Story! Have a transformational healthy-living tale of your own? Share it with us!

This article originally appeared as “Second Chance” in the March/April 2024 issue of Experience Life.

In the summer of 1997, Jennifer Crystal discovered a red, splotchy rash on her arm. A 19-year-old counselor at a camp in Maine at the time, Crystal had grown up in Connecticut; both states are epicenters of tick-borne diseases like Lyme.

Yet no one thought much of that rash — not even later, when, back at her Vermont college, she developed flulike symptoms: joint aches, fever, headache, and extreme fatigue. “I could barely get to class,” she recalls.

In the years that followed, the cluster of symptoms persisted. Crystal doggedly pushed through, completing a semester abroad, finishing college, and moving to Colorado to become a ski instructor — her lifelong dream — until it all became too much for her health. She ended up moving back to Connecticut to live with her family.

There, she sought the care of a ­naturopathic physician who sus­pected she had chronic fatigue syndrome. The condition is defined by exhaustion after exercise, unrefreshing sleep, concentration problems, and muscle pain lasting six months or more. Herbal treatments, an anti-­inflammatory diet, and acupuncture barely made a difference.

Her illness remained a mystery until 2005, the day Crystal noticed two new bull’s-eye rashes emerge spontaneously. Finally, a clue.

A Lyme-disease test proved positive, which led her physician to diagnose other tick-borne coinfec­tions. (Many persistent Lyme cases feature coinfections.) Months of IV antibiotics brought Crystal back to reasonable health. Believing she was cured, she took a job as an editor in Vermont.

Yet she remained fatigued, and working to support herself pushed her to the edge again. By 2007, at age 27, she was back home in Connecticut, in bed.

This time, with the help of her Lyme-disease specialist, Crystal approached her recovery differently. Along with antibiotics, supplements, and an anti-inflammatory diet, she pursued psychotherapy, integrative manual therapy, and neurofeedback. She regained traction, along with a new understanding that managing her illness would be an ongoing practice.

“I don’t consider myself sick,” Crystal says today — yet she also doesn’t consider herself cured. She has learned how to live with her chronic Lyme as well as symptoms from long COVID, and she is now documenting her experiences in a memoir called Long Hauler.

“I have needs from illness that come along with me, just the same way that diabetics have needs that they take along in their lives, to keep the illness in check.”

“I have needs from illness that come along with me, just the same way that diabetics have needs that they take along in their lives, to keep the illness in check.”

Crystal is one of up to 20 percent of Lyme patients whose symptoms are chronic, meaning they persist well past the initial course of treatment. In 2018, some estimates suggested there were more than 1 million Americans with chronic Lyme, or what the Centers for Disease Control and Prevention (CDC) calls posttreatment Lyme-disease syndrome (PTLDS).

Today we’re especially attuned to the long-haul fallout from COVID, where respiratory issues, brain fog, and depression hobble many patients for months. Those with chronic Lyme have faced similar hurdles for decades.

Doctors who are literate in chronic Lyme used to be rare. If you could find one, you’d likely be subjected to high doses of antibiotics and anti­malarials in harsh regimens that might’ve lasted months or years.

The success of this approach was mixed. Some chronic-Lyme ­sufferers regained their lives but endured ­grueling side effects, including ­destabilized microbiomes (see “Why Your Microbiome Matters” to learn more about this all important ecosystem that lives in you). Others suffered side effects but did not improve.

Perhaps because so many chronic Lyme cases involve coinfection, these treatments often didn’t resolve the problem.

Today, many of these same practitioners have taken a different path, a multipronged approach that combines the judicious use of drugs with more natural therapies. And many patients with intractable illness are finally getting their lives back.

When problems cascade, you must treat the whole patient before the person can clear the infection, says Lyme expert Daniel Kinderlehrer, MD, whose Denver-based integrative medical practice focuses on tick-borne disease. He starts treatment by addressing sleep and pain issues. The problem has “become so much bigger than that infection; there are so many things that are wrong that you can’t treat by just treating the infection,” he explains. “Even if you made the infection go away, you’d still have these other issues in the mix.”

