Thursday, October 12, 2023

Diagnosing & Treating Thyroid Dysfunction in ME/CFS and Long-COVID


NOTE: I am not a doctor. This post is based on my own experiences and what I have learned from my doctors and research. Always talk to your own doctor about any new treatments.

Key Points:

  • Thyroid function affects every part of the body.
  • Thyroid is very often dysfunctional in ME/CFS, long-COVID, tick infections., and related illnesses.
  • Testing just TSH is often not enough; a full thyroid panel is more helpful.
  • Treating thyroid can take a lot of patience and persistence to find just the right combination and dosages. Adjust dose in small increments to find the most effective dose for you.
  • After starting or changing thyroid treatment, wait 6-8 weeks to retest.
  • Evaluate treatments based on test results but also on symptoms and how you feel.
  • Effectively treating thyroid dysfunction should result in significant improvements in many ME/CFS and long-COVID symptoms.

ME/CFS and long-COVID are immune disorders that affect all parts of the body, with significant impacts on the endocrine system (this is also often true with Lyme disease and other tick infections). The endocrine system is made up of all the different hormones in the body and is responsible for regulating all bodily functions, including sleep, digestion, reproduction and sexual function, metabolism, and everything else. Hormones are the messengers of our body, released by various glands to tell our organs how to function.

What Does Thyroid Do?

The thyroid gland is one of these messenger centers, regulating metabolism (the rate at which your body uses energy), which is a key factor in ME/CFS, long-COVID, and tick infections. It also plays roles in controlling heart, muscle, and digestive functions, brain development, and bone maintenance. The thyroid gland, located at the base of the throat, releases thyroid hormones, including triiodothyronine (T3) and thyroxine (T4), which affect every cell and every organ in your body. Certain organs in your body transform T4 into T3 (the active thyroid hormone) so that it can be used by your cells. This article from the Cleveland Clinic explains thyroid function in greater detail.

T3 is named that because it contains 3 iodine molecules, while T4 contains 4 iodine molecules. Plenty of iodine must be present for your body to create enough T4 and convert it to T3. ME/CFS UK expert Dr. Sarah Myhill explains the critical role of iodine in this excellent, brief article, Iodine - What is the Correct Daily Dose? She's also written a book about treating thyroid dysfunction, The Underactive Thyroid - Do It Yourself Because Your Doctor Won't.

Clearly, the thyroid is critical to all functions in our bodies. Since endocrine dysfunction is an integral part of ME/CFS, long-COVID, and tick infections, thyroid dysfunction is very, very common in these diseases. Luckily, it is also very treatable, and treating thyroid dysfunction can help to improve just about everything.

I've recently come through a difficult period where my thyroid became extremely dysfunctional. At one point, I was bedridden for over a month. After a year of frequent thyroid testing and adjusting treatments, I am finally feeling quite good. My energy is good, my sleep is better, my symptoms are improved, and I am able to be more active without crashing. Oh, and I've lost 10 stubborn pounds over the past year (hypothyroidism aka low thyroid causes weight gain). I'll share some key details of my story, with respect to thyroid function (you can read my full 21-year illness history here) and then some lessons learned regarding testing and treating thyroid function.

My Thyroid Story

I am fortunate to have a primary care physician who understands ME/CFS and knows of the high potential for thyroid dysfunction in the disease. So, for the first 19 years of my ME/CFS and Lyme disease, she frequently checked my thyroid function with lab tests. Looking back, I see that some years she only tested TSH (thyroid stimulating hormone), which isn't enough to get a full picture of thyroid function (more on that below), but other years, she also tested T3 and T4, which were always in the normal range. In 2021, that changed. Here's a brief timeline:

March 2020 (no connection to COVID; the timing was coincidence) - I went into an unexplained relapse and began seeing my son's Lyme specialist (I hadn't seen one in a while and my Lyme was flared up). By May, I was improving. 

February 2021 - for the first time ever, lab testing showed low thyroid function (hypothyroidism) - T3 and T3 Uptake were slightly low; all other thyroid tests were normal. My Lyme specialist started me on a low dose (5 mcg) of liothyronine (artificial T3). Next lab tests were normal.

May/June 2021 - I got the first two COVID vaccines, and my ME/CFS worsened for the next 6 months.

October 2021 - slightly low T3, so my doctor increased liothyronine to 10 mcg.

January 2022 - I got COVID and my ME/CFS worsened for six months.

June 2022 - Thyroid labs mostly normal, except for slightly low T3 Uptake.

NOTE: See my Relapses and Recoveries post from June 2022 for details on all of the treatments that helped me to recover from the multiple relapses that began in March 2020, including those triggered by vaccines and COVID.

