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Hashimoto’s thyroiditis is the most common autoimmune thyroid condition in the world, and it hits women the hardest. Most people know that genetics, diet, and toxins can play a role in developing the disease. But here’s a lesser-known twist: viruses might be a hidden culprit, too. New research is shining a light on how certain viral infections can kickstart or worsen Hashimoto’s. The good news? Knowing about this viral connection opens up more ways—both conventional and holistic—to protect your thyroid and stay ahead of the disease.

At its core, Hashimoto’s is a case of mistaken identity: the immune system, which is designed to defend the body against invaders like bacteria and viruses, turns against the thyroid — a small, butterfly-shaped gland at the base of the neck that regulates metabolism, energy levels, and many other vital functions. This self-directed immune attack leads to chronic inflammation, which gradually impairs the thyroid’s ability to produce hormones efficiently, and usually results in hypothyroidism – an underactive thyroid.

The symptoms of Hashimoto’s often unfold slowly over months or even years, which can make the condition difficult to recognize at first. Fatigue is one of the earliest and most common complaints, often accompanied by subtle signs like weight gain despite no changes in diet, persistent constipation, brain fog, and increasingly dry skin. As thyroid hormone levels continue to decline, more noticeable effects like depression, hair thinning, slowed heart rate, and heightened sensitivity to cold may emerge. These symptoms can easily be mistaken for stress, aging, or other health issues, delaying diagnosis and treatment.

The underlying cause of Hashimoto’s is not fully understood, but researchers agree it’s multifactorial — a complex puzzle involving both inherited and environmental factors. People with a family history of thyroid disorders or other autoimmune diseases are at greater risk, suggesting a strong genetic component. But genetics alone doesn’t determine who develops Hashimoto’s. Environmental triggers such as stress, exposure to toxins, dietary factors (like excessive iodine or gluten sensitivity), and infections appear to play critical roles in “flipping the switch” that activates the autoimmune process.

One particularly intriguing and increasingly studied trigger for Hashimoto’s is viral infection, and experts now understand that certain viruses can trigger or worsen autoimmunity, including Hashimoto’s, in people with certain genetic or autoimmune tendencies. There are two ways that viruses can trigger Hashimoto’s:

Molecular mimicry and immune system confusion

Your immune system is designed to protect you from harmful invaders like viruses. But sometimes, after fighting off a viral infection, your immune system gets confused, and that’s when trouble can start. In the case of Hashimoto’s thyroiditis, here’s how it can happen:

1. A virus invades: You catch a virus, and your immune system kicks into gear to fight it off, launching a strong defense.
2. Friendly fire: Sometimes, parts of a virus can look similar to proteins found in your body, specifically, your thyroid gland. This is called “molecular mimicry.” Your immune system may accidentally mistake your thyroid cells for the virus.
3. Autoimmune response begins: Once your immune system is tricked, it starts attacking your thyroid tissue, thinking it’s an invader. This leads to inflammation and damage over time.
4. Hashimoto’s develops: Eventually, this attack on your thyroid becomes a chronic autoimmune disease. Your thyroid may not be able to keep up with hormone production, leading to hypothyroidism. This is when symptoms like fatigue, weight gain, depression, and hair loss can show up.
5. Ongoing triggers: Even after the initial virus is gone, your immune system may stay on high alert, continuing to target your thyroid. Other stressors, like more infections, gut issues, or hormonal shifts, can keep the autoimmune attack going.

Direct invasion of thyroid cells

Sometimes, it’s not just a case of mistaken identity. Some viruses don’t just confuse your immune system—they actually invade your thyroid cells directly. Here’s how that works.

1. Viruses enter thyroid cells: Certain viruses can enter your thyroid cells. Once inside, they take over the cell’s machinery to make more copies of themselves, just like they would in your lungs, liver, or other tissues.
2. Infection leads to inflammation: Your body notices something’s wrong. It sends immune cells to fight the infection inside the thyroid gland. This creates inflammation, which is your body’s natural way of fighting off invaders.
3. Inflammation = damage: That inflammation may help kill the virus, but also damages the thyroid tissue in the process. You might think of it like fighting a fire by flooding a house—the fire’s out, but the house is still damaged.
4. Autoimmunity is triggered: This damage can expose hidden parts of the thyroid that your immune system has never seen before. Your body may start treating those parts as foreign and begin an autoimmune response that doesn’t stop even after the virus is gone.
5. Hashimoto’s develops: Once your immune system is in attack mode, it may continue targeting your thyroid over time, causing more inflammation, scarring, and reduced hormone production. This is how Hashimoto’s thyroiditis can begin—and lead to hypothyroidism.

