This is part two of a five-part series decoding the biological evidence behind five of the most dismissed symptoms in Long COVID, ME/CFS, PoTS and related conditions. Yesterday we looked at brain fog and the PET scan evidence of dopamine system injury. Today: the PEM crash.
Post-exertional malaise is the symptom that perhaps attracts more scepticism than any other in these conditions. The idea that activity causes a delayed, disproportionate worsening that can last days or weeks is one that patients are routinely told is deconditioning, anxiety, or a learned fear of movement. The studies below do not support that interpretation. They support a different one: that specific, measurable cellular damage occurs during and after exertion in people with these conditions, damage that does not occur in healthy controls doing identical exercise and that is visible under a microscope.
Study 1: The muscle biopsy study that made post-exertional malaise impossible to dismiss
Appelman B, Charlton BT, Wüst RCI, et al. Muscle abnormalities worsen after post-exertional malaise in long COVID. Nature Communications. 2024;15:17.
Published in January 2024 in Nature Communications by researchers at Amsterdam UMC and Vrije Universiteit Amsterdam, this study took skeletal muscle biopsies from 25 Long COVID patients with post-exertional malaise before exercise and one day after exercise triggered a crash, running the same protocol in 21 healthy controls.
Before any exercise had taken place, Long COVID muscle was already different. Mitochondrial enzyme activity was reduced at baseline. The proportion of fast-twitch glycolytic fibres, the type that fatigue rapidly, was higher than in controls. Macrophages, immune cells associated with tissue damage and repair, were already present in greater numbers in patient muscle tissue before a single bout of exercise.
One day after exercise induced a crash, the findings worsened significantly. Oxidative phosphorylation capacity fell. Succinate dehydrogenase activity, a direct marker of mitochondrial function and a key enzyme in the Krebs cycle, dropped in Long COVID patients while remaining stable in controls. CD3 positive T cells accumulated in the muscle tissue, indicating an immune response to what the body was treating as injury. Areas of focal necrosis, localised cell death, were visible. Small atrophied fibres and signs of active muscle regeneration were present.
The blood supply to the muscle was identical in both groups. Capillary density and the capillary to fibre ratio showed no differences between patients and controls. This rules out the explanation that the damage was caused by reduced oxygen delivery, which is the hallmark finding of deconditioning. The muscles were being supplied with blood normally. They were still breaking down.
Study 2: The study that proved it is not deconditioning
Wüst RCI, et al. Skeletal muscle properties in long COVID and ME/CFS differ from those induced by bed rest. Nature Communications. 2026.
If post-exertional malaise were caused by deconditioning, the muscle changes seen in Long COVID and ME/CFS patients should look like the muscle changes caused by prolonged physical inactivity. In 2026, Rob Wüst and colleagues at Vrije Universiteit Amsterdam tested this directly by comparing muscle properties in Long COVID and ME/CFS patients against those produced by 60 days of enforced bed rest in healthy volunteers.
The profiles were not the same. Bed rest produced severe, widespread muscle atrophy. Long COVID and ME/CFS patients showed no equivalent general atrophy. ME/CFS patients showed selective shrinkage of type I slow-twitch fibres specifically, a pattern not seen after bed rest. Both patient groups showed higher proportions of glycolytic fast-twitch fibres compared to healthy controls, a shift not produced by inactivity. The mitochondrial impairments in the patient groups involved altered biochemical coupling that did not correlate with exercise capacity in the way deconditioning would predict.
The study concluded that physical inactivity cannot solely explain the lower exercise capacity or the muscle changes observed in these patients. The alterations are disease-specific. They are not a consequence of resting more.
Study 3: The exercise test that repeats itself to catch the crash
Davenport T, Stevens S, Stevens J, Van Ness M, et al. ME/CFS and Long COVID demonstrate similar bioenergetic impairment and recovery failure on two-day cardiopulmonary exercise testing. Clinical and Translational Metabolism.2026.
Cardiopulmonary exercise testing, known as CPET, measures how the cardiovascular and respiratory systems respond to increasing physical effort. A single CPET test in ME/CFS and Long COVID patients often returns results within normal limits because the test ends before the delayed crash begins. The two-day CPET protocol was designed specifically to capture what happens when exercise is repeated after a crash has been triggered.
