Long COVID Recovery Protocol: Peptides for Immune Dysfunction, Inflammation, and Mitochondrial Repair
A Restorative Approach to Long COVID Recovery
Long COVID refers to lingering symptoms like fatigue, brain fog, poor sleep, and inflammation that persist for weeks or months after a COVID-19 infection. Symptoms often result from ongoing immune dysfunction, mitochondrial disruption, and impaired tissue repair.
If you're still feeling unwell weeks or months after recovering from COVID-19, you're not alone. For many, symptoms like fatigue, brain fog, poor sleep, or ongoing inflammation reflect deeper disruptions in immune regulation, mitochondrial energy production, and tissue repair. These are not random side effects. They’re biological consequences of how the body responds to, and struggles to recover from, a viral assault.
Peptide therapy offers a science-based approach to help the body reset. Rather than masking symptoms, it works by restoring immune balance, rebuilding energy pathways, and supporting long-term healing from the inside out.
What Is Long COVID?
Long COVID, also known as post-viral syndrome or post-acute sequelae of SARS-CoV-2 infection (PASC), refers to symptoms that linger for weeks or months after the initial COVID-19 infection has resolved. These symptoms can include fatigue, brain fog, joint pain, gastrointestinal issues, poor sleep, and recurrent infections. For many, the struggle continues not because of ongoing infection, but because the immune system, mitochondria, and cellular repair pathways never fully recalibrate.
Why Does It Persist?
Unlike short-term illness, Long COVID creates a state of dysfunction: the immune system may remain overactive yet ineffective, inflammation persists at a low level, and mitochondrial energy output declines. These disruptions impact the nervous system, vascular tissue, and metabolic health, often leading to a complex cycle of fatigue and poor resilience.
At Scale Regenerative Health, we use targeted peptide protocols to restore immune function, support mitochondrial repair, and reduce systemic inflammation. Our goal is to help patients regain energy, mental clarity, and immune stability through individualized regenerative care.
Core Peptides for Immune Rebalancing and Viral Clearance
For individuals experiencing chronic immune fatigue, susceptibility to infections, or signs of unresolved inflammation, addressing immune system imbalances is the first step in effective Long COVID recovery. These peptides are often integrated into immune health protocols using advanced peptide therapies designed to restore balance and resilience across the immune system.
Thymosin Alpha-1 (Tα1)
Thymosin Alpha-1 is one of the most well-studied peptides in immunology. It supports the maturation and activity of T-cells, improves interferon production, and helps resolve chronic inflammation. In Long COVID, Tα1 is often used to rebuild immune vigilance that has become suppressed or dysregulated.
Tα1 may help by:
- Supporting T-cell survival and differentiation
- Enhancing antiviral defense and interferon response
- Modulating Th1/Th2 balance to calm immune overactivity
- Reducing chronic, unresolved inflammation
This peptide is particularly useful in patients with low lymphocyte counts, recurring infections, or signs of immune fatigue.
LL-37 (Cathelicidin)
LL-37 is a broad-spectrum antimicrobial peptide that bridges innate and adaptive immunity. It plays a key role in clearing residual viral particles and calming dysfunctional immune responses.
LL-37 supports recovery through:
- Promoting autophagy to remove intracellular viral debris
- Regulating cytokine production and immune signaling
- Enhancing pathogen clearance without overstimulating immunity
- Strengthening mucosal defenses in the respiratory and gut systems
LL-37 is a strong candidate for patients who experience repeated infections, sinus or GI symptoms, or signs of unresolved inflammation.
Peptides to Restore Mitochondrial Function and Tissue Repair
After addressing immune dysregulation, the next focus is rebuilding energy and repairing damage caused by chronic inflammation. The peptides in this category support mitochondrial health, tissue integrity, and neurovascular repair. This phase of recovery is especially important for patients experiencing fatigue, muscle soreness, or poor exercise tolerance.
SS-31 (Elamipretide)
Fatigue in Long COVID is often the result of mitochondrial dysfunction. SS-31 directly targets mitochondrial membranes to enhance energy production and reduce oxidative stress.
SS-31 works by:
- Improving electron transport and ATP generation
- Reducing mitochondrial DNA damage
- Supporting energy production in immune cells and neurons
- Enhancing overall metabolic resilience
This peptide is ideal for patients experiencing post-exertional crashes, energy plateaus, or neurological fatigue. You can learn more about how SS-31 supports mitochondrial health and resilience in this deep dive.
Thymosin Beta-4 (TB-500)
TB-500 supports vascular regeneration, microcirculation, and immune cell coordination. It is especially helpful when there is endothelial damage, fibrotic tissue, or poor recovery from exertion.
