Can the CIRS Protocol Help People with Long COVID Symptoms?

Can the CIRS Protocol Help People with Long COVID Symptoms?

“I Beat COVID. Why Am I Still Sick?”

Sarah thought the hardest part was over when her COVID test finally came back negative. But weeks later, she was still exhausted. Her brain fog was so thick she couldn’t focus on her job. Her joints ached like she had aged 20 years overnight. Every time she tried to exercise, she crashed for days.

Her doctor ran bloodwork: normal. An MRI: clear. She was told, “Your labs are fine. Just give it more time.”

But time didn’t fix it. Sarah’s story is not unique. Millions of people worldwide now live with long COVID, also known as Post-COVID Syndrome (PCS). And increasingly, research suggests it may have more in common with Chronic Inflammatory Response Syndrome (CIRS) than with traditional post-viral recovery.

Long COVID and CIRS: More Similar Than You’d Think

CIRS is a multi-system, multi-symptom illness caused by ongoing inflammation triggered by biotoxins (like mold, Lyme, dinoflagellates). What makes it unique is how it disrupts immune signaling, hormones, and mitochondrial function.

When researchers looked at long COVID through the same lens, they found striking overlaps.

A transcriptomic study led by Dr. Ritchie Shoemaker and colleagues analyzed the gene expression profiles of PCS patients. The results were eye-opening:

• Molecular hypometabolism (MHM): genes controlling mitochondrial energy production were suppressed—identical to patterns in CIRS.
• Innate immune activation: markers like TLR4 and CD14 were upregulated, showing persistent immune system overdrive.
• Inflammatory signaling: elevated TGFBR expression, linked to fibrosis and chronic inflammation.
• Symptom overlap: fatigue, cognitive decline, headaches, pain—all mirrored classic CIRS.

The conclusion?

PCS looks a lot like CIRS at the molecular and symptomatic level. (Surviving Mold, 2021)

The Lab Markers That Connect CIRS and Long COVID

TGF-β1 (Transforming Growth Factor Beta-1)

• Elevated in both CIRS and long COVID.
• Drives fibrosis, autoimmunity, and chronic inflammation.
• Explains persistent shortness of breath, lung scarring, and neurological symptoms.

VEGF (Vascular Endothelial Growth Factor)

• Often low in both conditions.
• Low VEGF means tissues struggle to get oxygen → fatigue, exercise intolerance, post-exertional malaise.

MMP-9 (Matrix Metalloproteinase-9)

• Elevated in both groups, reflecting leaky blood vessels and inflammatory cytokine damage.
• Explains joint pain, headaches, and migratory body aches.

C4a (Complement Component 4a)

• Part of innate immune activation, frequently spiking in CIRS and long COVID patients.
• Correlates with fatigue and brain fog.

These aren’t random overlaps—they’re evidence that long COVID and CIRS share a common inflammatory root.

How the Shoemaker Protocol Could Help Long COVID Patients

The Shoemaker Protocol is the only peer-reviewed, evidence-based framework for treating CIRS. Its stepwise approach may also apply to PCS:

Phase 1: Stop the Fire

• Remove exposures: While PCS isn’t caused by mold per se, environmental triggers like water-damaged buildings can add fuel to the fire. Many PCS patients improve once exposures are controlled.
• Binders: Cholestyramine and Welchol are used in CIRS to remove circulating biotoxins. In PCS, these may help bind and clear cell debris and inflammatory mediators driving symptoms.

Phase 2: Calm the Immune System

• Address MARCoNS if present (sinus colonization that suppresses MSH).
• Normalize inflammatory markers (TGF-β1, C4a, VEGF, MMP-9) with targeted therapies.

Phase 3: Repair and Restore

• Once inflammation is controlled, interventions like VIP nasal spray can restore normal hormone and immune signaling.
• This is critical for recovery of energy, cognition, and resilience.

What Patients Need to Know

1. Long COVID is Not Just “In Your Head.”

The molecular evidence is clear: PCS is a real, measurable illness with defined biological signatures.

2. Antivirals Alone Aren’t Enough.

Some PCS patients chase endless antiviral or immune-boosting regimens. But if your transcriptomic profile matches CIRS, the issue is immune dysregulation—not lingering virus.

3. You Need a Structured, Stepwise Plan.

Random supplements won’t fix mitochondrial suppression or leptin resistance. A protocol like Shoemaker’s provides a roadmap, with labs and objective milestones to track progress.

FAQ: CIRS Protocol and Long COVID

Q: Is long COVID the same as CIRS?

Not exactly. But they share many of the same gene expression abnormalities and symptoms. Some PCS patients may essentially be living with a “CIRS-like” condition triggered by viral injury.

Q: Do I need mold exposure to benefit from the protocol?

No. The Shoemaker Protocol isn’t just about mold—it’s about calming systemic inflammation and restoring normal gene expression. Long COVID patients without mold exposure may still benefit.

Q: Has this been studied?

Yes. The 2021 study on PCS patients showed clear transcriptomic overlaps with CIRS. (Surviving Mold)

Q: How long does it take?

Like CIRS, recovery is gradual. Patients may notice small improvements in months, with more stability after 12–18 months.

Q: Can I just try binders on my own?

Binders alone will not solve for PCS. They must be dosed carefully and combined with other steps to avoid setbacks. Always work with a CIRS-literate provider.

The Emotional Weight of PCS and CIRS

Beyond the biology, both CIRS and long COVID patients face dismissal, skepticism, and isolation. Being told “it’s just anxiety” or “give it time” is devastating. One of the greatest gifts of the Shoemaker Protocol is validation: your symptoms are real, measurable, and treatable.

At Flourish Clinic, we’ve seen firsthand how giving patients a clear roadmap changes not only their health but their hope.

In Summary… 

Long COVID is real. And its biology looks eerily similar to CIRS. That means the Shoemaker Protocol—a proven framework for treating chronic inflammatory illness—may also offer relief for PCS patients.

If you’ve been stuck with fatigue, brain fog, pain, or shortness of breath months after COVID, ask a CIRS-literate provider whether testing and treatment could help.