The 4 Hidden Viruses Triggering Your Chronic Fatigue + Autoimmune Problems


I see it all the time from people from all different backgrounds and places, in my telehealth functional medicine clinic. They tell me they can’t understand why one day they woke up feeling like “a train hit them,” no matter how much they slept. They are exhausted, craving caffeine and sugar foods just to get through the day. But what many people deem as “normal” and “just a part of getting older” often has to do with something else entirely: underlying viral infections. 

These hidden viruses tend to be the missing link to your health problems because they can wreak havoc on your health months or even years after the initial infection. And since they can trigger a variety of health problems, they can be difficult to identify and eradicate from your system unless you know exactly what you’re looking for. That’s why it is my job to help educate you on these hidden viruses so you can reclaim your health. So let’s dive into the four viruses I see most often, their symptoms, and exactly what you can do to start healing.


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What are viral infections?

Viral infections can range from the common cold to HIV and hepatitis. But in the case of viral infections that impact your long-term health, I am not necessarily talking about acute viral infections like the flu (influenza virus) - although it could be the case as everyone’s biochemistry is unique. What I am speaking about are certain chronic viral infections that are long standing and take up residence in your body.

The viral infections that I see most are actually part of the same family: The herpes family. When most people hear the word herpes they think of the sexually transmitted disease (STD) or cold sores. There are actually eight identified members of the human herpes virus family so far, though many in the integrative health world consider there to be more varieties. This is also the group of viruses that cause chickenpox and shingles! Herpes is one rough family.

The four members of the herpes family that I see being an underlying trigger with seemingly unrelated health problems are:

  • Varicella zoster virus (VZV) /Human Herpes Virus (HHV)-3
  • Epstein-Barr virus (EBV)/ HHV- 4
  • Cytomegalovirus (CMV)/HHV-5
  • Human herpes virus type 6 (HHV-6)

The viral-fatigue connection

EBV is one of the biggest contributors and the one I see the most in my clinic. In fact, a small-scale study (1) published in the medical journal PLoS One explored the link between antibodies against Epstein-Barr and chronic fatigue syndrome. Another 2015 Polish study (2) looked at the ability of EBV to “hide” in the thyroid and, once reactivated, stimulate the immune system to attack the thyroid, triggering autoimmune thyroid problems or Hashimoto’s disease, which is another common cause of fatigue. For a complete deep dive into EBV, read my article here.

Almost all of us have one or more of these viruses in our bodies, so the variable is not IF we have it, but will it be triggered and when? The name herpes comes from the Greek word ‘herpein’ or ‘to creep’ and that’s exactly what these viral infections do. They can stay dormant for years until an opportunity to strike occurs. A stressful time in your life, leaky gut syndrome, candida overgrowth, adrenal fatigue, or Lyme disease can all be the perfect time for the sleeping, latent viral infection to rise up, reactivate, and wreak havoc throughout your body.

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What health problems are caused by viral infections?

Since the symptoms of viral infections can mimic so many other health problems, researchers are still learning exactly how these infections can impact your health. However, these are some of the main health problems that have been clinically linked to underlying viral infections.

Brain problems

1. Depression and mood disorders

Depression and other brain health problems are on the rise worldwide. Multiple studies (3) including one in 2023 found an association (4) between mood disorders like depression and bipolar disorder and suicide rates with CMV, although we still don’t understand exactly the mechanism of how it does so. Similar studies have linked Epstein-Barr virus (5) with forms of anxiety such as panic attacks and attachment disorders. The virus is also implicated in Lyme disease.

2. Chronic fatigue

Epstein-Barr is the cause of “Mono” (mononucleosis) which causes extreme exhaustion, but it doesn’t stop there. Up to 2.5 million Americans (6) have Chronic fatigue syndrome (CFS). These viruses have also been implicated (7) in this debilitating condition.

Autoimmune conditions

1. Autoimmune thyroid problems

The most common cause of low thyroid dysfunction in the west is autoimmune reactivity against the thyroid - specifically Hashimoto’s disease or autoimmune thyroiditis. Hashimoto’s is also the most common autoimmune disease in the world. One 2015 study hypothesized (8) that latent EBV hides in the thyroid tissue, and once reactivated, stimulates the immune system to attack the thyroid. As a result, Epstein-Barr virus and thyroid are closely linked.

To read more about how to overcome thyroid problems, click here

2. Systemic lupus erythematosus (SLE)

A Journal of Clinical Rheumatology study (9) found that CMV was a possible trigger for Lupus.

