Fatigue, brain fog, shortness of breath, POTS-like symptoms, widespread inflammation… sound familiar?
Since the pandemic, more and more people have been dealing with lingering symptoms that don’t quite add up. Maybe you’ve heard the term “chronic viral syndrome” or “post-vaccine syndrome.” Whatever name it goes by, it’s exhausting, confusing, and often overlooked.
If you or someone you love is going through it, you know how frustrating it can be. Maybe doctors have brushed it off or said it’ll go away with time—but weeks or even months later, you’re still waking up in a body that doesn’t feel like yours.
At Boulder Holistic Functional Medicine in Boulder, Colorado, we approach health differently. We use a systems biology lens to understand how your body functions as a whole—i.e. what’s working, what isn’t, and the root cause of your symptoms.
And in case after case, one pattern keeps showing up: mitochondrial dysfunction.
Whether it’s from the virus itself, the spike protein, or an overactive immune response, something throws off your body’s energy production. This leads to fatigue, brain fog, and all the other symptoms that make up chronic viral or post-vaccine syndrome.
The good news? Functional medicine can help you recover. With the right plan, it’s possible to restore your energy, calm inflammation, and begin to feel like yourself again.
How Viruses and Spike Protein Impact Mitochondria
Viruses like SARS-CoV-2 cause a lot of stress in the body. They trigger systemic inflammation, activate your immune system, and do a lot of damage to your cells.
However, what many people don’t know is that stress from viruses also impacts your mitochondria.
The mitochondria are like tiny powerhouses inside each and every cell. Their job is to produce ATP (adenosine triphosphate), the energy source for all of the body’s critical functions. Thinking, breathing, digesting, healing— all require ATP.
But when you get hit by a virus like COVID, those power plants start to break down.
Over time, that stress can lead to:
- Less ATP production, which means less energy and more fatigue
- A buildup of free radicals, which increases inflammation throughout the body
- Low cellular energy, especially in the brain, which can lead to neurological symptoms like brain fog, memory issues, and trouble concentrating
To make matters worse, SARS-CoV-2 contains a spike protein which is proven to be particularly harmful to mitochondrial function. The spike protein is a structural part of the virus which helps it enter the cell— and it doesn’t just go away when the virus is gone. It causes a lingering disruption on the cellular level that leads to symptoms like chronic fatigue and brain fog often seen in long COVID.
And for some, even exposure to spike protein fragments from a vaccine can trigger a short-term inflammatory response or throw the immune system off balance—especially if there’s already underlying inflammation or a genetic predisposition.
Common Symptoms in Chronic Viral Syndrome or Post-Vaccine Syndrome
So how do you know if your symptoms are the result of chronic viral syndrome or post-vaccine syndrome? The signs are usually pretty easy to read once you know what to look for.
One or more of these symptoms is typically present if you are suffering from chronic viral syndrome or post-vaccine syndrome:
- Fatigue
- Exercise intolerance (post-exertional malaise)
- Brain fog, memory lapses, and anxiety
- Heart palpitations
- POTS/dysautonomia
- Shortness of breath, chest tightness
- Muscle weakness or pain
- Gastrointestinal dysregulation
- Menstrual irregularities and hormone imbalances
Because these symptoms affect multiple body systems, they can be difficult to treat, especially if you are treating each symptom individually. That’s where functional medicine comes in. We look at the body as a whole and treat the underlying issues, which in this case, is likely to include mitochondrial support.
Functional Testing: Data That Tells a Story
At Boulder Holistic Functional Medicine in Boulder, Colorado, we use functional testing to understand the effect the virus has had on your body. Each test reveals a piece of the puzzle and can help us to form a personalized treatment plan based on your unique needs and symptoms.
Our Recommended Tests for Post-Viral Fatigue
A few of the most valuable test for addressing chronic viral syndrome are:
NutraEval with Organic Acids Test (OAT)
This comprehensive panel looks at vitamin and mineral levels—including magnesium, B vitamins, zinc, CoQ10, and carnitine, which are all crucial for mitochondrial function.
The OAT portion measures key mitochondrial metabolites and provides insight into oxidative stress, detox pathways, and energy production. It’s one of the most useful tools we have for mapping out what’s happening at the cellular level.
Biotoxin Testing
Biotoxins like mold (mycotoxins), Lyme, and coinfections strain the immune system and mitochondria, making it harder to recover from chronic viral syndrome. Biotoxin testing helps uncover these hidden stressors so we can support detox and lighten the load.
Inflammatory markers
Labs like hsCRP, ferritin, and ESR help us assess whether chronic inflammation is present and how active it is. Elevated levels often correlate with lingering immune activation post-viral exposure.
Thyroid and adrenal testing (blood and saliva)
Fatigue isn’t always just about the mitochondria. Thyroid hormones and cortisol rhythms play a big role in energy regulation, and many post-viral patients show signs of burnout, adrenal dysregulation, or suboptimal thyroid function.
