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Encephalitis and Cytokines: When Viruses Like COVID-19 Have Long-Term Effects on the Brain
Dr. Jaycie Loewen

By: Dr. Jaycie Loewen Last Updated: May 23, 2022

Medically Reviewed by Dr. Alina Fong

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Encephalitis and Cytokines: When Viruses Like COVID-19 Have Long-Term Effects on the Brain

Brain Injury Awareness  |  Traumatic Brain Injury  |  Education & Resources  |  Brain Safety & Care

While the world wrestles with the COVID-19 pandemic, most news coverage is focused on what’s before us: death tolls, the emergence of new signs and symptoms, and the search for viable treatments. And this is as it should be. However, there’s something you should know that the news does not often emphasize: Of the many people who recover from COVID-19, a small percentage will have consequences of the disease that will outlast acute infection.

We know that certain viral and bacterial infections can have long-lasting consequences for the brain, if certain conditions are met (for example, if they cause encephalitis, which is inflammation of the brain). Given the ways that COVID-19 has caused neurological symptoms in some patients, we expect similar stories to emerge — stories of people who used to be healthy and now have fatigue, headaches, difficulty concentrating, or any number of symptoms similar to post-concussion patients.

The good news is that, in many cases, these symptoms are treatable if you know where to turn for help. While we primarily treat concussion patients whose symptoms never went away with time and rest, we’ve also treated patients who have recovered from conditions like bacterial and viral meningitis and carbon monoxide (CO) poisoning. The brain dysfunction they experienced was identical to that of concussion patients. Because of that, the same therapy that worked for the concussion patients worked for them as well.

In this post, we’ll cover:

Have your symptoms lingered for weeks or months after an infection? If you’ve experienced concussion, viral encephalitis, meningitis, hypoxia, carbon monoxide poisoning, or another source of brain trauma, sign up for a consultation. We’ll discuss your medical history and determine if you’re a good candidate for treatment. 95% of our patients experience statistically verified restoration of brain function after treatment at our clinic.

Note: Any data relating to brain function mentioned in this post is from our first generation fNCI scans. Gen 1 scans compared activation in various regions of the brain with a control database of healthy brains. Our clinic is now rolling out second-generation fNCI which looks both at the activation of individual brain regions and at the connections between brain regions. Results are interpreted and reported differently for Gen 2 than for Gen 1; reports will not look the same if you come into the clinic for treatment.

Can a Viral Infection Affect the Brain?

Yes, a viral infection can affect the brain, directly and indirectly. Bacterial infections and parasites can do so via similar mechanisms, but we’ll focus on viruses for the purposes of this post.

There’s a well-known cohort of viruses known to be capable of causing brain damage, such as herpesviruses (like herpes simplex virus [HSV], Epstein-Barr virus, and the varicella-zoster virus, which you know from chicken pox), mumps, rubella, and West Nile virus. But there’s more than one way to affect the brain, and more common viruses (even, on occasion, the common flu) are capable of causing brain trauma as well.

How Viral Infections Affect the Brain



There are five main ways we see patients suffering from neurological symptoms due to an infection:

Some patients may suffer from one; some may have more than one causing problems jointly. Here’s a quick explanation of each.

Direct Infection of Brain Tissues (Least Common)

Some viruses are capable of crossing the blood-brain barrier to infect brain cells (neurons, astrocytes, and so forth). It’s the least common of the methods listed in this post. But when an infectious disease is capable of directly infecting brain tissue, it’s a hard fight for survival. The virus (or your immune system attempting to fight the virus) could cause the death of infected brain cells, which is often permanent damage (and not something we can fix).

Patients who do survive will likely have lingering health issues to unravel and work through — something that we can help with. In fact, we’ve already helped many people with lasting brain damage from severe TBI (in which there was permanent damage we could see on the scan). We can’t reverse that damage, but we can help the rest of the brain adjust.