3. Inflammatory Bowel Disorders (IBD)

A study (10) out of the Scandinavian Journal of Gastroenterology actually found that the higher the level of HHV-6 and CMV that was found in an individual, the higher the severity of Inflammatory Bowel Disorders such as ulcerative colitis and Crohn’s disease.

4. Multiple Sclerosis (MS)

This neurological autoimmune disease affects 2.5 million people worldwide, and millions more have unexplained neurological autoimmune reactivity. EBV is clearly seen in the medical literature as a potential trigger to MS. In fact, according to the Journal of Infectious Diseases, a shingles outbreak can nearly quadruple the risk (11) of MS!

5. Guillain-Barré syndrome (GBS)

Another neurological autoimmune disease is Guillain-Barré syndrome. A 2021 study (12) published in the Iran Journal Of Child Neurology found that CMV is one of the most prominent viral triggers for GBS. Underlying Herpes zoster (shingles) can also be the culprit for other cases of unexplained nerve pain (neuropathy).

6. Alzheimer’s disease (AD)

Researchers have also looked (13) at the viral connection with yet another autoimmune-inflammatory neurological disease, Alzheimer’s, and found that there was an increased risk for Alzheimer’s disease with CMV.

Functional Medicine Tools To Boost Your Immune System

If you suspect you have an underlying viral infection here are my top tips to reboot your immune system and start the healing process:

1. Get viral labs

I suggest getting a full viral screen to see if you have these or other unexplained health problems. Labs are able to tell if there is an active or past infection.

2. Support methylation

Methylation is a process that acts like a big biochemical superhighway, and facilitating a healthy immune system is one of its major functions. Studies have shown that EBV messes up methylation, (14) so those of us who have genetic changes such as MTHFR mutations and other methylation impairments can’t necessarily handle as much dysfunction in this area as someone whose methylation is normally unimpaired.

Support methylation with activated B vitamin supplements and foods rich in B vitamins such as green leafy vegetables, onions, garlic, and grass-fed beef and liver.

Read More: Everything You Need To Know About HLA Gene Variants + Their Connection to Mold, Lyme, and Chronic Fatigue

3. Take high quality fish oil

Research shows that the healthy fats (15) EPA and DHA from fish oil decrease the chances of EBV being reactivated.

4. Increase vitamin D intake

A 2016 study found (16) that vitamin D was able to bring down Epstein-Barr antibodies in patients with the autoimmune disease multiple sclerosis. Make sure to have your vitamin D levels tested to determine dosage, and shoot for the optimal range of 60 to 80.

5. Supplement with the herb astragalus

This root herb is used in traditional Chinese medicine (17) to fight off viral infections.

6. Heal your gut

You can’t talk about the immune system without covering the area where the majority of your immune system resides: your microbiome. A study published in the Journal of Nuclear Medicine found (18) an increase in symptoms of fatigue and depression coinciding with an increase in bacterial endotoxins found in leaky gut syndrome.

I recommend having labs done to evaluate your gut health in the context of chronic fatigue. Endotoxins will raise immune labs, such as white blood cell count and inflammatory proteins such as C-reactive protein and IL-6.

7. Live your detox

Chronic exposure to mold (19) and mercury (20) and other toxins have been linked to chronic fatigue. To fight off their effects, bring more detoxing foods into your daily diet. Garlic, cilantro, parsley, spirulina, and sage are some of my favorites. You can use them in smoothies, on salads, or to flavor your meals. Try rotating these foods throughout your week for comprehensive detox support.

Read More: Worried About Mold Exposure? Here’s What You Need To Know

8. Calm stress and sleep better

Emotional suppression, psychological stress, (21) and a lack of sleep are all linked in the medical literature to a reactivation of EBV. Start and end your day with mindfulness meditations – apps such as Headspace and Calm are great tools to try.

An amino acid called theanine (22) has also been shown to improve sleep and helps you to feel rested and rejuvenated when you wake up. Low-caffeine teas like white tea or decaf green tea are great food sources for this sleepy-time medicine. I have a cup every night.

9. Test for and address nutrient deficiencies

Low levels of iron, magnesium, (23), B12, and folate can all contribute to fatigue and weaken your immune system. Get labs to check your nutrient levels. If you don’t already, focus on eating a clean diet with a wide variety of nutrient-dense whole foods such as vegetables, fruits, organic meats, and healthy fats.

10. Try olive leaf

The extract from the olive leaf has demonstrated (24) powerful antiviral and antibacterial capabilities, even in the case of COVID-19.

