Immune System Held hostage by Virus Protein Traces

My hypothesis is that the root cause of Long Covid is a malfunctioning immune system which is caused by:

• Damage from the initial Covid infection 
• Covid virus protein traces remaining in the body post infection
• A compromised gut microbiome 
• Unresolved chronic stress which can cause a 'fight-or-flight response' 

This compromised immune system enables the Covid RNA S1 Spike and Nucleocapsid Proteins to persist in the body weeks, months and even years after the initial Covid-19 infection has gone. 

This typically causes an overreactive immune response, which can result in autoimmune-like symptoms and hyperinflammation throughout the body. This can also cause autoantibodies and fibrin amyloid microclots to cause serious injuries to the body, brain and organs.

These virus traces also continue to keep the immune system malfunctioning.

In summary, I have learned and hypothesized that Long Covid comprises any combination of the following Eight Key Factors.

But the first and second ones, the virus protein remnants remaining in the body, and the malfunctioning immune system, are probably not only always present in most people’s systems, they together are also the likely root cause of Long Covid.  

The virus protein traces (spike protein) hold the immune system hostage, by keeping it in a damaged state so it can no longer eliminate these remaining troublesome virus protein traces.

In addition to the damage Covid causes to the immune system's dendritic cells, B-cells and T-cells,  I have also learned that a damaged gut microbiome, along with unresolved chronic stress, further weakens the immune system, making it even less capable of ridding the virus protein traces that persist in people with Long Covid. 

This protocol directly addresses the first seven factors through medicinal and behavioral therapies. Number Eight will be up to you to get your body and brain back in shape through exercise.

1. Covid-19 S1 (spike) and N (nucleocapsid) protein virus remnants remaining in body 
2. Malfunctioning Immune System which enables the virus protein remnants to persist in the body
3. Over-reactive Immune Response to Covid virus traces, causing hyper-inflammation and ongoing symptoms 
4. Covid-related Injuries & Damage to the body, gut microbiome, and major organs 
5. Brain and Neurological Issues, depression, anxiety, brain fog 
6. Depletion of NAD+, CoQ10, Tryptophan, and other key nutrients and energy reserves 
7. Buildup of Covid and immune system toxins 
8. Body & brain de-conditioning and loss of stamina 

Here’s a more detailed breakdown:  

1. Covid-19 S1 (Spike) and N (Nucleocapsid) Protein Virus Traces Remaining in the Body

For many people, an abundance of Covid-19 RNA virus S1 and N protein traces remain in the body after the initial Covid-19 infection. The body’s immune system reacts by flooding the organs with activated mast cells (usually histamines, cytokines, etc.).  

This causes major inflammation throughout the body, especially in parts of the body and specific organs with previously existing weaknesses. These biological processes are not well understood.    

My hypothesis is that most of these virus remnants become embedded and hidden in body tissue, biofilms, sinuses, ovaries (in women), and gut microbiome, and remain generally invisible to the immune system during periods of rest and low activity. That’s when you tend to feel better.  

But when you exert yourself or become "stressed out," these virus traces somehow "get loose" and enter your blood system and organs, which then triggers your immune system, creating an over-reactive immune response, causing Long Covid symptoms and inflammation. This can also somehow re-trigger the usually dormant Epstein-Barr virus found in 90% of the population.  

The virus protein remnants are also the likely root cause of the fibrin amyloid microclots, which can damage every organ in the body.

Removing these embedded Covid virus traces using the two stages of the “Eradicate Virus Remnants” part of the protocol is critical to healing from Long Covid. It is probably the most important purpose of this protocol.

https://www.biorxiv.org/content/10.1101/2021.06.25.449905v3

2. Malfunctioning Immune System which enables the virus protein remnants to persist in the body.

If you have Long Covid you probably have a compromised immune system, which enables the virus remnants to persist in the body. 