In this study, participants performed maximal CPET on two consecutive days. Healthy controls performed at essentially the same level on both days. ME/CFS and Long COVID patients showed significant deterioration on day two. The most pronounced abnormalities appeared at the ventilatory anaerobic threshold, the point at which the body shifts from aerobic to anaerobic metabolism, where effect sizes were larger than at peak exertion. Both conditions showed the same pattern, with no significant differences between them, consistent with shared underlying physiology.
This is the finding that matters most for the medical and legal context in which many patients find themselves. Post-exertional malaise is not a subjective report of feeling worse. It is a measurable, reproducible, physiological failure to recover from exertion, documentable on objective testing, that does not occur in healthy people performing identical exercise.
Study 4: The microclot evidence in muscle tissue
The Appelman 2024 study also documented something that connects the muscle findings to a broader vascular mechanism. Amyloid microclots, abnormal fibrin deposits that resist normal breakdown and obstruct microvascular blood flow, were found in increased quantities in Long COVID muscle tissue. Their presence in the muscle itself, not just in circulating blood, suggests that the microvascular obstruction documented in blood samples by Pretorius and colleagues is also occurring at the tissue level, in the muscles that patients are trying to use.
Ongoing research by Wüst’s group is directly investigating whether the same microclot pattern occurs in ME/CFS muscle tissue, with results expected from biopsies collected in 2024 and 2025.
Study 5: The immune response that should not be there
The immune cell findings across the Appelman study and the broader PEM literature are worth examining separately because they address one of the most common dismissals: that the crash is the body being oversensitive or overreacting psychologically to normal sensations.
In the Appelman biopsies, exercise triggered accumulation of CD3 positive T cells in Long COVID muscle tissue. T cells are adaptive immune cells that respond to what the body classifies as damage or foreign material. Their presence in muscle after exercise means the immune system identified the post-exercise tissue as something requiring an immune response. That is not an overreaction to a normal sensation. That is the immune system doing what it does when there is actual cellular damage to respond to.
The distinction matters because it closes the loop between the subjective experience of a crash and the objective biological event underlying it. The immune infiltration, the mitochondrial failure, the microclots, the necrosis: these are not the biological signatures of anxiety or deconditioning. They are the biological signatures of injury.
What this means
Five findings. Mitochondrial enzyme activity that drops in patients after exercise while holding stable in controls. Muscle fibre changes that do not match the pattern of deconditioning. Physiological performance deterioration on day two of exercise testing that is reproducible and measurable. Amyloid microclots in the muscle tissue itself. Immune cell infiltration treating post-exercise muscle as a site of damage.
None of these findings are what you would expect if the crash were caused by psychological factors, learned behaviour, or deconditioning. All of them are what you would expect if exertion caused specific, cumulative cellular damage in a system that is not recovering normally between bouts.
The biology of the crash is there. It is in the biopsies, in the exercise tests, in the immune cell counts, under the microscope. The question, as it always is with this research, is how long it takes that evidence to reach the clinical settings where patients are still being told to push through.
The views and opinions expressed in Dysautonomia Decoded are my own and do not represent those of my employer or any affiliated organisation.
References
Appelman B, Charlton BT, Wüst RCI, et al. Muscle abnormalities worsen after post-exertional malaise in long COVID. Nature Communications. 2024;15:17. https://doi.org/10.1038/s41467-023-44432-3
Wüst RCI, et al. Skeletal muscle properties in long COVID and ME/CFS differ from those induced by bed rest. Nature Communications. 2026. https://www.nature.com/articles/s41467-026-75725-y
Davenport T, Stevens S, Stevens J, Van Ness M, et al. ME/CFS and Long COVID demonstrate similar bioenergetic impairment and recovery failure on two-day cardiopulmonary exercise testing. Clinical and Translational Metabolism.2026. https://link.springer.com/article/10.1007/s12018-026-09326-0
Pretorius E, et al. Flow clotometry: measuring amyloid microclots in ME/CFS, Long COVID, and healthy samples with imaging flow cytometry. 2024. https://ouci.dntb.gov.ua/en/works/7AJqP684/
Validated and vindicated! Now let’s figure out how to prevent and/or treat it!
I call my brain fog 'Brian the Brain Frog'. Brian is too loud for me to read all of this properly, but I get the gist. Thank you!