The Autoimmune-COVID Connection and How to Safeguard Your Health

“You can’t control the virus, but you can control the host (that’s you!).”

— Rob Silverman, DC, CNC, author, Inside-Out Health

With massive action underway to vaccinate the population comes new hope of some end in sight for the coronavirus pandemic. I am hopeful that vaccines will be protective with minimal harm; and that in a reasonable amount of time, more semblance of life as we knew it will reemerge.

Personally, as someone who used to have multiple sclerosis (MS), I am being as cautious as ever, and doing what I can to proactively support my immune system and safeguard my health and wellbeing. I’m keeping my eyes on the research and have been noticing an increasing number of studies that are making the connection between COVID-19 and autoimmune disorders.

Scientists have known for more than a century that infections of all types including viruses like the Herpesvirus family (e.g., Epstein Barr (EBV) and HHV6), fungal infections like Candida albicans, and bacterial infections like Lyme disease and its numerous co-infections are known to trigger autoimmune conditions. Experts also observe that infections are more likely to take root in a host with a weakened immune system.

In my book, Beat Autoimmune, I delve deeply into the infection-autoimmune connection and how by targeting infections and supporting the “terrain” of the host naturally, we can potentially reverse autoimmune processes.

Infection-Autoimmune Mechanism of Action: Cross-Reactivity

It helps to have a high level understanding of how infections can trigger autoimmunity. At a cellular level, our bodies’ tissues are made up of proteins; and those proteins, at a microscopic level, are made up of amino acid sequences. Here’s where it gets crazy. At a molecular level, the infection (antigen) looks identical to the human tissue. Scientists call this molecular mimicry. As an example, it is known that the gluten, an inflammatory protein, when broken down to its smallest amino acid sequence, resembles human tissues including the thyroid, liver, pancreas, muscle, and brain. This is why it is imperative if you have an autoimmune condition or want to prevent one that you avoid gluten.

As with gluten, it turns out that some infectious pathogens, like COVID-19, when broken down to a molecular amino acid sequence level, resemble human tissue. You can imagine what happens next. The immune system, just doing it’s job to protect and defend you against the COVID-19 pathogen, tags the invader (antigen) for destruction and then produces antibodies (missiles) to destroy the tagged invader. Cross-reactivity occurs when the body’s own tissues inadvertently become the target of attack (autoantibodies). As autoantibody levels increase, the autoimmune process is initiated. If the person (the host) is inflammed, meaning the immune system is weakened from fighting other invaders like Candida, parasites, Lyme co-infections, glyphosate, and even chronic stress, it is likely that the individual has a leaky gut and what is referred to as “loss of tolerance,” too.

Mounting research reveals that COVID-19 is not just a one-time nasty virus, but that it can trigger autoimmunity and worsen existing autoimmune conditions.

Studies Link COVID With Autoimmunity:

  • Leading autoimmunologist, Aristo Vojdani, PhD, recently published a paper in Frontiers Immunology on the implications between COVID-19 and autoimmunity in which he, his son, Elroy Vojdani, MD, and leading Functional Medicine health expert, Datis Kharrazian, PhD, present research showing that SARS-CoV-2 (COVID-19) antibodies cross react with numerous human tissues, influencing disease severity, precipitating the onset of autoimmunity in susceptible people, and potentially exacerbating pre-existing autoimmune conditions.1
  • A large study of 1,700 COVID survivors shows that six months post-COVID hospitalization, 76% still had one of more symptoms, including fatigue, muscle weakness, sleep difficulties, anxiety, and depression. People with autoimmune disorders will be very familiar with this common constellation of symptoms. A note on age: in case you think long-COVID mostly affects the elderly, the average age in this study was 57. 2
  • In a smaller study of 31 people with a recent history of severe COVID and no preexisting autoimmune condition, 44% had a positive ANA (antinuclear antibody) test, a general autoimmune marker commonly observed in lupus and Sjogren’s Syndrome; and 19% had a positive RF (rheumatoid factor) commonly observed in rheumatoid arthritis (RA).3
  • A recent article called “Autoinflammatory and autoimmune conditions at the crossroad of COVID-19” published in the Journal of Autoimmunity shows a link between COVID-19 and Guillain-Barré syndrome (GBS), Kawasaki disease (KD), and Autoimmune hemolytic anemia.4

There is a chicken-egg situation with autoimmunity and COVID-19. Having an autoimmune disorder increases vulnerability to greater long-term complications from COVID-19; and COVID-19 may trigger autoimmunity in susceptible people.