August 2022 - After decades on birth control pills to keep my hormone levels steady, I had to stop taking them (I was fully in menopause and my OB/GYN of 30 years was retiring). A severe relapse resulted, and I was mostly bedridden through all of September and part of October, until I started using estrogen patches and progesterone.

November 2022 - Since the whole endocrine system is connected, that sudden shift in estrogen and progesterone sent my thyroid hormones into chaos! Tests showed low T4, low T3 Uptake, and low Free Thyroxine (T4) Index (see Lessons Learned below for tips on testing).

January 2023 - I switched my thyroid care from my Lyme specialist to my primary care physician (PCP), and she started me on Armour thyroid, 30 mg, in addition to the liothyronine. Armour is a natural product, real desiccated thyroid gland from pigs, and thus, it works most effectively to help normalize all thyroid function. Many experts say it's the most effective way to treat hypothyroidism.

March 2023 - Lab tests still showed low T3 and T4, so my PCP increased my dose of Armour thyroid to 45 mg.

June 2023 - Lab tests showed normal T3 and TSH but still low T4, so my PCP increased my dose of Armour thyroid to 60 mg.

August 2023 - Lab tests showed T3 barely in the normal range and T4 still low, so my PCP increased my dose of Armour thyroid to 75 mg.

October 2023 - I tested differently this time, getting the blood drawn before I took my morning thyroid meds (see Lessons Learned below), and the results were similar to the August results: low T4 and T3 barely in the normal range. My PCP increased my dose of Armour thyroid to 90 mg.

NOTE: Throughout 2023, with each dose increase of Armour thyroid, I was feeling better and better--more energy, better sleep, more stamina, fewer crashes. The dosage adjustments my PCP has been making have been tiny changes each time, rechecking lab results every two months, as recommended. I am still on just an average dose of Armour thyroid (average is between 60-120 mg).

December 2023 - Tests still showed low T4 and very low-normal (barely in the normal range) T3 and TSH. Based on advice from my Lyme specialist and Dr. Myhill's article, I started a small dose (6.25 mg) of Iodoral brand iodine (the one recommended by both of those sources). After 2 weeks, I increased my dose to 12.5 mg (2 pills), then to 18.75 mg (using the 6.25 mg pills and the 12.5 mg Iodoral pills). As of end of January 2024, I am testing out a dose of 25 mg. With each increase of iodine (Iodoral), my energy and overall well-being improved.

Lessons Learned


Many doctors only test for TSH, but TSH can be normal when T3 and T4 are abnormal. For maximum effectiveness, ask for a full thyroid panel, including:

  • TSH
  • Thyroxine (free T4)
  • T3 Uptake
  • Free Thyroxine Index
  • Triiodothyronine (free T3)
  • Reverse T3, serum

At a minimum, ask your doctor to request tests for free T3, free T4, and TSH. 

If you are taking any thyroid treatments, get blood drawn for testing first thing in the morning, before you take your thyroid medications. This will provide the most accurate picture of your thyroid function rather than just showing the immediate effect of the medications.

After starting or changing treatment for thyroid dysfunction, wait 6-8 weeks to retest. It can take that long for your body to fully adjust. It can take even longer for your body to fully absorb iodine supplements.

The goal is not only to get T3, T4, and TSH barely into the normal range, but to get to a point where your thyroid function is normalized, and you feel better, with T3 and T4 values in the middle of the normal range. In fact, the very helpful website Stop the Thyroid Madness, which is based on thousands' of patient experiences over the course of decades, says that optimal thyroid function will be when your free T3 is in the top part of the normal range and free T4 is in the middle of the normal range (remember that T4 converts to T3).

In addition to what the tests show, pay attention to how you feel and describe to your doctor any changes (positive or negative) after changes in treatment. As thyroid is normalized, you should begin to feel better.


Everyone is different. Finding exactly the right combination of treatments and dosage for you can take some trial and error (and patience and persistence!). 

Experts generally recommend Armour thyroid or other natural desiccated thyroid as most effective in normalizing thyroid function, either with or without a T3 treatment (like liothyronine). Some people do well on just a T3 treatment (as I was for the first 18 months), and some on a combination of T3 and T4 treatments or just natural desiccated thyroid.

The right treatment for you will depend in part on your lab results (for instance, in the first 18 months of my thyroid treatment, my T3 was a bit low and the other numbers were normal) and your own individual response to treatment. That's why some trial and error might be necessary.

I felt much better after starting Armour thyroid, and with each increase in dose, my condition further improved. 

Thyroid medication should be taken on an empty stomach and away from antacids, calcium, iron supplements, and cholesterol medications. Taking it upon waking and waiting at least an hour before you eat works well for many patients.