Encephalitis and Meningitis

Encephalitis is swelling and inflammation of the brain; meningitis is swelling and inflammation of the protective membrane that covers the brain and spinal cord (meninges). Encephalopathy is the term used to describe when the damage from either (or both) is permanent. All three can be caused by a virus.

Swelling and inflammation can interfere with the connection between brain cells and the blood vessels that supply them (neurovascular coupling, or NVC). Dysfunctional neurovascular coupling is at the heart of lingering symptoms for post-concussion patients, which is why we’re often able to help viral encephalitis survivors, too.

This is an example of indirect brain damage from a virus. The virus causes encephalitis (or meningitis), which in turn causes long-term brain dysfunction that can often only be resolved with treatment.

Cytokine Storms (Overactive Immune System)

Cytokines are chemicals your body produces for several jobs, including to help guide your immune response. Certain cytokines can ramp up your inflammation response to infection; others latch on to infected cells to mark them for death.

When cytokines overreact and harm — or even kill — healthy cells, that’s called a cytokine storm (or cytokine soup). It’s one of the more serious reactions you can have to a virus; many patients with a cytokine storm end up in the ICU (intensive care unit) at their local hospital. The results are widespread dysregulation and inflammation; one of the long-term effects can be concussion-like symptoms.

Autonomic Nervous System (ANS) Dysregulation


Almost any trauma can affect our autonomic nervous system, and viruses are no exception. For some patients, the sympathetic nervous system (think fight-or-flight response) may not relax after the threat (the virus) has been eliminated.

An overactivated nervous system can cause all kinds of symptoms, such as headaches, blood pressure issues, heart palpitations, light and noise sensitivity, gastrointestinal issues, and more.


Hypoxia — having low oxygen in some or all body tissues — can also cause long-term symptoms if it occurs in the brain. If a virus causes difficulty breathing (like COVID-19) or directly infects and interferes with lung cells, hypoxia could be the result.

Any disruption of oxygen to the brain could cause problems; for example, we’ve even seen and treated patients who had lingering symptoms from carbon monoxide poisoning (which deprived their brains of sufficient oxygen). When you disrupt the brain’s oxygen supply, dysregulation of neurovascular coupling (NVC) often follows.

Note: There is some disagreement in the literature as to whether NVC is directly damaged by hypoxia or whether there is another step in between (for example, perhaps the lack of oxygen in the brain leads to hypoxia-induced encephalopathy which leads to problems with NVC). Regardless, hypoxia is involved in leading to the decoupling, which in turn produces those concussion-like symptoms.

How Does COVID-19 Affect the Brain?

As of writing this post, we don’t know with certainty whether COVID-19 can directly infect brain cells. Some of the best ways to gather this data are via autopsy and lumbar puncture (spinal tap) for cerebrospinal fluid analysis; however, many hospitals do not have the resources to do the testing themselves, and independent labs are overwhelmed with COVID-19 detection. While we wait, the information from case studies is conflicting; some researchers think it can directly infect brain cells and brain stem tissue, while others do not.

Nevertheless, a notable number of patients have suffered neurological symptoms, including seizures (which we know can cause neurovascular decoupling). Doctors are using a variety of tests, including CT scans, MRI, blood tests, and EEG (electroencephalogram) to better understand what happens to these patients.

COVID-19 patients have reported symptoms of confusion, dizziness, headaches, muscle aches, and other symptoms related to nervous system function. There’s been a documented case of encephalitis in the United States and multiple instances of cytokine storms, which can result in some of the most severe cases of the illness. The breathing issues could cause disruption of the brain’s oxygen supply. And even the high fever, if sustained, could cause lingering brain dysfunction.

In other words, any of the mechanisms discussed above could be in play with COVID-19. We expect to see some fraction of COVID survivors facing lingering symptoms after their initial recovery.

Have your symptoms lingered for weeks or months after an infection? If you’ve experienced concussion, encephalitis, meningitis, hypoxia, carbon monoxide poisoning, or another source of brain injury, sign up for a consultation. We’ll discuss your medical history and determine if you’re a good candidate for treatment. 95% of our patients experience statistically verified restoration of brain function after treatment at our clinic.