People with Chronic Health Issues at Far Greater Risk

Most people will survive COVID-19, and the majority of those who get it will experience only mild symptoms. On the other hand, those with chronic health conditions like any of the 150 autoimmune conditions including MS, lupus, RA, Hashimoto’s thyroiditis, Sjogren’s, and IBD may be ten times more vulnerable to a severe form of COVID-19 illness and a  worsening of autoimmune symptoms.

Why I’m Extra Concerned

I’m personally extra concerned about COVID-19. Why? Because I’ve been in the higher risk group and continue to deal with underlying immune system challenges. In 2010, I beat a two-decade course of MS by finding and removing my triggers and healing my gut. Yet, health is not static. You don’t beat an autoimmune condition and that’s the end of the story. No. 

Health takes daily work, proactive maintenance, and a courageous commitment to oneself to stay on the healing and prevention path.

I may be more vulnerable to infection than most, because I have the genes — the latent potential — for MS, along with persistent immune system burdens like mycotoxins from recent mold exposure, persistent Lyme disease, and ongoing food sensitivities. This means I need to step up my game and do what I can to safeguard my health and protect my loved ones right now

How F.I.G.H.T.S.™ Can Help Safeguard Your Health

Immune system experts agree this is a time to help our immune systems function optimally. We can do this by embracing simple, healthy daily lifestyle habits. To help you remember the major root cause categories you can control, I created the mnemonic, F.I.G.H.T.S,™ which stands for Food, Infections, Gut health, Hormone balance, Toxins and Stress.

You can prevent COVID-19 and worse outcomes much in the same way you reverse or prevent autoimmune conditions with F.I.G.H.T.S.™

My clients, readers, and students who are following the F.I.G.H.T.S. framework to beat autoimmune are in a much better position to deal with the COVID-19 threat. There is no secret sauce, no mystery to their success. They are following a proven framework that works time and time again.

The strategies below focus on COVID-19 prevention, not what to do if you get COVID-19. This is not intended as medical advice. My own MS prevention strategies are specific to my healing journey. You may find many of the same strategies apply to you, but remember that healing is individual.

Start with Food

Food is the number one root cause category of autoimmune conditions. On the flip side, people with autoimmune issues often heal 60% to 100% just by changing what they eat. When you eat inflammatory foods, or foods you have developed sensitivities to, your immune system goes on high alert, creating antibodies (missiles) to attack foods (protein molecules) that have breached the gut barrier. When your immune system is distracted by fighting foods, it is not optimized to fight real infections like COVID-19. These are my top 3 immune-strengthening food strategies:

  • Eliminate inflammatory foods

    Gluten creates a leaky gut in anyone who eats it; 5and a leaky gut is the fast path to autoimmunity. Most people who are sensitive to gluten are also sensitive to casein, a protein in animal dairy. In addition to promoting obesity and diabetes — both risk factors for autoimmunity and COVID-19 — sugar and processed foods block the immune system from functioning for up to 5 hours after eating it. 6

  • Remove your food sensitivities

    Beyond the usual autoimmune culprits, gluten, dairy, and eggs, it turns out I’m sensitive to soy, corn, grains, almonds, sugar and vanilla (argh). This is not a life-sentence on all these foods, it just means that I need to remove them for six months to give my immune system and chance to calm down and stop fighting my foods so it is available to combat real threats like COVID.

  • Fast more, eat less often

    Intermittent fasting reduces inflammation, strengthens the gut barrier, and helps you move from being a sugar burner to a more metabolically beneficial fat burner. Fasting has also been shown to rejuvenate the immune system through a process called autophagy, which clears out old, “senolytic” (damaged) cells, making way for new, more robust immune cells. I typically stop eating at 5 pm and don’t eat anything until 9 am for a 16 hour fast, also known as 16:8, for the 8 hour eating window.