If you have Hashimoto’s thyroiditis, getting a viral infection after your diagnosis can also make your Hashimoto’s symptoms flare up or worsen, and even speed up the progression of the disease. Here’s how viruses can affect your Hashimoto’s:

• Old viruses can “wake up”: Viruses that are dormant after an initial infection and hiding in cells can become active again and resume replication. These dormant viruses can become reactivated due to physical or emotional stressors, hormonal changes 13, chemotherapy, or chronic inflammation.

• Your immune system can go off balance: Viral infections or reactivations can cause your body to release more inflammatory chemicals, which may ramp up your immune system and make it attack your thyroid more aggressively.
• More stress on your cells: Viruses can increase oxidative stress — a kind of damage to your cells, which can harm thyroid tissue and trigger stronger immune responses.

Recent research suggests that viral infections may play a significant role in triggering or exacerbating Hashimoto’s thyroiditis, particularly in people with a genetic predisposition. A 2022 study analyzing 53 thyroid biopsies found that 75% contained viral components, with 32% showing co-infections by two or more viruses. These findings indicate that a high viral “burden” could overwhelm the immune system and contribute to the onset or worsening of Hashimoto’s. Some of the viruses that are related to Hashimoto’s include the following:

Influenza virus: The influenza virus is considered a possible trigger for Hashimoto’s, as respiratory viruses can induce thyroid inflammation and immune dysregulation.

Epstein-Barr virus infection (EBV): EBV is a widespread herpesvirus infecting over 90% of the global population and is the cause of mononucleosis. EBV can remain dormant in cells and reactivate during periods of stress or illness. In people predisposed to Hashimoto’s, EBV antigens have been detected in thyroid tissue, suggesting a link between viral reactivation and autoimmune thyroid flares. EBV reactivation may also correlate with higher levels of anti-thyroglobulin antibodies.

Hepatitis C Virus (HCV): HCV infection is strongly associated with autoimmune thyroid disorders, including Hashimoto’s. The virus stimulates immune system activation and increases inflammatory cytokine production. Notably, interferon therapy for HCV has been shown to trigger or worsen thyroid autoimmunity in susceptible individuals.

Cytomegalovirus (CMV) and human herpesvirus 6 (HHV-6): Both CMV and HHV-6 can infect thyroid tissue and persist in a latent state. Reactivation of these viruses may disrupt immune balance and contribute to autoimmune flares. HHV-6, in particular, has been found in 82% of Hashimoto’s thyroid biopsies (compared to only 10% in controls), with evidence of active replication in thyroid cells. However, while the presence of these herpesviruses in thyroid tissue is well-documented, a direct causal relationship with Hashimoto’s remains unproven.

Parvovirus B19 and enteroviruses: Parvovirus B19 DNA has been detected in about 22% of Hashimoto’s thyroid samples, and it may provoke cytotoxic T-cell responses leading to thyroid inflammation. Enteroviruses have been found in 51% of thyroid tissues from Hashimoto’s patients. They are linked to the production of thyroid peroxidase antibodies, suggesting a role in persistent, low-grade infection and immune activation.

‍COVID-19 infection has been linked to the onset and worsening of Hashimoto’s thyroiditis, an autoimmune disease affecting the thyroid. Here’s what current studies and case reports reveal:

• Cases of new-onset or flare-ups of Hashimoto’s thyroiditis have been reported following COVID-19 infection, typically appearing 7 to 90 days after recovering from the virus.
• COVID-19 survivors are twice as likely to develop thyroid peroxidase (TPO) antibodies, a marker of autoimmune thyroid disease, compared to people who never had COVID-19 (15.7% vs. 7.7%).
• Some studies suggest that the overall prevalence of autoimmune thyroid disease has doubled in the population following the COVID-19 pandemic.