The Lyme Divide

Some 30,000 Lyme cases are reported to the CDC annually, but the agency also notes that around 476,000 people are treated for Lyme each year, according to insurance claims. It’s caused by the bite of a black-legged tick, commonly known as a deer tick, which transmits the spirochete Borrelia burgdorferi (and more rarely, Borrelia mayonii) into the bloodstream.

Lyme is one of a handful of illnesses transmitted by the hard-bodied deer tick in the United States; others include anaplasmosis, babesiosis, ehrlichiosis, and tularemia; all cause significant health issues, but Lyme is the most common and best-studied.

Lyme was first reported in the Northeast and Midwest; now rising temperatures are contributing to an expanded range for ticks. (Greater awareness has also led to increased reporting.) In the most recent CDC survey, infections were reported in every state but Hawaii and Oklahoma.

Other tick-borne diseases are also on the rise. California, where standard Lyme has long been endemic, is seeing the surge of Borrelia miyamotoi, a separate spirochete that can be carried by black-legged ticks. It causes a fever disease (called “hard tick relapsing ­fever”) that is often confused with Lyme.

Overall, two types of Lyme disease now prevail:

The first features a straightforward infection, diagnosed early, with no additional immune issues. Patients typically recover after a two-to-three-week antimicrobial course. If the infection isn’t cleared on this round, the Lyme spirochetes can invade cardiac, neurologic, and joint tissue; a month or two of IV antibiotics will usually clear it.

Then there are those with Lyme (or a mix of tick-borne infections) who remain sick after the stan­dard treatment. They are usually diagnosed late and may have contracted more than one infection. This is the second type: chronic, complicated Lyme, a systemic illness so ­profound that sufferers may be too disabled to go to work or school.

A study published in the New England Journal of Medicine found a group of such patients to be as impaired as those with congestive heart failure and sicker than those with type 2 diabetes. Researchers at Johns Hopkins Medicine have also documented a striking degree of neuro­inflammation in these patients.

Chronic Lyme causes the body to fall into general instability and disrepair. Yet a Lyme diagnosis remains controversial for the persistently sick group, and many physicians are reluctant to offer it. These patients are more likely to be labeled with chronic fatigue syndrome or fibromyalgia and offered ­scattershot ­treatment.

The contro­versy may stem partly from the inadequacy of Lyme tests, which don’t reliably register Lyme anti­bodies for about six weeks. And a significant subset of people with Lyme may never test positive on standard serologies. The disease can lie dormant within tissues, and some tests can’t register certain strains of Borrelia.

Some 30,000 Lyme cases are reported to the CDC annually, but the agency also notes that around 476,000 people are treated for Lyme each year. 

Many patients and providers may never think to test for Lyme, especially if a tick bite failed to trigger the mottled red Lyme rash, erythema migrans (EM). But the rash can take many forms beyond the iconic bull’s-eye, and it may be difficult to spot, especially on darker skin. It can also fail to appear at all.

Complicating matters, many doctors rely on the CDC’s surveillance case definition, which requires a positive test or the EM rash. But the criteria were not designed for diagnosis or treatment. In 2019, the CDC released a disclaimer, which may help more patients receive treatment early on.

Still, an early course of antibiotics does not eliminate the risk of chronic Lyme for those people who remain sick after standard treatment, says physician Elizabeth Maloney, MD, president of Partnership for Tick-Borne Diseases Education. The longer a patient has been misdiagnosed, the more likely treatment will fail.

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Lyme+: The Coinfection Problem

Lyme disease on its own can be debilitating, but when other tick-borne infections are also present, the problem can be exacerbated.

Zoonotic-disease expert Steven Phillips, MD, who treats a range of complex vector-borne diseases and is the coauthor of a recent book, Chronic: The Hidden Cause of the Autoimmune Pandemic and How to Get Healthy Again, calls these complex cases “Lyme+.” Treatment might be prolonged, and a cascade of other problems, incited by infection but sustained by immune dysfunction, can take hold.