After reading that splitting the dose can improve effectiveness and keep thyroid levels more stable throughout the day, I began splitting my daily dose in two, taking half when I first wake up and half after my nap, which is midway between lunch and dinner. (Note that I am talking about taking some pills in the morning and some in the afternoon, not cutting them in half; Armour thyroid can not be cut in half as it crumbles.)

There are several minerals that can be helpful to your thyroid--most of these are recommended for patients with ME/CFS or long-COVID or tick infections anyway (always start with a low dose, as listed, and check with your doctor):

  • Selenium 200 mcg - also supports healthy immune function.
  • Zinc - start low at 15-20 mg (increase if testing shows you're low); also supports healthy immune function.
  • Vitamin D3 (necessary for good immune function & often low in ME/CFS) - I take 5000 IU - you can test to see where your levels are to start.
  • Magnesium (look for glycinate, malate, or l-threonate; avoid oxide or citrate which are not well-absorbed and can cause diarrhea) - also helps with pain, sleep, energy, cognition, nervous system - I take Mg malate (1600 mg) and Mg-l-threonate (1200 mg), which is the only form of magnesium that can cross into the brain and is thus best for cognitive function.
  • Iodine - Iodoral brand is recommended by experts as pure and effective. Start at a low dose, like 6.25 or 12.5 mg or equivalent liquid and increase gradually if it is helping. Be sure to take iodine supplements away from vitamin C.

(NOTE: Check labels of supplements and medications if you are dairy intolerant; many use lactose as a filler. Pills that contain lactose are usually white and solid; gel caps don't contain lactose. Check labels or drug information online, looking for "inactive ingredients.")

Some experts say that low-dose naltrexone (LDN) can also help. This is a treatment that helps to normalize your immune system, so it is helpful for those with ME/CFS, long-COVID, and tick infections anyway. My son and I have taken it for about 15 years. Maybe that's why I didn't have any thyroid issues for so long!

If your doctor isn't willing to work with you on this--trying a treatment, waiting 6-8 weeks to get retested, listening to what you say about symptoms, adjusting treatment, repeat--then you should look for a different doctor (tips on finding a doctor). Treating thyroid dysfunction is often done by primary care physicians, family doctors, or general practitioners (GPs); however if your case seems particularly complex, your doctor may refer you to an endocrinologist. But, in most cases, a specialist isn't necessary.


I've found a couple of resources that have been very helpful in understanding how to diagnose and treat thyroid dysfunction:

  • Stop the Thyroid Madness - an excellent website packed full of information, based on decades of collected patient experience. If reading is difficult for you (congrats on getting this far in my post!), there are some audio options on the home page. Be sure to check out the article on achieving optimal thyroid function (can also print to share with your doctor).
  • Hypothyroidism in Lyme Disease from the Treat Lyme website by Marty Ross, MD - a well-respected website for those with tick infections, and the thyroid article is applicable for those with ME/CFS and long-COVID, too. Also good for sharing with your doctor.
  • Iodine - What is the Correct Daily Dose? by Dr. Myhill (who is an ME/CFS expert in the UK)

So, that's my story and what I've learned. 

What have been YOUR experiences with diagnosing and treating thyroid dysfunction?

Let me know in the comments below.

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Anonymous said...

I have low T3 but low normal tsh and t4. I’ve been dealing w chronic fatigue for 2 years after covid and a list of issues

Sue Jackson said...

Then you could definitely benefit from treating hypothyroidism and bringing the T3 and T4 up higher! Remember that optimal thyroid function is when T4 is in the MIDDLE of the normal range and T3 is at the higher end of the normal range - just barely into the normal range (low-normal) is still dysfunctional, especially with your T3 low.

I would definitely talk to your doctor about trying some treatments to bring those well into the normal range - it helps to improve everything! I feel SO much better than I did a year ago when I was just starting this process. Remember it can take some trial and error (which means time, patience, and persistence), testing every 2 months after a treatment change - but it is so worth it. Best of all, this is a measurable thing that any doctor can help you with.

Good luck! Please let me know if you have any questions, but please check out that Stop the Thyroid Madness website I linked to and I would also give the Iodoral (iodine supplements) a try.


Anonymous said...

T4 only needs to be in mid range if you're not on t3 meds. If you're on all or mostly t3 then t4 levels will be low and that's fine. The recommended dosage for t3 is between 50 and 100mcg. T3 should be raised every 1 to 2 weeks, not waiting as long as t4. Mid range isn't high enough for t3. It should be top quarter or very top of the range.

Sue Jackson said...

Thank you for taking the time to comment and share that info. Since it differs a bit (except for recommending that T3 be in the top part of the normal range - I said the same here) from the information I found in my research (I included the links to my sources in the blog post), can you share with me your sources? Thyroid function is so complicated! I would love to better understand it and the most effective approaches to treating it, both for myself and my readers.