Why People With Autoimmune Disease Face Hidden Risks During Disease Outbreaks

People living with autoimmune diseases face a double burden during infectious disease outbreaks: their own immune systems may be suppressed by necessary medications, and rising infection rates in their communities strip away a critical layer of protection they depend on. Unlike healthy individuals who gain strong immunity from vaccines, many autoimmune patients remain vulnerable even after vaccination because the very medications that control their disease also prevent their immune systems from building robust protection against infections.

How Do Infections Trigger Autoimmune Flares?

When infectious diseases spread through communities, people with autoimmune conditions often experience worsening symptoms. Researchers have identified several biological mechanisms that explain why viral infections can activate autoimmune disease pathways. These mechanisms include molecular mimicry (where viral proteins resemble the body's own proteins), bystander activation (where immune responses meant to fight the virus accidentally damage healthy tissue), epitope spreading (where the immune system begins attacking additional targets), and interferon signaling (a type of immune communication that can amplify inflammation).

After outbreaks occur, clinicians regularly observe increases in several serious conditions:

• Inflammatory Arthritis: Worsening joint pain and swelling in people already diagnosed with rheumatoid arthritis or other inflammatory joint diseases
• Lupus and Vasculitis Flares: Increased disease activity in systemic lupus erythematosus and blood vessel inflammation disorders
• Autoimmune Blood Disorders: Complications affecting red blood cells, white blood cells, or platelets
• Neurologic Immune Complications: Nervous system involvement including inflammation of nerves or the brain
• Post-Viral Fatigue and Dysautonomia: Persistent exhaustion and autonomic nervous system dysfunction lasting weeks or months after infection

Importantly, outbreaks can affect both people already diagnosed with autoimmune disease and those who have not yet developed symptoms but carry genetic susceptibility.

Why Don't Vaccines Protect Autoimmune Patients the Same Way?

Many autoimmune conditions are treated with medications that suppress immune activity to prevent the body from attacking its own tissues. These include corticosteroids, methotrexate, azathioprine, mycophenolate, biologic therapies, JAK inhibitors, and B-cell-depleting medications such as rituximab. Because these therapies directly affect the immune cells responsible for establishing long-term protection, vaccination does not always produce the same level of immunity seen in healthy individuals.

Autoimmune patients who receive vaccines may experience several limitations:

• Reduced Antibody Production: Their immune systems produce fewer protective antibodies in response to vaccination
• Shorter Duration of Protection: Any protection they do develop may fade more quickly than expected
• Partial Immunity: They may remain only partially protected even after completing a full vaccine series
• Vaccine Restrictions: Certain vaccines, particularly live attenuated vaccines like the measles, mumps, and rubella vaccine, may not be safely recommended during significant immunosuppression

This creates a critical difference during outbreaks. A vaccinated healthy person is usually well protected, while a vaccinated immunosuppressed person may still be vulnerable to infection. For this reason, community immunity functions as an additional layer of medical protection for autoimmune patients.

How Do Outbreaks Change Medical Treatment Plans?

When highly contagious infections are spreading locally, physicians often must delay or postpone intensification of immunosuppressive therapy. Medications such as rituximab or cyclophosphamide may be held back to avoid leaving a patient severely immunocompromised during periods of high exposure risk. As a result, outbreaks can influence disease management and sometimes prolong active disease in patients who would otherwise benefit from stronger immune suppression.

Measles presents a particularly concerning scenario. Unlike most respiratory viruses, measles infects memory B cells and T cells—the immune cells that store protection from past infections and vaccines. After measles infection, the immune system may lose part of this stored protection, a process sometimes called immune amnesia. This can increase susceptibility to other infections for months after the initial illness. For individuals with altered immune regulation, consequences may include higher rates of secondary infections, reactivation of dormant infections, prolonged recovery periods, and increased need for hospitalization after the acute illness.

These patients rely primarily on low levels of circulating virus in the community for protection. When outbreaks occur, that layer of protection is reduced, leaving them exposed to infections their compromised immune systems cannot adequately fight.

What Does This Mean for Autoimmune Patients Right Now?

Recent global events underscore the importance of this issue. In 2026, polio was detected again in Malawi, prompting vaccination campaigns for more than a million children. The World Health Organization approved a newer oral polio vaccine designed to stop outbreaks more quickly. Meanwhile, in the United States, some policymakers seek to repeal school vaccination mandates originally implemented to limit community spread of contagious diseases. At the same time, federal regulators declined to review an application for a new messenger RNA (mRNA) influenza vaccine despite completed trials and no identified safety or efficacy concerns.

For many people, these policy decisions and regulatory choices change little about daily life. For autoimmune patients, however, they determine whether vaccination is effective, whether treatment can continue safely, and whether routine activities pose an infection risk. For this group, infectious disease prevention is not just precaution—it is required for their medical safety.