These instances show that Lyme disease alone may not account for some of the most confounding cases. “Those most difficult to treat usually have more than one infection, such as babesiosis or bartonellosis,” says physician and Lyme researcher Richard Horowitz, MD, the author of How Can I Get Better? An Action Plan for Treating Resistant Lyme and Chronic Disease.

Researchers assessed 104 people with chronic-Lyme symptoms. They found that 48 percent had been infected by more than one microorganism, and 25 percent showed evidence of at least three.

The same ticks that carry Lyme-causing bacteria may also carry Anaplasma, which can cause the severe flulike anaplasmosis; the sometimes-fatal Powassan virus; and a series of other Borrelia microbes (including B. miyamotoi) that can cause relapsing fevers and other symptoms.

Bartonellosis may be the most disabling coinfection, because of its devastating neuropsychiatric impact, believe Horowitz and Kinderlehrer.  (Horowitz thinks that Bartonella can also amplify nearly every underlying Lyme symptom, including fatigue, neuropathy, muscle and joint pain, and sleep disorders.) Researchers previously doubted that bartonellosis and Lyme spread together via ticks, but some are now changing their positions. The Lyme and Tick-Borne Diseases Research Center at Columbia University now reports that “the evidence for ticks as vectors of Bartonella organisms is circumstantial but fairly strong.”

Evidence that coinfections add to illness continues to grow. In a study published in the European Journal of Microbiology and Immunology in 2021, researchers assessed 104 people with chronic-Lyme symptoms. They found that 48 percent had been infected by more than one microorganism, and 25 percent showed evidence of at least three.

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An Integrative Approach to Treatment

The current evolution in integrative treatment still includes pharmaceuticals, but for shorter courses than the former years-long treatments. It also often involves herbal treatments and a focus on overall health, including sleep and nutrition, since a long-term infection or immune dysfunction will destabilize multiple systems in the body.

Though quite experimental, emerging integrative approaches may focus on dormant or sluggish spirochetes, which are believed to be harder to conquer than others. The research, much of it coming from university labs, is new and remains controversial, but practitioners say that these discoveries have helped move the needle for some chronically ill patients for the first time in years.

These are some of the newest approaches.

Tackling Persister Cells and Biofilms

Recent research has identified more dogged forms of the Lyme spirochete. These “persister cells” are antibiotic-tolerant variants of Lyme bacteria, meaning they are generally unresponsive to drugs.

Researchers have also begun to consider the role of biofilms: starchy, gel-like coatings made of various microbes, including Lyme Borrelia. Microbes operate symbiotically to protect themselves in these films, making it particularly hard to eliminate them.

Stanford researchers subjected persister versions of the Lyme spirochete to more than 4,000 drugs to see which ones might have an effect on Borrelia. Kenneth Liegner, MD, an internist trained in critical-care medicine, has begun treating some Lyme patients with disulfiram, a drug that has FDA approval for treating alcohol dependence and can also be a potent agent against Lyme. Disulfiram has helped some Lyme patients — and caused especially severe side effects in others.

Other researchers continue to search for treatments beyond pharma­­ceuticals. Microbiologist and immun­ol­ogist Ying Zhang, MD, PhD, has tested Lyme-containing biofilms with a broad selection of antibiotics and herbal ­substances. For instance, he and other researchers have found that ­Japanese knotweed, black walnut, sweet wormwood, and Ghanaian quinine are all effective against Lyme Borrelia.

Although these tests were in vitro and studies of human subjects have yet to be done, many practitioners treating chronic-Lyme patients have been adapting these finds on the fly, using drugs as well as herbs when necessary.

Different Drug Protocols

Horowitz has tested a drug called dapsone. It’s normally used to treat leprosy, which also involves persister bacteria. A two-month course of dapsone combined with the biofilm-buster rifampin has helped almost half of the persistently ill Lyme patients in one study to return to health.

Fruitful developments have also occurred by accident. One of ­Horowitz’s patients was in the midst of a divorce and so caught up in grief that she took quadruple the study dose for four days, before stopping cold. Though she’d been chronically ill for years, this short-term, high-dose regimen put her symptoms into full remission, which has lasted nearly a year now.

“Perhaps the answer is to hit hard for several days three or four times a year,” says Horowitz.