How COVID-19 may trigger Hashimoto’s

There are several ways that COVID-19 may be triggering Hashimoto’s. 

• Direct viral impact: SARS-CoV-2, the virus behind COVID-19, can bind to receptors found on thyroid cells. Evidence of the virus has been detected in thyroid tissue during autopsies of COVID-19 patients, suggesting the virus may directly infect the gland.
• Immune system overdrive: The “cytokine storm” and heightened immune activation caused by COVID-19 may trigger or worsen autoimmune attacks on the thyroid.
• Molecular mimicry: The virus shares certain molecular similarities with thyroid proteins like thyroid peroxidase. This similarity may cause the immune system to produce cross-reactive antibodies that mistakenly attack thyroid tissue.

Conventional strategies to manage virus-triggered Hashimoto’s thyroiditis focus on stabilizing thyroid hormone levels and reducing immune system overactivity. While these approaches do not directly target the underlying viral trigger, they aim to control the resulting autoimmune response and alleviate symptoms.

Regular monitoring of thyroid function

Frequent thyroid testing is essential after any significant viral illness. The Paloma Complete Thyroid Test Kit offers a comprehensive and convenient way to assess thyroid health from home by measuring not only TSH but also free T3, free T4, and TPO antibodies, biomarkers often overlooked in standard blood tests. This broader panel helps detect overt and subtle thyroid dysfunctions, including autoimmune thyroid disease like Hashimoto’s, providing you with a complete understanding of your thyroid status. The kit is easy to use with a finger-prick sample, results are processed in CLIA-certified labs, and users receive personalized, physician-reviewed reports with the option for expert consultation and treatment from Paloma’s health care providers, making it especially valuable for those of you seeking accessible, thorough, and ongoing thyroid monitoring.

Thyroid hormone replacement treatment

Thyroid hormone replacement is the cornerstone of treatment for viral-triggered Hashimoto’s thyroiditis, especially once the autoimmune attack has led to significant thyroid damage and hypothyroidism. This medication helps restore normal metabolic function and can alleviate many of the symptoms caused by an underactive thyroid. While hormone replacement does not directly address the viral trigger or immune dysregulation, it is essential to maintain physiological balance and prevent further complications. Regular monitoring is vital to ensure proper dosage and to adjust treatment as the autoimmune process evolves.

Antiviral medications (in select cases)

Antiviral drugs may be considered for acute or chronic viral infections, but there is no substantial evidence that they prevent or reverse Hashimoto’s. In some cases, antiviral drugs (especially interferon for HCV) can actually worsen autoimmune thyroid disease9.

Influenza: Conventional antivirals for influenza include oseltamivir (Tamiflu) and zanamivir (Relenza), which are used to treat acute influenza infection. There’s no evidence that these antivirals are directly protective of the thyroid. 

EBV: There is no standard curative antiviral treatment. In certain chronic or severe cases, long-term valacyclovir (Valtrex) may be used to suppress reactivation, but this is not standard, and evidence for benefit in Hashimoto’s is limited.

HCV: The mainstay of treatment is direct-acting antiviral (DAA) tablets, which are highly effective and safe. DAAs include combinations such as ledipasvir/sofosbuvir (Harvoni), elbasvir/grazoprevir (Zepatier), sofosbuvir/velpatasvir (Epclusa), sofosbuvir/velpatasvir/voxilaprevir (Vosevi), and glecaprevir/pibrentasvir (Mavyret). These regimens target various steps in the HCV replication cycle and can cure over 90% of cases in 8–12 weeks. These therapies are not likely to trigger or worsen Hashimoto’s, but older interferon-based therapies are not recommended for Hashimoto’s patients. 

CMV and HHV-6: Antivirals such as ganciclovir (Cytovene) and valganciclovir (Valcyte) are used, primarily in severe or immunocompromised cases. Some studies have shown that valganciclovir can reduce the thyroid viral load in some patients. 

Parvovirus B19: There is no specific antiviral treatment. In severe cases, intravenous immunoglobulin (IVIG) may be considered. While IVIG is not a standard treatment for typical Hashimoto’s thyroiditis, it has the potential to improve the course of more severe Hashimoto’s.

Enteroviruses: No specific antiviral is widely available. Supportive care is the usual approach.