11. Consider ashwagandha

Research published in the Journal of Clinical Medicine found that this adaptogenic herb can increase (25) helpful immune cells and has next-level immunomodulatory effects. And since cortisol spikes (26) have been shown to also trigger a reactivation of EBV, ashwagandha is great because it has a balancing effect on this main stress hormone.

If you want to get a high-quality version of this adaptogen, check out The Ashwagandha, my curated blend.

12. Boost Vitamin C

An exciting study published in Medical Science Monitor found (27) that higher levels of vitamin C produced lower levels of EBV in people with mono and chronic fatigue syndrome. Check out this bioactive, absorbable form of Vitamin C, Brillian-C, if you're looking for a good supplement. 

13. Slay viruses with larrea tridentata

Try to say larrea tridentata three times fast! This traditional Native American medicine is the ancient antiviral medicine (28) of the desert.

Seeking help from a functional medicine expert

Navigating viral chronic fatigue can be overwhelming. Finding a qualified functional medicine practitioner to put the pieces of your health journey together can be invaluable to your health and well-being. You may need to try several different approaches before you find what works for you, but in my telehealth functional medicine clinic, my team and I work together to make make this happen more quickly and efficiently, as we look at your health case in its entirety to find holistic, long-term solutions rather than simply trying to put a bandaid over your symptoms. 

If you are struggling with unrelenting symptoms like fatigue and brain fog that you think are related to underlying viral infections, schedule a telehealth consultation today to learn more about how we can help you with functional medicine.

As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe.