A few other patients signed on for the four-day treatment with significant success. Horowitz now is conducting a clinical trial to see if shorter, higher-dose treatments can do the job consistently.

Recent success with short-term aggressive drug treatments has convinced Horowitz to change the focus of his practice and eliminate long-term antibiotics for good. “Perhaps the answer is to hit hard for several days three or four times a year,” says Horowitz.

The search for safer, even more effective protocols continues.

A Gentler Approach

Other Lyme doctors choose potent herbal treatments to help patients heal. These include many essential oils that academic researchers have found to be active against persisters and biofilms: garlic, cinnamon, oregano, and clove, among others.

To suppress the inflammation that makes people feel so sick, they look to turmeric, alpha-lipoic acid, glutathione, and more.

Such strategies have worked for Kinderlehrer, whose practice focuses on tick-borne-disease patients, some of whom are unable to tolerate antibiotics, even for short periods. His protocol includes lifestyle changes, antimicrobial and anti-inflammatory herbs, CBD, and efforts to restore normal hormone function.

In many of Kinderlehrer’s patients, a formerly straightforward infection has morphed into body-wide instability. They may have developed extreme sensitivities to foods, mold, and chemicals that never bothered them before. Some experience activation of mast cells, the white blood cells close to small blood vessels, provoking dangerous allergic reactions. These reactions can trigger brain fog, mood problems, pain syndromes, and profound fatigue.

Still other patients suffer from immune suppression, which likely occurs when Borrelia invade the lymphatic system, interfering in the process where antibodies are generated and sustained, according to University of California, Davis, immunologist Nicole Baumgarth, DVM, PhD.

This lowering of the guard, notes Kinderlehrer, could enable reactivation of yet other infections, such as the Epstein-Barr virus, as well as endocrine or neurological disruption. (Experts are also seeing this same reactivation happening in many patients with long COVID.)

Because no two chronic-Lyme patients are the same, treatments must be highly individualized.

Integrative physician Erica Lehman, MD, is another practitioner who now treads more softly in her treatment of Lyme patients. “A ­decade ago, I was more heavy-­handed with antibiotics,” she recalls. But a retrospective analysis of her patients’ outcomes has made her rethink her approach.

She still uses antibiotics, including IV treatment to reduce the load of infection, but then she switches to lower doses and herbs as soon as possible. “Slow and steady wins the race,” Lehman says.

Years of experience have helped her recognize patient clusters: those with neurologic disease versus illness that hits the gut, the endocrine system, joint tissue, and more. Each cluster has a different treatment protocol and separate path to wellness; though their problem may have started with a tick-borne disease, they face other issues now. (Much of her approach is informed by MyLymeData, a patient-powered Lyme-disease research project.)

Because no two chronic-Lyme patients are the same, treatments must be highly individualized.

Bill Rawls, MD, author of Unlocking Lyme, couldn’t agree more. He was almost 50 when he experienced a devastating descent into illness that was diagnosed as Lyme. After weeks of antibiotics, he was sicker than before. Ultimately, Rawls — who sought training in herbal medicine after his Lyme diagnosis — developed an herbal therapy protocol aimed at slowly killing tick-borne microbes while helping his immune system heal.

“Most of my patients don’t recall a tick bite,” he explains. Instead, they got sick after some extreme stress: a toxic exposure, head injury, overwork, or a traumatic life event. All can weaken the immune system and allow under-the-radar infections to gain purchase.

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Each Journey Is Unique

Many of the healthcare providers who specialize in chronic Lyme end up doing so because they’ve experienced it themselves. Like Rawls, naturopathic physician Mac Toohey, ND, was bitten by a tick in 2007. She was lucky enough to have a bull’s-eye rash, an incontrovertible sign of the disease. (Though not everyone who gets Lyme will have the rash, nearly everyone who has the rash ends up with Lyme.) Despite early diagnosis and treatment, she developed neurological symptoms.

When her stomach could no longer tolerate antibiotics after a yearlong course, she turned to herbs, such as Japanese knotweed and skullcap. That plus a shift to a more plant-based diet aided her in turning the corner.