Are Current Concussion and PCS Patients High Risk for Severe COVID-19 Symptoms?

Yes, concussion and post-concussion syndrome sufferers could be at risk for more severe symptoms. To clarify, they are no more likely to contract the illness than anyone else, but if they do contract COVID-19, then there are several reasons they may have a harder time handling the illness.

Many post-concussion patients have some level of ANS dysregulation. They can have problems with vasculature (blood vessels) regulation, and their breathing may be dysregulated as well. Therefore, they are more at risk for difficulty breathing and for an immune system overreaction — the cytokine storm mentioned earlier.

Keep in mind that the autonomic nervous system has some control over the cytokine response. In very general terms, the sympathetic nervous response (fight or flight) will promote the inflammatory cytokines; the parasympathetic nervous system (rest & digest) will promote anti-inflammatory chemicals. A nervous system skewed toward the first will be more likely to have serious difficulties during the fight against COVID-19.

If you’ve sustained a concussion (or another head injury) and still have symptoms, it’s a good idea to isolate yourself from society while social distancing measures are in effect. If you have a friend or family member who can handle store runs, it’s better to let them do so in your stead.

We hope that researchers will identify a vaccine and/or an effective antiviral treatment against COVID-19 soon, but for now, your best chance of staying healthy lies with being proactive and cautious.


Concussion Symptom Checklist

Ways You Can Be Proactive

In addition to following guidelines from the Centers for Disease Control and Prevention (CDC) — such as wearing a mask in public spaces, not touching your face, and frequently washing your hands — there are some things you can do to give your body the best chance at fighting the coronavirus, should you get sick:

  • Even though it’s harder to find what you need at the grocery store, try your best to have well-rounded meals. If you can, make healthy meals in batches, and store portions in the freezer for use if you get sick. Look for anti-inflammatory foods.
  • Keep exercising! Get out on those walks, runs, or whatever you can do for exercise. Just remember to stay far away from other people who are exercising — since we don’t yet know how infectious COVID-19 is outdoors, it’s better to give people more than 6 ft when they’re in motion.
  • Quality sleep after a concussion, or when you’re stressed, or when you’re cooped up at home all day (and so forth) can be difficult. Do your best to stick to a sleep routine (even if you don’t have a commute anymore), and stay as well rested as you can.
  • Do things to relax your nervous system, like gardening, reading, meditating, or listening to calming music. As difficult as it may be, try not to let anxiety and fear dictate the state of your nervous system. If you’re having trouble, consider writing down your worries in a journal and then putting it away for the day.
  • Get enough Vitamin D. Vitamin D deficiency is more likely when we’re all stuck inside; take some time each day to get in the sunlight and look for foods that are high in Vitamin D. If those aren’t enough, consult with your doctor on an appropriate supplemental dose.
  • If you do get sick, tell your primary care doctor immediately, especially if you have any problems breathing. They can advise you on next steps.
  • Sick or not, do your best to get up and move around multiple times per day. Sitting and lying down all the time will negatively affect your body chemistry.

What if You Don’t Feel Like Yourself After Recovery from COVID-19, Encephalitis, Etc.?

Many COVID patients report feeling fatigued for weeks after contracting the virus. Fatigue after an infection isn’t abnormal, but it shouldn’t drag on past the first few weeks after initial recovery. If you haven’t made a full recovery, there may be some long-term symptoms you need to get in check.

We’ve seen and treated patients who have recovered from meningitis, CO poisoning, and even hypoxia induced by sleep apnea! Their brains looked like the brains of post-concussion patients, with hyperactive and hypoactive brain regions appearing on their fNCI scans (a type of fMRI, or functional magnetic resonance imaging).