This is due to the initial Covid infection having damaged and reduced the number of critical Dendritic Cells, immune cells critical for fighting infections and other threats such as lingering Covid virus remnants. https://www.sciencedaily.com/releases/2021/10/211028125803.htm 

Covid has also been shown to damage or deplete several other critical immune system cells such as naïve T-cells and Natural Killer (NK) T-cells. 

It additionally inhibits B-cell maturation and can erase the antibody knowledge that B-cells store. This could be why people who have had a Covid infection tend to be more susceptible to head colds and influenza. https://pingthread.com/thread/1605958004163084292 

People with Long Covid also tend to have an “uncoordinated adaptive immune response” where the B-Cells and T-Cells no longer work together in a coordinated manner, which can severely cripple the immune system’s effectiveness. There are also increased frequencies of CD4+ T-cells migrating to inflamed tissues, and exhausted (no longer fully functioning) Covid-specific CD8+ T cells.

https://www.biorxiv.org/content/10.1101/2023.02.09.527892v1#F7 

A Covid infection can also reduce Immunoglobulin-G3 levels. Research has shown that people with Long Covid have lower levels Immunoglobulin-G3 serum concentrations in their blood. This has been shown to be a precursor of Long Covid.

https://www.nature.com/articles/s41467-021-27797-1 

The Covid infection and remaining virus protein remnants can also cause the immune system to function incorrectly and cause autoantibodies to attack every organ in the body, causing Long Covid-related bodily injuries. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8440763/ 

So, on one hand the damaged immune system is underreacting in that it doesn't know how to respond to some real threats correctly such as getting rid of the dangerous Covid virus remnants (spike protein) remaining in the body, and on the other hand it's overreacting causing organ injuries and the typical Long Covid symptoms such as Mast Cell Activation Syndrome (MCAS), POTS, Chronic Fatigue Syndrome, etc.

I have learned through personal experience and research that there are five conditions associated with Long Covid that cause the immune system to malfunction:

• Insufficient and/or damaged Dendritic Cells, T-cells, B-cells and lowered Immunoglobulin-G3 levels
• Covid virus protein remnants still in body causing organ damaging autoantibodies 
• Damaged gut microbiome 
• Depleted NAD+, CoQ10, Tryptophan, Selenium, Magnesium, and most vitamin levels.
• Chronic stress

I found that all five had to be addressed for a complete recovery from Long Covid to be achieved.

The first three can be addressed via the supplements in the protocol. But I had to solve the chronic stress through separate behavioral therapies. 

Let’s take a closer look at these four: 

  A. Insufficient and/or damaged Dendritic Cells, T-cells, B-cells and lowered Immunoglobulin-G3 levels. The Covid infection depletes and damages the infection-fighting immune system cells that are critical for eliminating the Covid virus protein remnants, such as the Spike protein, and protecting the body from secondary infections. 

For me, these immune system cells seemed to have healed over time probably due to the immune repairing supplements in the protocol and good nutrition. 

  B. Autoantibodies caused by the remaining Covid virus protein remnants. It appears that the Covid virus remnants remaining in the body also play havoc with the immune system, causing it to attack the body’s organs and causing a lot of Covid-related injuries. So, deactivating and eradicating these virus traces was a high priority.

  C. Damaged Gut Microbiome. The health and quality of the microbiota in the digestive tract has been shown to have an effect on both the immune system and your mental health via the gut-brain axis. 

The initial Covid infection and the lingering Covid virus protein traces appear to somehow damage and negatively affect the diversity and quality of the microbiota in the gut, further compromising the immune system and affecting mental well-being.

Healing the gut microbiome was critical in my full recovery.

  D.  Depleted NAD+, CoQ10, Tryptophan, Selenium, Magnesium, and most vitamin levels. . 

These vital nutrients are depleted by the Covid infection and possibly Long Covid as well. 

They are replenished via the “Replenish Body” and “Recover Brain” regimens.

  E. Chronic Stress. It was very difficult for me to hear and admit that chronic stress played a significant role in my Long Covid. 

That’s because so many medical professionals were initially claiming that Long Covid was psychosomatic or “all in my head”. 