Then she contracted Lyme again in 2015, and the same treatments didn’t help. Toohey soon learned she had yeast overgrowth and small-intestinal bacterial overgrowth (SIBO), which had to be treated first.

Based on what she learned, she now treats chronic-Lyme patients with IV antibiotics, addresses microbiome imbalance, and focuses on patients’ overall nutrition and sleep habits.

Toohey’s experience has shown her that when a tick-borne disease causes a patient to remain ill for months or years, it is always a journey of one. Much depends on the infections involved and the person’s own biology: Complex chronic illnesses damage different systems and present in unique ways. Practitioners like Toohey, trained in the integrative arts, gently strip the layers of illness, relying on research to guide the way.

Many other practitioners have taken note. Some of the most aggressive, antibiotic-focused Lyme doctors have begun to adapt their treatment protocol, creating new hope in the chronic-Lyme community. The long-term, heavy-dose pharmaceuticals these physicians offered have been controversial, harsh, and costly to maintain. Lyme patients who couldn’t tolerate them often sought support in the world of alternative care, where they may have faced quackery and scams, such as the groundless promotion of malaria treatments.

Today, a well-considered integrative approach is backed by a growing body of peer-reviewed research. Though more clinical studies are still necessary to validate treatments and elevate the level of care for chronic Lyme, the integrative world is a good place to turn when the fallout from tick-borne illness just won’t end.

And as the rates of other complex chronic illnesses, like long COVID, continue to climb, the hard-won experience of chronic-Lyme survivors may be able to provide a road map for us all.

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Your immune system lives to protect you. Like an elite security detail, it guards your body’s perimeters and swiftly deals with troublemakers, such as minor pathogens and cancer cells. It uses a range of tools, including the inflammatory response and specialized immune cells that attack invaders. Once it has vanquished the enemy, the immune system settles back into a state of cool, calm surveillance.

Or at least that’s how it’s supposed to work.

Sometimes the immune system gets confused and attacks the body it’s meant to protect. This is called autoimmunity, or, literally, immunity to self.

Autoimmunity encompasses more than 100 known conditions, including type 1 diabetes, rheumatoid arthritis, lupus, multiple sclerosis, and inflammatory bowel disease. And the number of such diagnoses has continued to rise as healthcare providers have begun to recognize the prevalence of ­immune ­dysregulation.

“Twenty-five to 50 million Americans have some kind of disease characterized by dysregu­lation of the immune system,” says Leonard Calabrese, DO, director of the Cleveland Clinic’s R. J. Fasenmyer Center for Clin­ical Immunology. Symptoms can include joint pain, recurring fever, skin problems, fatigue, swollen glands, and gastrointestinal issues.

But diagnosing autoimmune conditions can be tough. There’s typically no single conclusive test, and many conditions mirror each other. A care provider may need to consider symptoms (which often fluctuate), blood markers, and other factors.

According to the Institute for Functional Medicine, latent or pre-autoimmune disease often exists for seven to 14 years before diagnosis.

The Challenge of Autoimmunity

Autoimmunity rates have been rising steadily for decades, and experts suspect that increasing exposure to environmental toxins may be to blame (more on this later). But the COVID-19 pandemic could be responsible for a massive influx of members to this club that no one wants to join.

The virus that causes COVID was dubbed the “autoimmune virus” in a 2020 article in Autoimmunity Reviews; the authors cited a strong association between the viral infection and the development of autoimmunity. Research shows that the novel coronavirus may activate preexisting “autoantibodies” — the immune proteins that target a person’s own tissues — as well as prompt the body to make new ones.

How can a virus cause the immune system to turn on itself? It apparently has to do with the delicate balance and regulation of this complicated system.

“How viruses interact with our immune system is at the forefront of understanding autoimmunity.”

“The immune system doesn’t work like a radio with a volume control,” explains functional-medicine internist Leo Galland, MD. “It’s more like an orchestra with many different sections that interact with each other. The interactions are dynamic and complex, and the outcome of a novel interaction can be hard to predict.”

