Autoimmune Disease and Vaccine-Preventable Disease Outbreaks
In 2026, vaccines are back in the headlines worldwide.
Infectious diseases do not disappear all at once. They fade when enough people remain protected, and they return when protection drops.
Several recent events show this process happening in real time.
In Malawi, health workers began vaccinating more than a million children after polio was detected again. The virus is close to global eradication, but it can reappear when immunity gaps develop. The World Health Organization (WHO) recently approved a newer oral polio vaccine designed to stop outbreaks more quickly and raised concerns about a proposed study that would delay a proven hepatitis B birth-dose vaccine for some newborns, noting that the vaccine prevents serious liver disease later in life.
In the United States, some policymakers seek to repeal school vaccination mandates originally implemented to limit the community spread of contagious diseases. At the same time, federal regulators recently declined to review an application for a new mRNA influenza vaccine despite completed trials and no identified safety or efficacy concerns, raising questions about future vaccine availability.*
*update available about this decision, read more here
These events are often discussed in terms of policy decisions or public debate. Medically, they describe something simpler: how much virus is likely to circulate in daily life.
For many people, that changes little. For others, it determines whether vaccination is effective, whether treatment can continue safely, and whether routine activities pose an infection risk.
Not everyone relies on vaccines in the same way.
People living with autoimmune disease and other immune-related chronic illnesses are part of this second group. Their safety depends not only on their own immune system, but also on how much infection is circulating around them. The effects appear in several predictable ways.
To learn more about navigating infection risk while immunocompromised, read A Guide for Immunocompromised Individuals in a Post-Pandemic World.
Infections Can Trigger Autoimmune Activity
Immune responses meant to eliminate pathogens can also activate pathways involved in autoimmune disease. Researchers have identified several mechanisms, including molecular mimicry, bystander activation, epitope spreading, and interferon signaling.
After outbreaks, clinicians often observe increases in:
- worsening inflammatory arthritis
- lupus and vasculitis flares
- autoimmune blood disorders
- neurologic immune complications
- post-viral fatigue and dysautonomia
Outbreaks may therefore affect both people already diagnosed and those who have not yet developed symptoms.
Outbreaks Can Change Treatment Decisions
When highly contagious infections are spreading locally, physicians may delay initiation or intensification of immunosuppressive therapy. Medications such as rituximab or cyclophosphamide may be postponed to avoid leaving a patient severely immunocompromised during exposure risk.
As a result, outbreaks can influence disease management and sometimes prolong active disease.
Measles Can Weaken Existing Immune Protection
Measles is unusual among respiratory viruses because it affects immune memory. The virus infects memory B cells and T cells, which store protection from past infections and vaccines. After recovery, 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
- increased need for hospitalization after the acute illness
Some Cannot Receive Live Vaccines
The measles, mumps, and rubella vaccine is a live attenuated vaccine. While safe for healthy individuals, it may not be recommended during significant immunosuppression.
These patients rely primarily on low levels of circulating virus in the community for protection. When outbreaks occur, that layer of protection is reduced.
Infection Risk Can Remain High Even After Vaccination
Many autoimmune conditions are treated with medications that suppress immune activity to prevent tissue damage. These include corticosteroids, methotrexate, azathioprine, mycophenolate, biologic therapies, JAK inhibitors, and B-cell–depleting medications such as rituximab.
Because these therapies affect immune cells responsible for establishing long-term protection, vaccination does not always elicit the same level of immunity observed in healthy individuals. Patients may:
- produce fewer protective antibodies
- lose protection sooner than expected
- remain only partially protected
- be unable to safely receive certain vaccines
During outbreaks, this creates an important difference. A vaccinated healthy person is usually well protected, while a vaccinated immunosuppressed person may still be vulnerable to infection.
For this group, community immunity functions as an additional layer of medical protection.