Long Covid Protocol

The most common symptom of long covid is fatigue, most often extreme fatigue. And all cases of long covid have microclotting. A theory to explain this combination is that covid virions persist in the body after the acute phase has passed, constantly topping up the microclots as the microclot load is being dissolved by the body’s processes.

The microclots make the blood too viscous to flow through the body’s narrowest capilliaries, starving the surrounding tissue of oxygen. Thus any exertion by a long covid sufferer results in extreme fatigue.

Persistent viral infection, even at a low level, would cause inflamation.  Persistent inflammation depletes vitamin D and magnesium, in turn making it hard for the body’s immune system to overcome the inflammation.

It follows that overcoming long covid, in theory, would start with reducing the covid virion load. Of secondary importance is speeding up the dissolution of the microclots. Third is restoring the immune system. What follows is not medical advice:

Reducing the Covid Virion Load

While most of the general public currently think that the covid virus dissappears from the body between bouts of covid, it appears to persist in many individuals.

A recent study reports that: “We find evidence of viral presence in the lung up to 359 days after the acute phase of disease, including in patients with negative nasopharyngeal swab tests. The lung of post covid patients are characterized by the accumulation of senescent alveolar type 2 cells, fibrosis with hypervascularization of peribronchial areas and alveolar septa, as the most pronounced pathophysiological features. At the cellular level, lung disease of post covid patients, while distinct, shares pathological features with the chronic pulmonary disease of idiopathic pulmonary fibrosis.”

There is one widely available molecule known to bind to covid virions and inactivate them. That is ivermectin. Though doctors are banned from prescribing it in Australia to treat covid, it can be bought in bulk from rural supply stores such as Elders.

Prior to the appearnace of covid, several studies reported antiviral effects of ivermectin on RNA viruses such as Zika, dengue, yellow fever, West Nile, Hendra, Newcastle, Venezuelan equine encephalitis, chikungunya, Semliki Forest, Sindbis, avian influenza A, porcine reproductive and respiratory syndrome, human immunodeficiency virus type 1. Furthermore, there are some studies showing antiviral effects of ivermectin against DNA viruses such as equine herpes type 1, BK polyomavirus, pseudorabies, porcine circovirus 2, and bovine herpesvirus 1. So clinical efficacy against covid should not be surprising.

One doctor using ivermectin to treat long covid has reported that 70 to 90 percent of patients respond to the respond, generally within 10 days: “Patients can be classified as ivermectin responders or non-responders”.

Ivermectin can be taken orally or absorbed through the skin. The optimum dosing rate is considered to be 0.4 mg/kg of body weight per day. Ivermectin is lipid soluble and is stored in the body’s fat reserves. This may explain the conundrum of central Africa being largely spared covid despite taking ivermection against parasitic worms only once or twice a year.

An Argentinian study published in March 2021 is the only peer-reviewed study evaluating ivermectin for long covid. The study found that in patients reporting long covid symptoms—including coughing, brain fog, headaches, and fatigue—ivermectin alleviated their symptoms.

A typical long covid anecdote on ivermectin: “I’m taking 12mg of ivermectin a day. It’s working for me. Fatigue, numbness, headache, inflammation of lymph node are better.”

In silico screening of plant molecules followed by in vitro work has found some that have anti-covid efficacy at clinically achievable levels. For example ursolic acid from elderberry and tanshinone IIA from red sage which has an IC50 against covid of 4.1 µg/ml.

Dissolution of the Microclots

It has been reported that all long covid cases have microclots in the blood. Long covid is also characterised by extreme fatigue and post-exertional malaise. A theory uniting these facts is that the microclotting restricts the flow of blood through the smallest capilliaries and thus organs and muscles are starved of oxygen.

What many long covid sufferers have used to dissolve the microclots in the blood is nattokinase. This is an enzyme produced by fermenting boiled soybeans with the bacteria Bacillus natto. A typical dosing rate is 100 mg twice daily to be taken on an empty stomach: at least 30 minutes before a meal or 2 hours after.

Bottle of nattokinase capsules

Other supplements also used include serrapeptase which is a proteolytic enzyme produced by the enterobacterium Serratia marcescens, originally isolated from silkworm intestine. And lumbrokinase, an enzyme isolated from earthworms.

An anecdote on nattokinase use in long covid: “Huge difference after taking a combo pill of Natto/Serra, 2x in the morning upon waking and one in the late afternoon. I felt like exercising for the first time in 2+ years and managed 4 minutes!”

Most benefit is achieved using enteric-coated nattokine, preserving the capsule from the highly acid conditions of the stomach so that it is all delivered to the small intestine.

Restoring the Immune System

Another theory to explain the extreme fatigue of long covid has been proposed by Dr Patrick Chambers and it does explain a lot, including why younger females are over-represented in long covid statistics.  His theory:

Inflammation causes reactive oxygen species (ROS) production in the mitochondria. Normally ROS are soaked up by antioxidants.

These oxidizing agents, if not reduced, are very toxic to cells and threaten their destruction. In order to avoid this, cells shut down their mitochondria, the source of the ROS, to survive.

The glycolytic pathway from glucose to pyruvate normally proceeds to the Krebs cycle for oxidative phosphorylation and ATP production within mitochondria. Instead pyruvate proceeds to lactate only.

ATP production goes from 38 ATP molecules per glucose molecule to 2. Mitochondria are especially dense in muscle cells (skeletal, cardiac, smooth). Fatigue becomes unavoidable.