Heal Your Gut

The gut is ground zero for health and disease. It turns out about 75% of the immune system is housed right there in the lining of the gut. A leaky gut and imbalanced microbiome are central to the development of  autoimmune conditions; and if our immune systems are impaired, they are less able to fight nasty infections like COVID-19. I tend to my gut with these daily strategies:

  • Seed with probiotics

    This is one of my most important COVID-19 prevention strategies: seeding my gut microbiome with probiotics (beneficial bacteria). LactobacillusBifidobacterium, and spore (soil-based) based probiotic species have been found to have a beneficial, modulating effect on the immune system. I take several brands to make sure I’m getting an assortment of immune-enhancing strains. Right now I rotate or layer: General Biotics’ Equilibrium and Microbiome Labs’ MegaSporeBiotic. If you can tolerate fermented foods without a histamine reaction, there are more probiotics in a forkful of sauerkraut or kimchi than in most probiotic supplements.

  • Feed the probiotics with prebiotics

    Prebiotics are fiber and fiber is what probiotics eat. If you don’t eat enough fiber, those beneficial bugs will start gnawing on your own mucus lining. When you eat fiber, your probiotics will pay you in dividends with myriad beneficial functions like creating hormones and neurotransmitters, protecting your gut lining, and modulating your immune response. I make sure to eat plenty of different types of vegetables such as dandelion greens, artichokes, avocados, flax, and chia seeds, plus supplemental powders like organic psyllium husk, acacia, and inulin. 

  • Seal a leaky gut with collagen

    Collagen is the most abundant protein in our bodies, acting as a structural matrix and glue. It also helps repair a leaky gut, helping to protect and support the immune system, 80% of which resides in the gut lining. I use 100% grass fed beef bone broth, collagen or gelatin. I make beef stew with bone broth and add extra gelatin to thicken; and I add collagen, gelatin or bone broth powder per day in smoothies, soups, stews, curries, coffee and my keto cardamom pudding.

Clear Infections

Any number of infections can trigger autoimmune conditions; and having an autoimmune condition makes you more susceptible to further infections, especially if you’re taking immunosuppressive medication. Excess inflammation from hidden infections puts your immune system in overdrive, weakening immunity. This is what I’m doing to bolster my defenses against COVID-19 and deal with existing stealthy infections:

  • Optimize your immune function

    Supplementing with targeted nutrients long-term is one of the best strategies to replenish depleted stores and defend against COVID-19. I take supplements known to improve resilience to infection, including 2 gr corn-free vitamin C; 5K IU D3 + 200 mcg K2; 30 mg zinc carnosine; 1000 mg quercetin; 1 ml liposomal glutathione; 300 mg Co-Q10; 200 mg R-lipoic acid; 500 mg resveratrol; and 3 mg timed-release melatonin. I am currently offering a 15% discount normally reserved for my clients on professional-grade supplements in my Fullscript supplement dispensary.

  • Rev up your metabolism

    Autoimmunity is a hypometabolic state, meaning the metabolism is typically low and slow. Being in a hypometabolic state not only decreases your vitality, it decreases the robustness of your immune system. To improve my metabolism and strengthen my immune system I lift heavy weights several times per week (muscle is more metabolically active than fat); I hike in the morning in a fasted state; and I finish every shower with cold water for the hormetic effect — a little stress is beneficial. 

  • Take infection-fighting herbs

    Herbal antimicrobials and coconut-based compounds are safe and effective for infections of all types, and are often more effective than antibiotics.7 I love simplicity so select herbs that cover all the bases. To deal with lingering Lyme co-infections, reactivated Epstein Barr Virus (EBV), and any candida overgrowth I take 600 mg Ecological Formula’s monolaurin, 1000 mg Karuna Olive Leaf extract, and Apex Energetics’ GI-Synergy,™ which is a powerful infection-flighting blend of herbs including wormwood, black walnut, cat’s claw, pau d’arco, organo extract, and Oregon grape

Minimize Toxins

Each of us carries a “toxin bucket” into which go all the potential inflammatory factors — think bad F.I.G.H.T.S.™ — that enter or are created as byproducts within our bodies. When the bucket overflows, our bodies buckle under the burden, inflammation increases, our guts become leaky, and we become vulnerable to infections like COVID-19 and autoimmunity. We must proactively minimize what comes into our toxin buckets and reduce what’s already in there. Here are the top things I’m doing to keep my bucket as empty as possible:

  • Go organic

    Organic produce has up to 60% more antioxidants—protection against autoimmune disease and COVID-19—and up to 100 times lower pesticide residue than conventionally farmed produce.8 By going organic with 100% grass-fed, organic meats, oils, and veggies we massively reduce our consumption of chemicals. Remember, you are what you eat ate!