Of course, we now know that Long Covid is biologically based via the remaining virus protein remnants. 

But we also know that chronic stress plays a physiological role via brain circuitry in the amygdala and hypothalamus areas of the brain that manifest as a ‘fight-or-flight response’. This has been shown to seriously compromise the immune system making it unable to get rid of the virus remnants in a timely manner, if ever. 

There has also been research from the DNA company 23andMe showing that people who report a history of depression and anxiety develop Long Covid at twice the rate as people who don't. Anxiety and depression are often symptoms of chronic stress. https://blog.23andme.com/articles/anxiety-depression-long-covid 

Constant worry, old negative stories we tell ourselves, or non-resolved emotional trauma, or other ongoing stressful situations in your life can create an  ongoing low-level ‘fight-or-flight response’ in the body, which is known to result in the suppression of the immune system and gastrointestinal system. 

I discovered that resolving chronic stress was critical to my full recovery from Long Covid. I shared exactly how I did that in the section called “Resolving Chronic Stress”.

In conclusion, a suppressed immune system has been shown to make your body more susceptible to disease such as Long Covid. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1361287/ 

I believe a malfunctioning immune system somehow enables the Covid spike protein to persist and take over by exploiting and colonizing itself throughout the body.

3. Over-Reactive Immune Response to Spike Protein causing Inflammation and Ongoing Symptoms

I posit that Long Covid is primarily an over-reactive immune response to the virus protein remnants in your body. The symptoms can be similar to an autoimmune disease.  

When you are suffering from Long Covid, you probably have extensive inflammation in the body, which can damage organs and slow down the healing process. It is vital to reduce this inflammation as quickly as possible.   

I designed the “Deactivate Hyper-Immune Response” part of the protocol to lower both symptoms and inflammation, and to reduce the Covid proteins viral load and activity in the body. 

This was based on an extensive trial and error process involving many thoroughly researched medicinal herbs and supplements. Many that I initially tried ended up having no positive effect, but I ended up using the ones that did work in this protocol. 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7529115/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7946344/

4. Covid Injuries & Damage to the Body and Major Organs

The initial Covid-19 infection along with Long Covid can injure and damage several areas of the body, which will need time and the proper nutrients to heal completely. 

Two major culprits causing these injuries are likely the fibrin amyloid microclots and autoantibodies, which appear to affect every area of the body. These are probably due the Covid virus protein remnants remaining in the body.

The parts of the body and organs typically affected are:

• Blood vessels and the entire circulatory system, which can become torn or even clogged from the inside. These are the arteries, veins, and capillaries.
• Heart: Covid-19 can damage the heart directly by causing high blood pressure and inflammation of the heart muscle called myocarditis, which makes it harder for the heart to pump. 
• Lungs:  Covid-19 can affect the lungs, bronchial tubes, and air sacs. While most people recover from Covid-19 without any lasting lung damage, the pneumonia associated with COVID-19 can be severe. Even after the disease has passed, lung injury may result in breathing difficulties that might take months to improve. 
• Liver: Covid-19 can cause inflammation of the liver which can damage it long term. 
• Kidneys: Inflammation is also responsible for kidney damage, especially for Covid patients who were hospitalized. 
• Pancreas: Covid-19 and Long Covid appear to be responsible for people experiencing both acute pancreatitis (infection of the pancreas) and diabetes. 
• Gut Microbiome: Covid and Long Covid appear to compromise the healthy bacteria in the gut.
• Scalp: Covid-19 and Long Covid seem to affect many people with hair loss. 
• Gut microbiome, which is critical for a strong immune system. Covid can damage the gut microbiome making it difficult to heal properly. A damaged gut microbiome may also be responsible for harboring the virus protein remnants via biofilms, which further worsens Long Covid symptoms

Obviously, healing the body from the damage caused by Covid is critical, but it can take months, or maybe even years. And of course, all the injuries may not heal completely.   

About six months after completing the protocol, my night vision was still more glary than it was pre-Covid.  I am also aware that I have not yet recovered some potentially lost memories. These are examples of physical damage caused by Covid that I may never heal from, or will take time.  

