Can the CIRS Protocol Help People with Long COVID Symptoms?

When someone tells me, “I beat COVID… so why am I still sick?” my heart goes out to them. I hear this story weekly in clinic. And it almost always sounds like this:

Sarah’s COVID test finally came back negative, and she expected life to go back to normal. But instead of recovering, she kept sinking. Her exhaustion was bone-deep. Her brain fog felt impenetrable. Her joints ached like she had aged overnight. Anytime she tried to exercise, she paid for it with two or three days in bed.

Her doctor ran the usual tests: labs, MRI, general screening; all of which are always “normal.” And she was told the same line I hear over and over:

Everything looks fine. Just give it more time.

But time didn’t help. And if this is your story… please know you are not alone. Millions of people now live with persistent symptoms after COVID — often called long COVID or Post-COVID Syndrome (PCS). What’s becoming increasingly clear is this:

Long COVID shares surprising overlap with Chronic Inflammatory Response Syndrome (CIRS). And understanding that overlap may finally offer a roadmap forward.

Long COVID and CIRS: A Shared Pattern Beneath the Symptoms

CIRS is a multi-system, multi-symptom illness triggered by biotoxins such as mold, Lyme, or dinoflagellates. What makes CIRS unique is how it disrupts hormone signaling, immune balance, and mitochondrial function.

When researchers analyzed long COVID through that same lens, they found something astonishing. A transcriptomic study led by Dr. Ritchie Shoemaker and colleagues looked at gene expression patterns in PCS patients. (source) What they found mirrored the CIRS picture almost exactly:

1. Molecular Hypometabolism (MHM)

Key mitochondrial genes were switched off. An identical pattern to what we see in CIRS.

2. Innate Immune Activation

Markers like TLR4 and CD14 were elevated, showing the immune system was stuck in overdrive.

3. Inflammatory Signaling

TGFBR expression was significantly elevated. This is tied to fibrosis and chronic inflammation.

4. Symptom Overlap

Fatigue, brain fog, headaches, pain, shortness of breath… All classic CIRS symptoms.

The takeaway:

Long COVID and CIRS aren’t identical… but the biological overlap is undeniable.

Lab Markers That Connect Long COVID and CIRS

Inside the lab data, the overlap becomes even clearer.

TGF-β1

Elevated in both CIRS and PCS
Tied to chronic inflammation, autoimmunity, and fibrosis
Helps explain shortness of breath, brain fog, and neurological symptoms

VEGF

Often low in both CIRS and PCS
Leads to poor oxygen delivery. Resulting effects include: fatigue, exercise intolerance, PEM

MMP-9

Elevated in both CIRS and PCS
Indicates leaky blood vessels and cytokine-driven inflammation
Explains migratory body pain and headaches

C4a

A key driver of innate immune activation
Frequently elevated in both conditions
Correlates strongly with fatigue and cognitive decline

These aren’t random findings, they’re a shared inflammatory fingerprint.

So… Could the Shoemaker Protocol Help Long COVID Patients?

Remember, to develop CIRS we need three things:

HLA mutation
Exposure to biotoxins
A priming or triggering event

PCS is not caused by mold, but here’s something you need to know… it is the perfect priming/triggering event. Since the pandemic, I have seen a similar story in patients. So many people have got so incredibly sick after contracting COVID.

What’s not often discussed is what was happening before the COVID infection. For a lot of people, there was an unknown but ongoing biotoxin exposure. And this is how the Shoemaker protocol can help:

Phase 1: Remove What’s Fueling the Fire

For PCS patients, this often means:

Evaluating the Environment

Even if COVID triggered the initial crash, a water-damaged building can keep the inflammation going. Many PCS patients don’t realize they’re living or working in a mold-contaminated space.

Using Binders Strategically

Cholestyramine or Welchol help remove circulating biotoxins in CIRS. In PCS, you may find binders to cause all sorts of unwanted reactions. Make sure you test your environment. A ongoing (albeit hidden) exposure could be keeping your immune system reactive.

Phase 2: Calm and Rebalance the Immune System

This includes:

Treating MARCoNS if it’s present
Normalizing inflammatory markers such as TGF-β1, C4a, VEGF, and MMP-9
Supporting mitochondria as they come back online

This is where many long COVID patients begin to experience early improvements: clearer thinking, more stable energy, and better sleep.

Phase 3: Repair and Restore Normal Physiology

Once inflammation stabilizes, therapies like VIP nasal spray help normalize neuroimmune signaling, hormonal balance, and mitochondrial function. For many people — CIRS or PCS — this is the phase where resilience returns.

What Patients Need to Know

Long COVID is real and measurable.

This is not anxiety. Not deconditioning. Not “just stress.” PCS has a biological fingerprint.

Antivirals aren’t the solution.

If the virus is gone but the immune system is dysregulated, antivirals won’t fix the underlying problem.

The Shoemaker Protocol offers structure.

Long COVID patients often come to me exhausted from trying random supplements with no guidance. The protocol provides objective markers, clear milestones, and a stepwise process.

FAQ: The CIRS Protocol & Long COVID

Is long COVID the same as CIRS?

Not exactly. Many PCS patients show the same inflammatory pathway disruptions we see in CIRS.

I think of COVID as the priming or triggering event that pushes the immune system into overdrive thus causing CIRS.

Do I need mold exposure for the protocol to help?

No. The protocol works on immune regulation and gene expression, not just mold.

Just remember that a lot of you may be unknowingly exposed to biotoxins. Remember to test, not guess.

Has this been studied?

Yes. Dr. Shoemaker’s 2021 PCS transcriptomic study showed significant overlap with CIRS biology.

How long does recovery take?

Gradual improvements often begin over months, with more stability at the 12–18 month mark.

Can I try binders on my own?

I strongly recommend working with a trained provider. Poorly timed or incorrectly dosed binders can worsen symptoms.

The Emotional Weight of PCS and CIRS

Beyond biology, both CIRS and long COVID patients face something even harder: dismissal.

“Your labs are fine.”

“Just push through it.”

“Try exercising more.”

This is devastating to hear. Especially when you know your body isn’t functioning the way it used to. What I want you to know is this:

Your symptoms are real.

They’re measurable.

And there is a roadmap forward.

At Flourish Clinic, I’ve seen patients move from fear and confusion into clarity and hope once they finally understand what’s driving their symptoms.

In Summary…

Long COVID is real. It has a biological signature. And it shares profound overlap with CIRS. This is good news. It means we’re not flying blind.

The Shoemaker Protocol, a proven framework for chronic inflammatory illness, may offer long COVID patients a path toward recovery that’s structured, evidence-based, and grounded in physiology.

If you’re months past COVID and still struggling with fatigue, brain fog, pain, or shortness of breath, consider speaking with a CIRS-literate practitioner to explore whether testing or treatment might help.

There is hope. You’re not alone. And your body can find its way back to balance.