COVID-19 and the Autoimmune Connection

Some people face a greater risk from COVID because of their immune system's inability to respond to the virus without hurting the body
April 15, 2021 Updated: April 22, 2021

What is Autoimmunity?

While the medical community at large does not recognize an exact root cause of autoimmune disease, the research is clear that many variables may contribute to  autoimmune disease including genetic expression, internal and external environmental triggers, and hormonal changes. Seasons of stress and trauma have also been correlated with manifestations of autoimmune disease. All of these factors have the ability to disrupt the immune system and trigger autoimmune disease.

To understand autoimmunity we need a foundational understanding of the immune system. The immune system is an intricate organization of various immune cells, organs, and biochemical messengers that work together to protect the body from foreign invaders. These foreign invaders include viruses, bacteria, parasites, environmental toxins, food, mold, and mycotoxins. When the body comes in contact with any of these threats, the immune system responds with an attack to overcome the threat. This is the body’s innate, natural defense mechanism often referred to as the inflammatory response.

In normal physiology, the body easily differentiates between your own cells and tissues and foreign invaders. Autoimmunity occurs when the immune system can no longer distinguish between the body and threats from the outside world. Basically, the body starts attacking its own tissue.

In one scenario common to autoimmune disease, an individual has permeable barriers within the gut, lungs, or brain. This allows certain proteins to pass through these damaged barriers. The immune system then starts producing antibodies against these internal foreign invaders.

Viruses & Autoimmunity

The misfiring of the immune system can look different for each individual and oftentimes there are many factors that impact the immune response. We know that viral illness can trigger autoimmunity. Research shows a link between autoimmunity and viruses including Parvovirus B19, Epstein-Barr-virus (EBV), cytomegalovirus (CMV), herpes virus-6, HTLV-1, hepatitis A, hepatitis C, West Nile Virus, and rubella virus.

These viruses have a strong correlation with the onset of autoimmune conditions like rheumatoid arthritis, systemic lupus, Sjogren’s syndrome, multiple sclerosis, Hashimoto’s autoimmune thyroiditis, and many others.

Several mechanisms within the immune system can trigger a misguided immune response due to a viral illness. These include epitope spreading, bystander activation, and cryptic signaling. Let’s take a deeper look into one of the most common—molecular mimicry.

In the process of molecular mimicry, the body initiates an autoimmune response because it sees similar amino acid sequences between foreign invaders and its own tissue. This case of mistaken identity leads the immune system to think specific tissues are the problem. The autoimmune condition that manifests is determined by what tissue(s) are being attacked.

For example, when the body has an immune response against the thyroid tissue, the result could be Hashimoto’s thyroiditis or Grave’s disease. These amino acid sequences or partial proteins become targets for the immune system if one of the barrier systems in the body is broken down and these partial proteins get into the bloodstream. The most common barrier to be broken down would be the single cell layer making up the epithelial lining of the intestines. If the gut remains “leaky,” an individual can develop more autoimmunity as this process perpetuates itself over time.

COVID-19 and the Immune System

COVID-19 is the disease caused by the virus SARS-CoV-2. The immune system is the best defense against COVID-19. Once the body becomes aware of the viral invasion, it mounts an immune response that includes a cascade of chemical messengers and an inflammatory response within the body.

Most often, people experience a mild case of COVID-19 where the immune system is able to quickly and efficiently fight the virus and restore normal function. Some people develop severe cases of COVID-19 where the body has an exaggerated, sometimes uncontrolled response to the infection. In these circumstances, an abundance of pro-inflammatory cytokines and other immune factors are released very aggressively. This causes a state of hyper-inflammation and results in dangerous levels of oxidative stress. This has the potential to injure various tissues within the body and cause respiratory failure. People that suffer this type of  immune response have more severe symptoms and can sometimes fall into post viral syndrome for many months after their initial illness.