Its benefits include:
- Enhancing blood flow and capillary repair
- Reducing fibrosis in lungs, connective tissue, or heart
- Supporting repair of soft tissue and endothelial lining
- Calming tissue-level inflammation
TB-500 is often used alongside SS-31 in patients with circulation-related symptoms or systemic stiffness. TB-500 is also commonly used in peptide protocols supporting athletic performance and injury recovery.
BPC-157
BPC-157 helps restore gut integrity and reduce neuroinflammation, making it a key peptide for patients with GI symptoms, food intolerance, or brain fog. It supports the gut-brain-immune axis through tissue repair and improved blood flow.
Key actions of BPC-157:
- Regenerating mucosal and endothelial tissue
- Reducing inflammation across the digestive tract
- Supporting nitric oxide signaling and microcirculation
- Enhancing communication between the gut and central nervous system
BPC-157 is often foundational for patients experiencing bloating, gut pain, or autoimmune flares triggered by food or stress.
GHK-Cu
GHK-Cu is a naturally occurring copper peptide that encourages DNA repair, reduces oxidative stress, and promotes wound healing. In Long COVID, it helps restore redox balance and tissue resilience.
GHK-Cu offers:
- Potent antioxidant and anti-inflammatory effects
- Support for fibroblast activity and tissue regeneration
- DNA repair signaling for damaged or aging cells
- Recovery support for skin, connective tissue, and organs
This peptide is particularly useful in patients with chronic inflammation or slow recovery from soft tissue damage.
Additional Supportive Peptides
Not every patient requires an extensive protocol. However, for those experiencing neurological disruption, severe inflammation, or circadian imbalance, additional peptides may offer targeted support. These are typically introduced after core systems show signs of stabilization or when symptom patterns point toward deeper hormonal or neuroimmune dysfunction.
Epitalon
Supports melatonin regulation, pineal gland health, and circadian rhythm stability. Can help restore nighttime immune signaling and support restful sleep in patients with hormonal or neurological disruption.
KPV
A small peptide that modulates inflammation through the melanocortin pathway. Particularly effective in gut, lung, and brain inflammation associated with cytokine dysregulation or histamine sensitivity.
How These Peptides Work Together
Peptides work best when thoughtfully combined. In Long COVID, symptoms rarely arise from one isolated dysfunction. Instead, we see overlapping issues across the immune, nervous, vascular, and metabolic systems.
Protocols are often layered in a way that addresses each patient's most pressing concerns. For example:
- For fatigue and brain fog: SS-31, Tα1, and BPC-157
- For recurring infections: LL-37, Tα1, and KPV
- For gut-brain axis repair: BPC-157, KPV, and Epitalon
- For tissue and vascular recovery: TB-500 and GHK-Cu
These combinations are adjusted based on clinical markers, symptoms, and patient response. Most peptides are delivered via subcutaneous injection on a rotating or cyclical schedule to support sustained recovery.
Frequently Asked Questions
Peptides are not a cure, but they can address many root causes of Long COVID by supporting the immune system, repairing energy pathways, and reducing inflammation. They are often part of a broader recovery strategy that includes nutrition, movement, and stress reduction.
Many peptides are considered investigational and are not FDA-approved for treating Long COVID. However, several, such as Thymosin Alpha-1 and LL-37, have been studied extensively and may be prescribed off-label by qualified clinicians.
Some patients notice improvement in energy, mood, or digestion within 2 to 4 weeks. For others, progress may be more gradual. Full benefits often emerge over 8 to 12 weeks as immune and metabolic systems stabilize.
Yes. Many patients use peptides alongside medications, supplements, or other therapies. Our team carefully evaluates your history to ensure compatibility and avoid interference.
Ready to Explore a Personalized Recovery Plan?
If you're struggling with persistent symptoms following COVID-19 and looking for a structured path forward, we offer comprehensive consultations to help determine whether peptide therapy is right for your recovery. Our team builds treatment plans tailored to your biology, symptoms, and goals—backed by evidence, not guesswork.
Request a consultation and take the next step toward restoring your immune health, energy, and resilience.
Here’s what you can expect during your first peptide therapy consultation to help you prepare.
References
Chapter Seven – Immune Modulation with Thymosin Alpha 1 Treatment
Immune Modulation with Thymosin Alpha 1 Treatment (PubMed)
Mitochondrial protein interaction landscape of SS-31
SS-31 as a Mitochondrial Protectant in the Treatment of Tendinopathy
Stable Gastric Pentadecapeptide BPC 157 May Recover Brain-Gut Axis and Gut-Brain Axis Function
BPC 157 and Standard Angiogenic Growth Factors. Gastrointestinal Tract Healing
human tri-peptide GHK and tissue remodeling (2008)
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