COVID-19: Antivirals such as nirmatrelvir/ritonavir (Paxlovid) and remdesivir are used for acute treatment in certain high-risk patients.

Vaccination

Vaccines against influenza, COVID-19, and other viral infections can help prevent the triggering of autoimmune flares. Many studies have shown that COVID-19 vaccines are generally safe for people with Hashimoto’s and may reduce the risk of post-COVID thyroid complications.

Holistic and integrative strategies are gaining attention as complementary ways to protect thyroid health, especially in the context of viral activity and autoimmune thyroid disease. While conventional medicine remains the foundation of thyroid care, evidence-based lifestyle and nutritional interventions can offer additional support.

Nutritional support 

Several nutrients play pivotal roles in both immune defense and thyroid hormone balance:

• Selenium: Essential for thyroid hormone metabolism and may help lower thyroid peroxidase (TPO) antibody levels, particularly in autoimmune thyroid disease like Hashimoto’s. Supplementation can benefit those with low selenium status, but should be guided by a healthcare provider to avoid excess.
• Zinc: Supports T cell function and the conversion of T4 to the active T3 hormone. Zinc deficiency can impair both immune and thyroid function.
• Vitamin D: Modulates immune responses and may reduce the production of thyroid autoantibodies. Maintaining optimal vitamin D levels is associated with better immune regulation.
• Vitamins C and E: Provide antioxidant protection, which is especially valuable during viral illnesses that may stress the thyroid.
• Vitamin B12: Often low in hypothyroid individuals, B12 supplementation can help manage fatigue and support nerve health.
• L-lysine: May suppress the replication of certain viruses, such as Epstein-Barr virus (EBV), which has been linked to thyroid autoimmunity (though more research is needed).

A note about iodine: Excess iodine intake can accelerate thyroid antibody production and worsen autoimmune thyroiditis. Supplement only if you are iodine-deficient, and avoid high-iodine diets unless advised by a healthcare provider.

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Herbals/botanicals 

Certain botanicals have long been valued for their potential to support the body’s defenses against viral infections. These plant-based remedies—such as olive leaf, astragalus, cat’s claw, and elderberry—are renowned in traditional medicine for their broad-spectrum antiviral and immune-modulating properties. They may work by enhancing the body’s natural antiviral response, inhibiting viral replication, or supporting overall immune resilience. As interest in natural approaches to immune health grows, these botanicals have gained popularity as supportive tools during times of illness or increased exposure to viruses.

Olive leaf extract, for instance, contains a compound called oleuropein, which has demonstrated antiviral activity in laboratory studies. It disrupts viral entry into cells and interferes with viral replication. Astragalus, a staple of Traditional Chinese Medicine, is known for its immune-boosting qualities and is often used to help the body adapt to stress and enhance resistance to illness. Cat’s claw, a vine native to the Amazon rainforest, is believed to possess antiviral and anti-inflammatory properties. Elderberry is commonly used to reduce the duration and severity of cold and flu symptoms due to its rich content of flavonoids and anthocyanins.

However, despite their promising benefits, these herbs must be used with care, especially by individuals with autoimmune conditions like Hashimoto’s thyroiditis. While some botanicals may help regulate the immune system, others can stimulate immune activity in ways that may inadvertently trigger a flare. For example, herbs like astragalus and cat’s claw are considered immune-stimulants and might provoke an exaggerated immune response in sensitive individuals. This is especially important to consider in autoimmune thyroid disease, where immune dysregulation is already at play.

For those managing Hashimoto’s, it’s wise to approach immune-supportive herbs cautiously and under the guidance of a knowledgeable healthcare provider. A personalized approach—taking into account individual reactivity, disease activity, and coexisting health concerns—is essential when integrating botanicals into a wellness regimen. What works for one person may not be suitable for another, highlighting the need for careful experimentation and professional supervision.

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Gut health and the microbiome

A healthy gut microbiome supports immune regulation and may help reduce inappropriate autoimmunity:

• Probiotics and prebiotic fiber: Supplementation has shown benefits in thyroid function and fatigue reduction in clinical trials, especially for those on thyroid medication.
• Fermented foods: Including yogurt, kefir, and sauerkraut can help maintain gut resilience, particularly after illness or antibiotic use.