  • Filter your water

    While the EPA sets guidelines for allowable limits of contaminants in drinking water, there is no guarantee that those standards are being met. Our local county public water supply is treated with fluoride, and may also contain any number of 2,100 known toxins commonly found in water, like lead, pesticides, bacteria, iron, nitrates, nitrites, chlorine, and copper. To avoid these baddies we use simple water filters in our kitchen, shower and tub faucets.

  • Detox daily

    Sweating is one of the most effective methods of detoxing the body of hundreds of different toxins, including heavy metals, PCBs, flame retardants, pesticides, herbicides, and many other harmful chemicals. I try to sweat at least a little every day, mostly through exercise, but also through sitting in a low EMF infrared sauna. If you don’t have access to a sauna right now, you can get similar benefits from soaking in a hot bath. Make it even more nourishing with epsom salts and lavender essential oil.

Address Stress

There are three types of stress: tame, tolerable and toxic. Tame is the mild form you quickly get over, like taking a cold shower or doing something a little out of your comfort zone. Tolerable is the kind you may feel after a job loss, break up, or death of a loved one. You eventually get over it if you have the resources and support. Toxic stress is unrelenting, chronic, and includes buried emotional trauma from childhood. Ongoing stress is toxic and causes mega inflammation throughout the body, keeping your immune system weak. These are the top ways I address stress today:

  • Breathe slowly and deeply

    You can quickly and easily activate the relaxation response by breathing consciously, deeply and slowly. When you hold your in-breath for a comfortable period and then exhale slowly and deeply, you stimulate the vagus nerve, which helps you move out of the stress response and into the relaxation response. 9 I do a few minutes of soft belly breathing at least twice a day: during my morning meditation, before bed, and anytime I need instant relaxation during the day.

  • Go to bed earlier

    Research is clear that sleep deprivation, defined as 6 or fewer hours a night, negatively impacts gene expression and makes you more vulnerable to infections. 10 11 If you have an autoimmune disorder you may need 8 or more hours. I’ve always needed more sleep than most, but now I’m getting extra sleep — for me that’s getting in bed at 8 or 8:30 pm. I monitor my sleep with an Oura ring and keep track of my deep sleep, temperature and heart rate variability (HRV). 

  • Connect with loved ones

    Studies show that lack of social connection is a greater detriment to health than obesity, smoking and high blood pressure. 12 On the other hand, strong social connection strengthens your immune system, helps you recover from disease faster, and may even lengthen your life!13 I am an introvert who works from home, and now, further isolated with COVID-19, I must be super proactive in staying connected with loved ones. Every day I make sure to reach out to at least one friend or colleagueparticipate in an online yoga, wellness, or meditation class, and engage in supportive group discussions inside Beat Autoimmune Academy. It is especially heartening during tough times to be part of a group that is committed to healing together. Every week also we enjoy having video dinners with friends.

Balance Your Hormones

Thankfully, hormone balance usually follows addressing the other F.I.G.H.T.S. factors. As you optimize your diet, heal your gut, clear infections, minimize toxins, and address stress, your hormones should naturally fall into line. As I revealed in my book, Beat Autoimmune, I suffered from the 6 biggest hormonal imbalances in America: low vitamin D, low (hypo) thyroid, low DHEA, high estrogen, high insulin, and high cortisol, so continue to take a more assertive approach. These are my top hormone balancing strategies:

  • Get your D levels up

    This one is the easiest way to fill up your immune system reserves and protect against autoimmunity and viral threats. Experts argue about optimal levels. Personally I get my D levels tested twice a year and optimize my level to 70 – 100 ng/ml, often with sun exposure, but also with 5K IU Quicksilver Scientific Liposomal D3 + K2.

  • Consider bioidentical hormones

    Low hormones, like postmenopausal levels of estrogen or low thyroid levels, can suppress the immune response. Conversely, when hormones are too high, like estrogen dominance, there are less available immune-protective T-cells in the bloodstream. With hormones, it’s a Goldilocks goal: not too high or too low, but just right. My Goldilocks regime is a combination of oral progesterone before bed; compounded cream called Bi-est that contains estriol/estradiol, testosterone and DHEA once a day in the morning.