Brain oxygen consumption represents 20% of the total. So, eventually some degree of cognitive compromise is inevitable.

The resulting hypoxia and increased lactic acid trigger release of TGF-β, the primary cytokine of the Warburg effect. This cytokine is elevated in chronic fatigue syndrome and many other chronic fatigue diseases.”  And;

“The interface between insufficient magnesium and elevation of TGF- β in long covid begins with cellular hypoxia. Long covid afflicts a younger age group, predominantly female, the opposite of the Covid-19 group.”

It could be that the extreme fatigue of long covid is caused by both microclotting and persistent mitochondrial hypoxia and the proportions vary from individual to individual. Certainly many sufferers report an improvement of symptoms using nattokinase. Others have reported improvement using magnesium supplementation: “Magnesium helps my palpitations tremendously.”

Why long covid in younger women? They are the most magnesium deficient cohort in our society and magnesium is involved in all the endogenous antioxidant synthesis in the body.

Glutathione, the master antioxidant, is a tripeptide made from amino acids glycine, cysteine, and glutamic acid. It occurs at surprisingly high levels  – 5 milli molar – in cells.

Glutathione can be regenerated from several sources, e.g., alpha lipoic acid, cysteine, NAC but several ATP molecules are required for each pathway to glutathione synthesis. The currency of regeneration is in short supply under oxidative stress conditions.

Magnesium is essential to the synthesis of glutathione and melatonin. It could be that long covid is largely a disease of magnesium deficiency with the body trapped in that state by hypoxic inflammation.

Magnesium supplementation itself must also be approached carefully. Most have a laxative effect, especially magnesium citrate. Exceeding bowel tolerance results in loss of magnesium and potassium. Magnesium in chelated form to malate, taurate, threonate, glycinate, or another amino acid is recommended. An increase in palpitations has been reported with magnesium glutamate and magnesium aspartate.

So restoration of the immune system starts with a foundation of magnesium supplementation. And it will be supplements because the same foods that are sources of magnesium are also sources of calcium, and for most of us our calcium to magnesium ratio is out of whack. That suppresses magnesium availability as both atoms bind to the same receptor. The Western diet has seen this ratio escalate from 2.3 – 2.9:1 in 1977 to 2.9 – 3.5:1 in 2007 with a rise in magnesium deficiency. The optimum blood calcium to magnesium ratio is 2:1.

On that foundation of magnesium, the following should be added:

Glutathione              – the most powerful endogenous antioxident, so the body doesn’t have to expend energy to make it.

Melatonin                 – antioxidant

Vitamin D                 – antioxidant, adults could dose at 10,000 IU per day. Inflammation chews through the body’s vitamin D stores

Vitamin C                  – antioxidant

Quercetin                  – zinc ionophore, vitamin D receptor activator, antiviral

CoQ10                        – antioxidant

Zinc                           – antiviral

N-acetyl cysteine      – precursor to glutathione

Selenium                   – involved in glutathione synthesis

Boron                         – antiviral

Vitamin B 6               – immune system maintenance

Vitamin B 12             – immune system maintenance

Vitamin B 9               – immune system maintenance

D-ribose                    – helps produce ATP (adenosine triphosphate)

Antihistamines such famotadine or low dose naltrexone will reduce inflammation.

Long Covid Blood Test Panel

Lactate Dehydrogenase

Is your body trapped in a low energy state by inflammation shutting down mitochondrial conversion of glucose? This test will quantify that.

Vitamin D

Vitamin D is a major regulator of the immune system. The more you have, the more your immune system can do. Most Australians live, less happily than they might, with less than half the ideal level of vitamin D, and then along comes long covid. Knowing what your vitamin D level is will indicate the size of the vitamin D bolus dose you should take along with at least 10,000 IU daily.

C Reactive Protein

This test indicates the level of severity of inflammation.

Glutathione Peroxidase

The body’s main antioxidant, soaking up hydrogen peroxide.


Not many Australians are actually deficient in selenium though a lot of pastoral and crop-growing areas are. Glutathione contains selenium.


Magnesium is a co-factor in the production of many of the molecules of the immune system.

The Gut-Brain Axis

A study in mice found that infection with covid led to a loss of species diversity in the gut microbes of these mice. Infected mice also had changes to their gut lining. The number of goblet cells, which produce mucus, increased. Meanwhile, the number of Paneth cells, which produce antimicrobial compounds, decreased. The remaining Paneth cells had abnormalities resembling those found in inflammatory bowel disease. These changes in the gut lining correlated with disruptions to the microbiome.

Some long covid patients have benefited from re-establishing their gut flora. A keto diet may also help cognitive function.

The Importance of Resolving Long Covid Quickly

The persitent hyperinflammation of long covid affects many organs, resulting in slow or incomplete recovery. The heightened inflammatory state of many individuals gives rise to a long term increase in disease risk. The most important of these disease risks relate to:

  1. New onset diabetes
  2. Multiple cardiovascular risk outcomes including new onset atherosclerosis and myocardial infection risks.
  3. Neurodegenerative conditions including Alzheimer’s disease and other dementias.

The sooner that long covid cases are resolved, the lower the subsequent health burden, individually and collectively.

There is a parallel with the Spanish Flu. There is evidence for excess deaths throughout the late 1920’s and 30’s, long after the Spanish flu epidemic was over. No one made the connection. All they knew was that there were excess deaths in cardiac and respiratory disease.

David Archibald is the author of The Anticancer Garden in Australia