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5 Common Long COVID Questions

During a recent interview with Dr. Eric Gordon, Dr. Jamie Kunkle spoke about his experience treating Long COVID patients and how he uncovers what is at the root of their symptoms.

Dr. Kunkle applies his depth of knowledge treating chronic cases of lyme, mold, Chronic Fatigue Syndrome, and Mast Cell Activation over the years to help patients struggling with Long COVID and vaccine reactions.

He uses classic, foundational supportive naturopathic therapies as well as herbs, peptides, and prescriptions to help patients find a path back to health. Below, he answers some of the most common questions we see around treating this relatively new condition.

covid virus surrounded by question marks

There are several different types of patients we see. 

One population of patients that I have seen with Long COVID have been previously healthy and often referred to our clinic by Dr. Bruce Patterson’s team or other practitioners. A lot of these folks, if you really dig deep, may have had some symptoms and soft signs of illness, but generally they were healthy by modern standards. Examples I’ve seen are occasional fatigue and other relapsing symptoms, metabolic disorders (prediabetes), difficulty with weight management that may come and go. However, most people chalk it up to a typical age related decline in health and function. 

Others did not have obvious symptoms at all and were considered optimally healthy, but I consider that to be a rare, truly healthy pre-COVID population. Things like infections and toxins can be present and the body stays regulated and they are often quite resilient to stress in general. Then COVID comes on the scene and suddenly their system dysregulates. Perhaps there are genetics here not yet known, or it has something to do with the unique features of COVID, such as spike protein, to dysregulate the immune system.

This “optimally healthy” prior to COVID population is interesting in that they can heal quicker with minimal intervention. Occasionally time itself, along with attention to the foundations of health; diet, lifestyle, sleep, spiritual/emotional balance, these people may return to normal health in 6-12 months . 

Another patient profile we see often has experienced chronic infection or other complex illnesses in the past. They were able to heal from them to a significant degree, then COVID entered their system and created massive dysregulation with new layers of illness and sometimes return of the old symptoms they had had previously. 

Aside from infections, mold/mycotoxin and environmental illnesses can predispose one to Long COVID in our experience. They may not necessarily be symptomatic but the presentation of COVID exposes the struggle the body has been experiencing secondary to toxin illness. Active environmental exposure needs to be identified and removed. There are also increasing concerns not discussed here of COVID heightening autoimmune and even certain forms of cancer, but more studies will need to be done on larger populations for longer periods of time to determine this connection.

I started off treating this as a typical post viral syndrome. However, as we started learning the unique features of COVID, we began using Dr. Bruce Patterson’s cytokine testing and treatment protocol as a general framework. We also integrated the Front Line COVID-19 Critical Care Alliance (F.L.C.C.C.) program along with more of the typical integrative natural medicine approach with herbs, nutrients, and pharmaceuticals together. I have also found success with some of my classic foundational supportive naturopathic therapies as well, like hydrotherapy. There seemed to be enough synergy between those systems that this population was responding well. Each one of these protocols has its strengths and weaknesses and there are people who it will work for.


For the few patients who didn’t respond, we would rethink our situation, and figure out what we were missing. Maybe there was more of a mast cell activation issue going on. Maybe the immune system was subdued and slower to recover function. Maybe it was something we didn’t immediately see when they were coming in, an occult infection or toxin illness. Maybe it was the damage of COVID itself on an organ system that needed more time to heal. Recent models have compared neurologic manifestations in post COVID to traumatic brain injury.

Long COVID is similar to many other chronic illnesses we treat in that we start by looking for root causes underneath the presenting symptoms and constitutional (individual) features of illness.  

I have been looking very intently at infections. What’s been discovered with COVID is that there were possible Lyme coinfections reactivated from the spike protein’s toxicity to the innate immune system. Also, dormant viruses, bacteria, or fungus/fungal elements that were within their system.

Some patients have had mold or heavy metals in their environment prior or they’ve worked occupationally in toxic places. This usually requires a deeper investigation. Many toxins, including mold toxins (mycotoxins), and heavy metals can cause inflammation in the blood and the endothelium (walls of the vascular system). The spike protein pushes this inflammation over the edge, creating long COVID symptoms. Finding these factors can allow for appropriate integration of therapies around toxin management and neurovascular support. 