  • Go keto periodically

    By emphasizing healthy fats, moderating protein intake, and restricting carbs to roughly 70% fat, 25% protein and 5% carbs) with the ketogenic (keto) diet, energy soars, brain function improves, inflammation is lowered, insulin resistance can be reversed; and the ketogenic diet might be protective against viral infections like the flu. Yale University published a recent study showing that mice fed a ketogenic diet and infected with the influenza virus had a higher survival rate than mice on a normal, high-carb diet.

Prevent COVID-19 and Beat Autoimmune with F.I.G.H.T.S.™

For those of us with underlying health conditions, the risk for worse outcomes with COVID-19 is real. The time to take proactive action to safeguard your health is right now.

While this information and the situation itself may be overwhelming, the F.I.G.H.T.S. framework can help you get organized. And whether you address each category one at a time or all at once, doesn’t matter, as long as you get going. As you feel empowered by taking one step forward, you’ll find the motivation to take another, and then another, until the momentum of healthy habits carries you toward a life of vibrant health and wellbeing.

As you get your immune system in good fighting shape, you’ll also be protecting your loved ones and the broader community, and that will help us all get back to normal faster.

Stay safe, stay connected, and take very good care!

Photo credit: Allef Vinicius

P.S: Want my help beating an autoimmune condition and optimizing your immunity?

If you live the U.S. and are ready, willing, and able to invest in your best health, I offer Functional Medicine Total Health Transformation Programs over Zoom. I collaborate with a naturopath who is an expert in resolving chronic infections and toxic burdens which are almost always part of the autoimmune puzzle. Together we provide comprehensive, customized treatment plans, and collaborative, caring support. Sign up for a complimentary 15 min discovery call to discuss how we might work together. If you’re truly ready to invest in your best health and life, I’d love to talk with you.

1 Reaction of Human Monoclonal Antibodies to SARS-CoV-2 Proteins With Tissue Antigens: Implications for Autoimmune Diseases; Vojdani, A. et. al., Front. Immunol., 19 January 2021 | Reference
2 6-month consequences of COVID-19 in patients discharged from hospital: a cohort study; Huang, C. et. al., pub Jan 8, 2021, The Lancet, Reference
3 Broadly-targeted autoreactivity is common in severe SARS-CoV-2 Infection, Woodruff, M., et. al., Reference
4 “Autoinflammatory and autoimmune conditions at the crossroad of COVID-19”; Rodriguez, Y., et. al.,  Journal of Autoimmunity; Reference
5 Effect of Gliadin on Permeability of Intestinal Biopsy Explants from Celiac Disease Patients and Patients with Non-Celiac Gluten Sensitivity, Hollon, J. et. al., Nutrients. 2015 Mar; 7(3): 1565–1576, Reference
6 Sanchez, A., et al.; Role of Sugars in Human Neutrophilic Phagocytosis; American Journal of Clinical Nutrition; Nov 1973; 261:1180-1184; Reference
7 Liu Q, Meng X, Li Y, Zhao CN, Tang GY, Li HB. Antibacterial and Antifungal Activities of Spices. Int J Mol Sci. 2017;18(6):1283. Published 2017 Jun 16. doi:10.3390/ijms18061283; Reference
8 19. Baranski, M., et. al., Higher antioxidant and lower cadmium concentrations and lower incidence of pesticide residues in organically grown crops: a systematic literature review and meta-analyses, British Journal of Nutrition, Volume 112, Issue 5 14 September 2014, pp. 794-811; Reference
9 Cleveland Clinic Wellness; “What Happens in Vagus” Reference
10 Asif N, Iqbal R, Nazir CF. Human immune system during sleep. Am J Clin Exp Immunol. 2017;6(6):92–96. Published 2017 Dec 20 Reference
11 Effects of insufficient sleep on circadian rhythmicity and expression amplitude of the human blood transcriptome; Möller-Levet, Carla S., et al.; Reference
12 Klinenberg E. Social Isolation, Loneliness, and Living Alone: Identifying the Risks for Public Health. Am J Public Health. 2016;106(5):786–787. doi:10.2105/AJPH.2016.303166; Reference
13 Social relationships and health; JS House, KR Landis, D Um




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Palmer is a certified Functional Medicine Health Coach who has helped thousands of people reverse autoimmune conditions based on her own two-decade battle to successfully beat multiple sclerosis (MS). She’s the author of the Amazon #1 bestselling book, Beat Autoimmune, which has a powerful foreword by Functional Medicine pioneer, Mark Hyman, MD.

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