Several factors can make us more likely to develop autoimmunity, and genes are one of them. “Some genetic polymorphisms put people more at risk,” says functional-medicine practitioner Keesha Ewers, PhD, ARNP, FNPc, MSN, author of Solving the Autoimmune Puzzle. Polymorphisms on the major histocompatibility complex (MHC) genes that code proteins for the adaptive immune system, for example, can create greater susceptibility.

But a genetic proclivity doesn’t guarantee autoimmunity. “Genes are the cards you’re dealt at birth, but it’s how you play your cards that determines how your genes function throughout your life,” explains Calabrese.

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Calculating Risk

Autoimmune conditions require five basic ingredients, according to pediatric gastroenterologist Alessio Fasano, MD: genetics, environmental triggers, loss of gut-barrier function, a belligerent immune system, and an imbalanced microbiome (dysbiosis).

For instance, if you have a genetic intolerance to gluten, eat a gluten-heavy diet, and develop a leaky gut, “your immune system is already angry,” says Ewers. A baseline state of chronic inflammation sets the stage for an environmental trigger, such as a virus or parasite, to activate a dysregulated immune response.

Traditional approaches to treating autoimmunity involve medications that suppress symptoms without ­addressing root causes, so many people with one autoimmune condition soon develop others. One study found that a single autoimmune diagnosis ­increases the likelihood of a second (or third) diagnosis by up to 34 percent.

By contrast, addressing the root causes of a dysfunctional immune response makes it less likely that the immune system will expand its attack in other areas of the body, forgoing the need for ever more band-aids that simply suppress symptoms.

One study found that a single autoimmune diagnosis ­increases the likelihood of a second (or third) diagnosis by up to 34 percent.

Although the presence of autoantibodies is usually a critical indicator in diagnosing autoimmune conditions, not everyone who has detectable autoantibodies has active autoimmune disease. Those with autoantibodies but no auto­immune symptoms are considered to have “pre-autoimmunity.”

Yet because the internal environment is a key influence on autoantibodies’ behavior, certain precautions can enable these people to remain symptom-free. “Some of the most common autoantibodies we produce only create damage when there’s also systemic inflammation,” explains Galland.

The exact provocations for autoimmunity are still poorly understood. Stress, which includes toxic relationships and thought patterns, is a known trigger, says Ewers. But so are many pathogens, such as the bacteria that cause Lyme disease, and viruses such as Epstein-Barr, herpes, human papillomavirus (HPV), and coronaviruses such as SARS-CoV-2.

Ewers suspects that environmental toxins such as cigarette smoke, pesticides, allergens, and molds can potentially activate autoimmunity. She also focuses on estrogen-mimicking chemicals, including bisphenol A (BPA), which is found in plastic, canned foods, and personal-care ­products. These chemicals can disrupt the modulation of inflammatory proteins called cytokines, which may be one reason women appear to be more susceptible than men to autoimmunity, representing nearly 80 percent of all cases.

It sounds like a hodgepodge, but these suspected triggers are more alike than they seem. Calabrese notes that they are all part of the body’s “exposome,” or the sum total of its exposure to environmental stressors.

“The exposome is everything from pollution and chemicals in food and water to how we eat, exercise, sleep, and handle stress,” he explains. Researchers are just starting to understand the exposome’s role in autoimmunity.

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The Virus Question

Viruses outnumber everything on the planet. Some we catch, like SARS-CoV-2 or HPV; others have been incorporated into the human genome and bestow benefits such as disease resistance or starch digestion.

As journalist Moises Velasquez-Manoff writes in An Epidemic of Absence: A New Way of Understanding Allergies and Autoimmune Diseases, viruses we catch help with training and balancing the adaptive immune system, providing external stimuli that may help prevent autoimmunity.

But viruses have also long been suspected as autoimmune triggers. Epstein-Barr (best known for causing mononucleosis) has been linked to lupus, and influenza can trigger a blood-clotting disorder called autoimmune thrombocytopenia. Chikungunya, a mosquito-borne virus, can cause chronic inflammatory rheumatic diseases.

Now SARS-CoV-2 appears to trigger its own autoimmune cascade, which is revitalizing researchers’ urgency to understand the role of viruses in these conditions. “How viruses interact with our immune system is at the forefront of understanding autoimmunity,” says Calabrese.