Autoantibodies and mast cell mediators
For patients with symptoms like histamine intolerance, unexplained rashes, or light and sound sensitivity, we may test for immune dysregulation or mast cell activation, which is common in post-viral and post-vaccine syndromes. Markers like ANA, blood histamine levels, MMP-9, and TGF-beta help us evaluate whether your immune system is stuck in overdrive or reacting in ways it shouldn’t.
Coagulation studies
One emerging area of concern is microclot formation—tiny, persistent clots that impair oxygen delivery and fuel fatigue. Coagulation markers can help us identify and address this issue when other tests come back normal but symptoms persist.
Each of these tests reveals a different piece of the puzzle. Once you and your functional medicine provider know the full story, you can work together to find your best path to healing.
Supplements for Post Viral Fatigue
Once we know the root cause of your symptoms, then we can start to rebuild your resilience from the inside out. Often, that means using supplements to support your mitochondria, calm the immune system, and reduce inflammation.
These are some of the most common supplements we recommend for post viral fatigue and vaccine-related symptoms:
- CoQ10 and PQQ – Powerful antioxidants that help recharge mitochondrial energy production
- Acetyl-L-Carnitine – Supports the transport of fatty acids into mitochondria, helping your body burn fuel more efficiently
- Magnesium – Crucial for ATP production and muscle recovery; often depleted after viral illness
- Methylated B-complex – Supports mitochondrial enzyme function, nervous system health, and detoxification
- NAD+ precursors (NMN or NR) – Fuel cellular repair and boost resilience
- Omega-3s – Anti-inflammatory support for the brain, heart, and immune system
- Plasmalogens (Prodrome Neuro, Prodrome Glia) – Specialized lipids that support brain health and help calm inflammation
- Glutathione or NAC – Strengthen your antioxidant defenses and help detox lingering viral byproducts
- Low-dose methylene blue (if indicated) – May enhance mitochondrial function and improve oxygen utilization
- Quercetin and luteolin – Calms mast cell activation and reduces neuroinflammation
- N1O1 (Nitric Oxide support) – Improves circulation and reduces vascular inflammation
- Lumbrokinase, Nattokinase, and Serrapeptase – Enzymes that help break down microclots and biofilms that can form after viral exposure
- High dose melatonin – Help squelch the inflammasome in those with post viral syndrome
These supplements are a typical part of a personalized plan based on testing, symptom patterns, and underlying imbalances. They’re not one-size-fits-all, but rather chosen to meet your body where it is and help guide it toward healing.
Advanced and Adjunctive Therapies for Chronic Viral Syndrome
Sometimes, supplements aren’t enough—and that’s when we turn to advanced therapies for deeper support. These modalities help speed up healing, especially in patients dealing with stubborn fatigue, brain fog, or dysautonomia after a viral infection or vaccine reaction.
Depending on your individual case, we may consider:
- Hyperbaric Oxygen Therapy (HBOT): This helps get more oxygen into your tissues and supports cellular repair.
- Nutrient IV Therapy: High doses of vitamins, minerals, and antioxidants—like glutathione, vitamin C, and phosphatidylcholine—delivered straight into your bloodstream for a quick boost.
- Peptides (like BPC-157, Thymosin Alpha-1, TB4, and KVP): These support your immune system, help heal tissues, and aid recovery from lingering viral fragments.
- Detox and Antiviral Protocols: Customized plans for people who still have signs of spike protein toxicity or viral remnants hanging around.
- Low-Dose Nicotine Patches: In some cases, these can help regulate your nervous system, support memory, and improve blood flow by boosting acetylcholine—especially if certain receptors aren’t working quite right.
- Senolytic Supplements: Products like Qualia Senolytic or Healthgevity Rejuvinate/Senolytic help clear out old, worn-out cells so your body can refresh itself.
- Methylene Blue: A powerhouse for your mitochondria that can help boost energy and oxygen use at the cellular level.
- Prescription Medications: There are some prescription options that can support your immune system or help clear spike proteins and viral leftovers. These vary by case and your provider can talk through what might be right for you.
- Limbic Retraining and Vagus Nerve Stimulation: Techniques to calm your nervous system and support overall healing.
For many patients, a combination of supplements, advanced therapies, and lifestyle changes are essential to help the mitochondria recover. As always, you should consult with a knowledgeable provider before changing your healthcare plan or adding anything new.
Work with Boulder Holistic Functional Medicine
If you’re dealing with post viral fatigue, vaccine side effects, or symptoms that don’t make sense to anyone else, please know: You are not alone, and you are not imagining it. These symptoms are real, and they deserve a real solution—not a band-aid or dismissal.
Functional medicine helps uncover why your body is stuck in survival mode and the best way to move forward with your healing. Ready to rebuild your resilience and heal from the inside out? Schedule a consultation with Boulder Holistic Functional Medicine today!