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  1. Lerner, A Martin et al. “Antibody to Epstein-Barr virus deoxyuridine triphosphate nucleotidohydrolase and deoxyribonucleotide polymerase in a chronic fatigue syndrome subset.” PloS one vol. 7,11 (2012): e47891. doi:10.1371/journal.pone.0047891
  2. Janegova, Andrea et al. “The role of Epstein-Barr virus infection in the development of autoimmune thyroid diseases.” Endokrynologia Polska vol. 66,2 (2015): 132-6. doi:10.5603/EP.2015.0020
  3. Phillips, Anna C et al. “Cytomegalovirus is associated with depression and anxiety in older adults.” Brain, behavior, and immunity vol. 22,1 (2008): 52-5. doi:10.1016/j.bbi.2007.06.012
  4. Zheng, Haixia et al. “Cytomegalovirus antibodies are associated with mood disorders, suicide, markers of neuroinflammation, and microglia activation in postmortem brain samples.” Molecular psychiatry, 10.1038/s41380-023-02162-4. 30 Jun. 2023, doi:10.1038/s41380-023-02162-4
  5. Fagundes, Christopher P et al. “Attachment anxiety is related to Epstein-Barr virus latency.” Brain, behavior, and immunity vol. 41 (2014): 232-8. doi:10.1016/j.bbi.2014.04.002
  6. Myalgic Encephalomyelitis/Chronic Fatigue Syndrome CDC December 19th, 2023
  7. Wallace, H L 2nd et al. “Human herpesviruses in chronic fatigue syndrome.” Clinical and diagnostic laboratory immunology vol. 6,2 (1999): 216-23. doi:10.1128/CDLI.6.2.216-223.1999
  8. Janegova, Andrea et al. “The role of Epstein-Barr virus infection in the development of autoimmune thyroid diseases.” Endokrynologia Polska vol. 66,2 (2015): 132-6. doi:10.5603/EP.2015.0020
  9. Pérez-Mercado, Arnaldo E, and Salvador Vilá-Pérez. “Cytomegalovirus as a trigger for systemic lupus erythematosus.” Journal of clinical rheumatology : practical reports on rheumatic & musculoskeletal diseases vol. 16,7 (2010): 335-7. doi:10.1097/RHU.0b013e3181f4cf52
  10. Sipponen, Taina et al. “Human herpesvirus 6 and cytomegalovirus in ileocolonic mucosa in inflammatory bowel disease.” Scandinavian journal of gastroenterology vol. 46,11 (2011): 1324-33. doi:10.3109/00365521.2011.605466
  11. Jiunn-Horng Kang, Jau-Jiuan Sheu, Senyeong Kao, Herng-Ching Lin, Increased Risk of Multiple Sclerosis Following Herpes Zoster: A Nationwide, Population-Based Study, The Journal of Infectious Diseases, Volume 204, Issue 2, 15 July 2011, Pages 188–192,
  12. Mamishi, Setareh et al. “Cytomegalovirus Infection and Guillain-Barré Syndrome: The First Case-Control Study in Iran.” Iranian journal of child neurology vol. 15,4 (2021): 35-41. doi:10.22037/ijcn.v15i4.31285
  13. Barnes, Lisa L et al. “Cytomegalovirus infection and risk of Alzheimer disease in older black and white individuals.” The Journal of infectious diseases vol. 211,2 (2015): 230-7. doi:10.1093/infdis/jiu437
  14. Caliskan, Minal et al. “The effects of EBV transformation on gene expression levels and methylation profiles.” Human molecular genetics vol. 20,8 (2011): 1643-52. doi:10.1093/hmg/ddr041
  15. Akihisa, Toshihiro et al. “Cancer chemopreventive effects of polyunsaturated fatty acids.” Cancer letters vol. 205,1 (2004): 9-13. doi:10.1016/S0304-3835(03)00284-2
  16. Røsjø, Egil et al. “Effect of high-dose vitamin D3 supplementation on antibody responses against Epstein-Barr virus in relapsing-remitting multiple sclerosis.” Multiple sclerosis (Houndmills, Basingstoke, England) vol. 23,3 (2017): 395-402. doi:10.1177/1352458516654310
  17. Du, Xiaogang et al. “Astragalus polysaccharides enhance the humoral and cellular immune responses of hepatitis B surface antigen vaccination through inhibiting the expression of transforming growth factor β and the frequency of regulatory T cells.” FEMS immunology and medical microbiology vol. 63,2 (2011): 228-35. doi:10.1111/j.1574-695X.2011.00845.x
  18. Hannestad, Jonas et al. “Glucose metabolism in the insula and cingulate is affected by systemic inflammation in humans.” Journal of nuclear medicine : official publication, Society of Nuclear Medicine vol. 53,4 (2012): 601-7. doi:10.2967/jnumed.111.097014
  19. Brewer, Joseph H et al. “Detection of mycotoxins in patients with chronic fatigue syndrome.” Toxins vol. 5,4 605-17. 11 Apr. 2013, doi:10.3390/toxins5040605
  20. Shin, Sae-Ron, and A-Lum Han. “Improved chronic fatigue symptoms after removal of mercury in patient with increased mercury concentration in hair toxic mineral assay: a case.” Korean journal of family medicine vol. 33,5 (2012): 320-5. doi:10.4082/kjfm.2012.33.5.320
  21. Sausen, Daniel G et al. “Stress-Induced Epstein-Barr Virus Reactivation.” Biomolecules vol. 11,9 1380. 18 Sep. 2021, doi:10.3390/biom11091380
  22. Vuong, Quan V et al. “L-Theanine: properties, synthesis and isolation from tea.” Journal of the science of food and agriculture vol. 91,11 (2011): 1931-9. doi:10.1002/jsfa.4373
  23. Chaigne-Delalande, Benjamin et al. “Mg2+ regulates cytotoxic functions of NK and CD8 T cells in chronic EBV infection through NKG2D.” Science (New York, N.Y.) vol. 341,6142 (2013): 186-91. doi:10.1126/science.1240094
  24. Ahmadpour, Elham et al. “Efficacy of olive leaves extract on the outcomes of hospitalized covid-19 patients: A randomized, triple-blinded clinical trial.” Explore (New York, N.Y.) vol. 19,4 (2023): 536-543. doi:10.1016/j.explore.2022.10.020
  25. Tharakan, Ajit et al. “Immunomodulatory Effect of Withania somnifera (Ashwagandha) Extract-A Randomized, Double-Blind, Placebo Controlled Trial with an Open Label Extension on Healthy Participants.” Journal of clinical medicine vol. 10,16 3644. 18 Aug. 2021, doi:10.3390/jcm10163644
  26. Quaia, M et al. “Glucocorticoids promote the proliferation and antagonize the retinoic acid-mediated growth suppression of Epstein-Barr virus-immortalized B lymphocytes.” Blood vol. 96,2 (2000): 711-8.
  27. Mikirova, Nina, and Ronald Hunninghake. “Effect of high dose vitamin C on Epstein-Barr viral infection.” Medical science monitor : international medical journal of experimental and clinical research vol. 20 725-32. 3 May. 2014, doi:10.12659/MSM.890423
  28. Reyes-Melo, Karen Y et al. “Larrea tridentata and its Biological Activities.” Current topics in medicinal chemistry vol. 21,26 (2021): 2352-2364. doi:10.2174/1568026621666210727170908

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Dr. Will Cole, DNM, IFMCP, DC is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is the host of the popular The Art Of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian, The Inflammation Spectrum, and Gut Feelings: Healing the Shame-Fueled Relationship Between What You Eat and How You Feel.

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Gut Feelings

Healing The Shame-Fueled Relationship
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