The SARS-CoV-2 and the Autoimmune Connection

New research shows that various proteins within the body are cross reactive with monoclonal anti-SARS-CoV-2 antibodies and polyclonal anti-SARS-CoV-2 antibodies. That means these proteins are prone tof molecular mimicry and a SARS-CoV-2 infection has the potential to trigger chronic disease.

When cross reactivity, or similar amino acid structures were studied between SARS-CoV-2 antibodies and various proteins within the body, it was discovered that SARS-CoV-2 antibodies initiated reactions in various tissues including barrier proteins (gut, brain, and lungs), gastrointestinal proteins, thyroid proteins, neural tissues, and more. This research shows that the extensive immune cross-reactivity between SARS-CoV-2 antibodies and different tissues within the body likely influence the severity of illness, initiate an autoimmune disease in certain individuals, and exacerbate autoimmunity in those with pre-existing autoimmune conditions.

It may go without saying, but we clearly need more research to help us understand the long term impacts of COVID-19 on autoimmunity and overall health. Thankfully, there are many strategies that can protect you from both COVID-19 and autoimmune disease.

Strategies for Supporting the Immune System Against Autoimmunity

Many dietary and lifestyle factors can go a long way in protecting you and your loved ones from viral infection and autoimmune disease. Making these changes can have a profound impact on the immune system.


Eating a clean, nutrient-dense diet is foundational to a properly functioning immune system. Prioritize eating quality fats, proteins, and phytonutrient-rich vegetables and fruits. Consuming probiotic-rich lacto-fermented foods, bone broth, and collagen helps to maintain proper barrier function within the gut.

Meanwhile, refined sugars, processed carbohydrates, and processed foods drastically suppress immune function, so it is important to stay away from these foods. For some people, certain foods significantly contribute to immune system dysregulation. These include conventional gluten and dairy; however uncovering an individual’s unique food sensitivities can help immune system function.

Immune Support

Not only is eating an anti-inflammatory diet crucial for a strong immune system, supporting immune function through various supplements can also help to bolster it. While it is best to get some functional lab testing done to understand your body’s unique physiology, optimizing vitamin A, vitamin C, vitamin D, zinc, and glutathione status have been shown to support the body in the face of a COVID-19 illness and help prevent autoimmune disease.  We cannot underestimate the importance that proper sleep, movement, diet, and stress have on the immune system.

Support Barriers

As mentioned above, proper barrier function is crucial for safeguarding the body from developing autoimmune disease. Foundational to ensuring proper barrier integrity is supporting the microbiota. The microbiome, or the overall microbial balance of the body, impacts barrier function of the gut, lung, and brain. Eating an anti-inflammatory diet and supplementing with prebiotics and probiotics have been shown to protect barrier function as well as nourish the microbiome. If there is an underlying infection within the body, identifying and uprooting it will help restore barrier function.

Avoid Toxins

Harmful toxins are ubiquitous in our environment today. Environmental toxins include pesticides and herbicides, heavy metals, chemicals, molds, and mycotoxins. On-going exposure to these toxins causes systemic inflammation. Environmental toxins have been shown to hurt the microbiome, and damage the gut, lung, and blood brain barriers. They also contribute to hormone imbalances, hinder phase one and phase two detoxification, and disrupt immune function.

Manage Stress

We know that both acute and chronic stress can undermine immune function.  Additionally, chronically elevated stress hormones wreak havoc on the gut, lung, and blood brain barriers. Emotional trauma and adverse childhood experiences (ACEs) are intimately intertwined with the overall stress load on the body. Working with a skilled clinician to work through trauma can have a profound impact on the way you see the world, overall stress, and immune function.

We are just scratching the surface on how to prevent COVID-19, post viral syndrome, and autoimmunity. Future articles will provide more detail on how to work through a viral illness. In the meantime, if you are experiencing post viral syndrome or would like to put an autoimmune disease into remission, please see a functional medicine doctor who can help you work through your many options.

Dr. Ashley Turner is a board-certified doctor of holistic health, traditionally-trained naturopath, author, homesteader, and homeschooling mother of three sweet daughters. You can reach her at Restorative Wellness Center where she practices functional medicine.