Stress, sleep, and toxin reduction

• Mind-body practices: Yoga and meditation can reduce stress hormones and may improve thyroid function. For example, yoga has been shown to lower TSH levels in Hashimoto’s thyroiditis.
• Sleep optimization: Prioritizing 7–9 hours of sleep nightly supports immune repair and reduces inflammatory markers.
• Toxin reduction: Avoiding endocrine disruptors like BPA is associated with lower thyroid antibody levels.
• Chronic stress: Managing stress is crucial, as it impairs immunity and increases susceptibility to both infections and autoimmune flares.

Post-viral recovery

After viral illnesses, you should also allow time for immune recalibration:

• Return to activity gradually: Avoid overexertion to prevent setbacks.
• Support your mitochondria: Nutrients like CoQ10, magnesium, and B vitamins may help restore energy and cellular resilience.
• Monitor symptoms: Watch for new or worsening thyroid symptoms in the weeks following recovery and consult your healthcare provider as needed.

In our modern, hyperconnected world, exposure to viruses is nearly impossible to avoid. And for those with autoimmune Hashimoto’s, this reality carries added weight. Mounting research shows that viruses may not only trigger the onset of Hashimoto’s but also worsen existing disease. Viral infections can ignite immune system misfires, leading to thyroid tissue damage, hormone imbalances, and debilitating flares.

The good news? You’re not powerless. While we can’t seal ourselves off from every viral invader, we can strengthen our defenses and protect thyroid function. It starts with building a resilient immune foundation, not through quick fixes but sustainable strategies. Prioritize sleep, eat nutrient-dense, anti-inflammatory foods, and support your gut health, which houses over 70% of your immune system. These steps lay the groundwork for a balanced immune response that’s less likely to overreact or turn inward against the thyroid or result in autoimmune disease.

Smart supplementation is also key. Nutrients like selenium, zinc, and vitamin D have antiviral properties and support thyroid hormone metabolism and immune regulation. Botanical antivirals may provide gentle, ongoing support for those prone to viral reactivation — such as individuals with EBV. And don’t underestimate the role of stress: chronic stress weakens immune resilience and can flare autoimmunity. Mind-body practices like breathwork, yoga, and meditation aren’t luxuries — they’re thyroid-saving tools.

You will also want to be watchful after viral infections for any signs of new or worsening Hashimoto’s. Vigilance post-infection could enable earlier intervention.

Finally, staying proactive with regular lab monitoring allows you to spot changes early. If a viral infection hits, addressing it promptly with rest, hydration, antiviral nutrients, and physician-guided care can reduce the likelihood of a thyroid flare-up. In an era where new viruses can emerge quickly and stealthily, protecting your thyroid is about preparation, not panic. With thoughtful care and consistent habits, you can create a buffer between viral threats and thyroid damage — and reclaim a sense of control in an unpredictable world.

Because each case of Hashimoto’s is unique, people benefit most from a personalized approach that integrates conventional medicine with holistic care. That’s where Paloma Health stands out. As a virtual medical practice specializing in hypothyroidism and Hashimoto’s, Paloma Health offers comprehensive, evidence-based care tailored to your unique needs. Their team of board-certified doctors, nutritionists, and health coaches understands the complex triggers of autoimmunity, including the often-overlooked connection between viral infections and Hashimoto’s. By working with practitioners who recognize these links, you can create a long-term thyroid protection plan that addresses root causes, reduces flare-ups, and supports your overall well-being.

Viral infections may act as hidden triggers for Hashimoto’s thyroiditis through immune confusion or direct thyroid invasion.

• Mechanisms include molecular mimicry and viral-induced inflammation, which can start or perpetuate thyroid autoimmunity.
• Common symptoms of Hashimoto’s include fatigue, weight gain, constipation, and depression, often developing gradually.
• Viruses implicated include EBV, HCV, CMV, HHV-6, influenza, parvovirus B19, enteroviruses, and SARS-CoV-2 (COVID-19).
• COVID-19 has been linked to new-onset and worsened Hashimoto’s, possibly due to immune overactivation and molecular mimicry.
• Management includes regular thyroid testing, antiviral treatments in select cases, vaccination, holistic approaches, and individualized care to support a healthy immune system and thyroid health.