While the protocol stopped the over-reactive immune response, eliminated the root cause of Long Covid (virus protein remnants), and provided the nutrients to help my body and brain heal almost completely, it has not yet fully healed all of the neurological damage that affects my eyes and memories. 

https://nyulangone.org/news/platelets-are-key-blood-vessel-damage-patients-covid-19 

https://pubmed.ncbi.nlm.nih.gov/35195253/ 

5. Brain and Neurological Issues 

Both the initial Covid-19 infection and Long Covid can cause injury to the brain and nervous system. This includes:  

1. The myelin sheath which surrounds and protects the nerve fibers in the brain, as well as the nervous system throughout the body. 
2. The all-important Vagus nerve, which is actually two long nerves that impact the area of your body between the head and digestive tract. 
3. Overall brain inflammation caused by both the initial Covid-19 infection, as well as Long Covid, which acts like encephalitis and is probably responsible for a significant number of neurological Long Covid symptoms.  

The typical symptoms of brain and neurological issues are: 

1. Depression and/or anxiety 
2. Brain fog - it was hard to think deeply about things 
3. Difficulty speaking - it was hard to turn thoughts into speech without stuttering 
4. Lost memories
5. Neuropathy - my hands and fingers were not functioning 100%; I could no longer strum a guitar or play piano well
6. Extreme brain exhaustion - even by simple tasks, such as driving (especially during rush hour), having conversations, or trying to solve a problem

There has also been research showing that people who report a history of depression and anxiety develop Long Covid at twice the rate as people who don't. Non-fully resolved emotional trauma can create a low-level chronic stress or fight-or-flight response in the body, which results in a compromised immune system and gastrointestinal system. 

I discovered that resolving this fight-or-flight response was critical in my Long Covid healing process.

https://www.ninds.nih.gov/Current-Research/Coronavirus-and-NINDS/nervous-system

https://www.nature.com/articles/s41467-022-30932-1

https://www.nih.gov/news-events/news-releases/small-nih-study-reveals-how-immune-response-triggered-covid-19-may-damage-brain

6. Depletion of NAD+, CoQ10, Tryptophan and other Key Nutrients, and Energy Reserves

The initial Covid-19 infection can deplete several vital nutrients that the body depends on to heal properly. These are predominantly NAD+, CoQ10, L-Tryptophan, key vitamins and minerals such as selenium, magnesium and zinc. Covid can also deplete your vital deep energy reserves.

Since our cells use NAD+ to regenerate, low NAD+ levels can slow down the healing process as well as making cells more vulnerable to infection.  Additionally, Covid has been shown to deplete Coenzyme Q10 (CoQ10) that can damage platelet mitochondrial function, which can also block cells from healing and functioning properly as well as worsen Microclotting issues.

Low serum and muscle Tryptophan levels may be responsible for most the common Long Covid symptoms, such as depression, sleep disturbances, fatigue, and muscle weakness  

It is critical that your body has the correct amount of nutrients and energy reserves to protect itself and heal properly. 

https://pubmed.ncbi.nlm.nih.gov/34180141/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418699/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9395797/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8087860/ 

7. Buildup of Covid and Immune System Toxins 

The initial Covid infection, followed by Long Covid, appears to leave toxins in the body.  Also, the process of eliminating the spike protein can flood the body with all types of debris and heavy metals that the body must eliminate. This can overstress the liver and kidneys and potentially slow down the healing process. It can also make you feel lousy.   

I found that a critical part of healing from Long Covid is fully detoxing the body and brain. 

8. Body De-conditioning and Loss of Stamina

Due to a lack of exercise during the initial Covid infection and Long Covid, the body becomes deconditioned or to put it bluntly, out-of-shape.  This can add to feeling lousy.  

It is critical to keep moving your body every day, even just a little. As you successfully start removing all the remaining Covid virus traces from your body, you can slowly increase exercise weekly until you are back to your pre-Covid body stamina and conditioning.