Many COVID victims die not from the virus itself but from an overactive immune response to it, characterized by the “cytokine storm.”

One of the most potent effects of SARS-CoV-2 is on the human immune system. Many COVID victims die not from the virus itself but from an overactive immune response to it, characterized by the “cytokine storm.” (Cytokines are inflammatory immune proteins that, in large quantities, can destroy the body’s tissues and organs.) And many who survive COVID seem to generate copious amounts of autoantibodies — the proteins that target the body’s own tissues.

“The question is, What are those autoantibodies doing?” says Calabrese. “Are they predisposing people to inflammation and autoimmunity? Are they contributing to the pathogenesis of long COVID?”

There are multiple theories on how SARS-CoV-2 may be triggering the autoimmune symptoms (including brain fog, fatigue, headaches, dizziness, joint pain, fever, and mood disorders) that have come to be associated with long COVID. The first theory is called molecular mimicry, in which viral proteins that resemble proteins in the body spur the creation of antibodies that attack the body’s own cells.

Another possibility is that inflammation from the infection primes the immune system to mistake the spilled contents of destroyed cells as foreign and create autoantibodies against these cellular pieces.

Again, the health of the gut seems to play an important role. “People with COVID-19 have changes in the gut microbiome of a type that fosters inflammatory reactions,” says Galland. “The bacteria that provoke more inflammation grow, and anti-inflammatory bacteria are suppressed in the GI tract.”

(For more on how mRNA COVID vaccines may resolve some auto­immune symptoms, see “Long-Haul-COVID Recovery and Vaccines”.)

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Repairing the Terrain

One of the greatest challenges with autoimmune conditions is that they can affect multiple body systems. A 2020 study in the Journal of Autoimmunity examined how autoimmune processes may account for the widespread damage caused by some COVID infections, including inflammation of the heart and circulatory system. Circulatory damage can lead to loss of oxygen in the body’s tissues; this in turn slows the function of mitochondria, the energy-producing powerhouses in our cells.

“Immune cells require energy to work properly,” says Galland. “If you have a smart TV and the remote’s battery starts to die, the TV starts doing screwy things. When the power source diminishes, it’s not just that everything gets dim — it gets wacky. That’s the impact of mitochondrial damage on the immune system.”

While researchers still have much more to learn about long COVID, functional-medicine practitioners are already reaching for proven strategies that have helped people manage other autoimmune conditions. There is no one-size-fits-all protocol, but some basic principles apply.

“I go to individualization — what’s at the root?” asks Ewers. “Why was this terrain susceptible to this virus, and what form did it take? Then the treatment protocol matches those things.”

Keep reading to learn about the main tenets of a functional-medicine approach to treating autoimmunity.

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The Functional-Medicine Approach to Treating Autoimmunity

An Anti-Inflammatory Diet

An anti-inflammatory diet is one of the most important tools for managing autoimmune conditions. “Many predisposing factors to poor outcomes [from autoimmunity] come from chronic inflammation, and a largely plant-based diet is a great start toward lowering inflammation,” says Calabrese.

Several special diets have proven to be helpful for people with autoimmune disease, including the Wahls Protocol, Autoimmune Protocol, and variations on the paleo diet. While they vary in their specifics, they share an emphasis on fresh, whole, unprocessed foods; plenty of colorful vegetables; abundant fermented foods; bone broth; and healthy fats. They also minimize sugar, processed carbs, alcohol, dairy, and caffeine.

Ewers recommends working with a functional-medicine provider to identify specific food sensitivities, absorption issues, or nutrient deficiencies. Using diet to manage inflammation and support circulation and mitochondrial function can make a huge difference in autoimmune symptoms and quality of life.

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Microbiome Management

The gut microbiome plays a crucial role in immune function. “The microbiome controls so much of how the immune system responds to invaders,” says Ewers. A comprehensive stool analysis can help identify imbalances in the microbiome, such as a lack of beneficial bacteria or an overabundance of harmful microbes, parasites, or yeast.