So, we suspect that you might experience any of the symptoms we’ve seen in PCS patients, including:

Cognitive Symptoms

  • Brain fog
  • Difficulty concentrating
  • Difficulty finding things
  • Distractibility
  • Easily feeling overwhelmed
  • Fatigue
  • Headache
  • Migraine
  • Memory loss
  • Memory problems
  • Sleep disturbances

Visual Symptoms

  • Blurry vision
  • Difficulty reading
  • Functional vision changes
  • Sensitivity to light
  • Sensitivity to screens
  • Tired eyes

ANS-Related Symptoms

  • Balance problems
  • Blood pressure changes
  • Change in or loss of taste
  • Dizziness
  • Exercise intolerance
  • Gastrointestinal issues
  • Heart rate irregularities
  • Nausea
  • Ringing ears
  • Sensitivity to noise
  • Sensitivity to temperatures
  • Stiff neck

Emotional Symptoms

  • Anxiety
  • Depression
  • Irritability
  • Low motivation
  • Personality changes not otherwise mentioned in this list

Note: Acute stiff neck is a sign of meningitis and should be taken seriously. If you have signs and symptoms of meningitis, see a doctor as soon as possible.


Be attentive to your body. If you think something is wrong, don’t let other people brush you off, especially when it comes to your mental health. Well-meaning people can say things like, “Oh, you’re just stressed right now,” or “You’re not the only one who’s depressed right now; it’s just because we’re all struggling with the pandemic.” But a common cause of depression in brain injury survivors, in addition to trauma or situational issues, is a chemical imbalance. If you think there’s something more to your post-illness mood changes, it’s worth seeking help rather than trying to wait it out on your own.

If you’re experiencing the above symptoms long after your battle with the virus has ended, seek help from a trained medical professional who can provide therapy, or refer you to someone.

Brain Dysfunction After Viral Infection Is Treatable 

It is incredibly frustrating to experience lingering symptoms and not know why. Some of our patients suffered for decades before finding our clinic and undergoing treatment. Many doctors simply don’t know what causes these symptoms, and are therefore poorly equipped to diagnose and treat them. Sometimes, our patients have been told by other doctors that they’re imagining their pain or making up symptoms to get attention.

Lingering symptoms after a viral infection, concussion, or other source of brain trauma are real, and we can see the changes in your brain to prove it using functional neurocognitive imaging (fNCI). This imaging technique allows us to see which regions of your brain were affected and whether they are hypoactive or hyperactive.

Using that information, we then administer a week-long regimen of therapy designed to kickstart the brain’s inherent neuroplasticity (its ability to adapt and improve based on external and internal stimuli). Therapy — consisting of neuromuscular therapy, sensorimotor therapy, cognitive therapy, occupational therapy, and more — is tailored to your specific needs, as identified during the fNCI and other in-person examinations.

With our extensive, multidisciplinary staff, we’re able to accomplish what many clinics don’t have the resources to do. 

Want to learn more? Read about our EPIC treatment program, or see what our patients have said about their journey to recovery.

If you want to learn if you are a good candidate for treatment, sign up for a consultation.

About Dr. Jaycie Loewen

Dr. Jaycie Loewen is a Clinical Neuroscientist who received her Doctorate of Neuroscience at the University of Utah. Her background includes the study of basic and clinical brain injury, including the publication of research regarding mechanisms of epilepsy pathophysiology. Her work has elucidated the role of glial and neuronal cell profiles in viral-induced brain injury and acute seizures. Dr. Loewen is further a Howard Hughes Medical Institute Scholar, with a Master's in Clinical Investigation awarded in 2018, as well as a recipient of the Higher Education Teaching Specialist Certificate. Through these degrees, she obtained experience with patient care and education as well as an understanding of the necessity of respecting patient experience and symptoms. Dr. Loewen’s focus is firstly patient care and education. She also provides literature analysis and aids in the publication of Cognitive FX’s research. Her goal is to improve Cognitive Fx’s ability to help patients through equal interaction and communication, as well as the furthering of concussion and mild traumatic brain injury treatment and science.

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