I will also look at the endocrine (hormone) system and see if there are irregularities there, since I have occasionally found the system can dysregulate here as well. This may include sudden declines in thyroid, adrenal, sex hormones, and blood sugar regulation systems.

The cases that are the toughest are often when there are more neurologic (and neuropsychologic) symptom manifestations in my experience. They might have a specific neurologic disease or these symptoms may be completely new. They may have neuropathies or immense fatigue, brain fog, autonomic and neuropsych disturbances (anxiety, depression, insomnia, panic attacks). 

I had a case that involved a possible MRNA vaccine injury. This person developed a lot of neuroinflammation with multiple debilitating symptoms.  We worked through a lot of the very basic protocols with this person and were not able to achieve a lot of progress until I found out that there were high levels of tick borne infection in their system. As I started working with the infections more intently, I started to see more gains. 

This patient had been treated prior for tick borne infection, and felt they had healed from it, but then some of that started to come back. With testing, we found Bartonella and other viruses like Epstein barr virus and cytomegalovirus. Variations of this multiple infection presentation are common in post COVID illness. I’ve made significant progress in relieving symptoms caused by the spike protein by treating these infections.

When it comes to COVID, treating it early is best. For our patients, we monitor their symptoms with the understanding that if they do harbor other infections, patterns of illness, or if they have sensitivity reactions that all of this should be considered in how we treat them individually. The people that I have started on protocols very quickly generally do the best. I ask them to tell me when they are positive right away, or have had exposure. Once we know, we can begin supporting very quickly. They may already have a protocol in place that we had discussed before, and that doesn’t always mean pharmaceutical treatments, it can be as simple as vitamin C, zinc, biotin, and vitamin D.

For most, antioxidants including vitamin C, NAC, Vitamin E are a good place to start.  If a patient is at higher risk, I will sometimes give them Paxlovid in the first five days. I will recommend ivermectin sometimes as well. I’ve found that time helps best with the inflammation response of COVID and vaccine responses as well. 

Taking action against the infection quickly is really the key feature and then monitoring for those post-infection phases. Watching if there are issues with coagulation or clotting systems is very important. If a patient does happen to have lingering or reactivated respiratory infections, then addressing this early is a priority. I will monitor their oxygen saturation, decline of symptoms, then treat with antibiotics and steroid therapies if appropriate. I have fortunately avoided hospitalization in my patients treated this way. 

Preparing people for the vaccine can be more challenging. It’s important for them to tell me if they plan on getting it. With advance notice, I can usually prepare people around it. In these cases, I will often use a lot of antioxidants. Similar to a COVID infection, I will use vitamin C, vitamin A, NAC, and vitamin E. Basically all the coagulation support. Some patients still get triggered from that, though not right away, which makes it more challenging. I’ve had a few patients with bad reactions the next day where the vaccine flared out their existing chronic symptoms. 

One patient with Stiff Person Syndrome (SPS) got a vaccine with the first generation MRNA. The two years of progress that we had made on her illness all back slid quite a bit and it took us another year and a half or so to get her back to where she was before.

This was the very early stages of the vaccine and I didn’t have the same level of protocols that I do now. The only known common factor between viral illness and vaccination is spike protein.  The  surge of spike that comes from the MRNA vaccine is quite robust and can be difficult to mitigate in those susceptible. The best practice right now is still to use similar principles of treatment as we do for infections, minus the antiviral treatments. 

I’ve seen a lot of infections reactivate from the vaccine too, so some of the same reactions that happen with the virus can happen with the vaccine in terms of suppression of immune system response or dysregulation of the immune system response. 

It’s also interesting to see people with repetitive COVID infections and how that presents. I try to pay attention to how many times a patient has had COVID and how many times they’ve been vaccinated on top of it. I feel like if they didn’t dysregulate from the first experience, there’s still a chance that they could from subsequent experiences. 

Even though there are risks with multiple exposures, I try to tell people not to live in a bubble. We still want to communicate on these types of events, and monitor them appropriately to ideally prevent them from escalating the next time. Early treatment is the most important factor for these individuals.

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