“We see similarities between long COVID and chronic fatigue syndrome in the microbiome,” says Galland. For long COVID, he recommends supplementing with specific bacteria strains, such as Bifidobacterium longum BB536 and a form of Bacillus subtilis, which may help stabilize and reorganize the gut microbiome. Studies show that eating avocados and chickpeas may also support the growth of anti-inflammatory bacteria, he notes. (For more on microbiome health, see “Your Microbiome: The Ecosystem Inside“.)

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Adequate Sleep

Sleep helps restore the immune system. Insufficient sleep (less than seven or eight hours per night) has been linked to the production of inflammatory cytokines. But many people with autoimmune conditions have disturbed sleep patterns; they may suffer from profound fatigue and struggle to regularly sleep through the night.

Working with a functional-medicine provider to integrate sleep-hygiene techniques, such as ritualized sleep–wake cycles, environmental and dietary modifications, and (potentially) melatonin therapy, can help restore healing and supportive sleep patterns. (For more on sleep, see “Sleep It Off“.)

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Moderate Movement

Exercise is key for healthy immune function. Multiple studies have shown that moderate exercise offers benefits for patients with autoimmune conditions — including improvements in joint mobility, mood, cognitive ability, energy, and quality of life. If you’ve received a diagnosis recently or are easing into exercise after being sedentary, start with gentle, moderate movement as you build up strength and stamina, and be sure to consult with your provider.

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Supplements

There is no singular supplement protocol that will achieve the same results in everyone with autoimmunity. Most functional-medicine providers make supplement recommendations based on a person’s specific test results and symptoms. Still, these are some of the most common supplements used to support better health and function for a variety of autoimmune conditions, including long COVID, and each one has a range of salutary effects.

• Vitamin D3: Insufficient vitamin D is associated with a number of autoimmune diseases. Raising low levels may help mitigate disease severity and progression and help repair a leaky gut.
• Curcumin: This potent anti-inflammatory chemical is found naturally in turmeric.
• Resveratrol: A polyphenol found in peanuts, berries, and red grapes, resveratrol may help reduce the production of autoantibodies, among other immunomodulating effects.
• Fish oil: This oil contains EPA and DHA, anti-inflammatory omega-3 fatty acids that Ewers says help with healthy gene expression.
• NAC: Short for “N-acetylcysteine,” NAC helps the body make the antioxidant glutathione, which protects against cellular damage and supports immune health. Combining NAC with niacin can help support mitochondrial function, says Galland.
• CoQ10: Naturally produced by the body and also available in supplement form, this antioxidant supports circulation and mitochondrial function.

Stress Relief

Psychoneuroimmunology is a burgeoning area of immune science based on the insight that the central nervous system and immune system are intertwined. “The brain and the immune system are one organ,” explains Calabrese.

To manage the stress of autoimmunity itself, Ewers believes we may also need to look directly at the “autoimmune mindset” — a sense of being at war with oneself.

“People are always looking to be done,” notes Ewers. “The expectation is that we kill the yeast in our gut, get our hormones balanced, and the body should shape up.”

But people with autoimmune conditions need to accept that creating health is a long-term process that involves all the layers of our being — physical, energetic, mental, emotional, and spiritual. “There are no quick fixes or tricks for immune health,” notes Calabrese. “It’s a process.”

Autoimmune patients need to treat their bodies with unconditional love. . . . Praise them when they get it right, and when things go wrong, offer some help and support.

We can use tools like mindfulness meditation, which has shown a capacity to lower inflammation and tamp down inflammatory genes. Mind–body techniques such as yoga, tai chi, and qigong can reduce autoimmune activity. But overall, the recovery process requires patience and lots of self-love.

“When we have expectations that aren’t being met, that’s one thing that sets the immune system off the worst,” says Ewers. She believes autoimmune patients need to treat their bodies with unconditional love, the way we would children who are learning a new skill: Praise them when they get it right, and when things go wrong, offer some help and support.

“It’s about getting into a collaborative instead of a combative relationship with yourself.”

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This article originally appeared as “Autoimmunity Now” in the January/February 2022 issue of Experience Life.