Etiology, pathology, genomics, physiology, and clinical course
Abstract
Long COVID, or post-acute sequelae of SARS-CoV-2 infection (PASC), is a heterogeneous multisystem disorder in which fatigue, post-exertional malaise, cognitive dysfunction, autonomic disturbance, exercise intolerance, myalgia and cardiopulmonary symptoms frequently coexist. Although no single mechanism explains the syndrome, accumulating evidence implicates persistent disturbances of cellular energy metabolism. Mitochondria occupy a central position in this hypothesis because they integrate oxidative phosphorylation, substrate utilization, redox homeostasis, calcium signaling, apoptosis, innate immunity and cellular stress responses.
A growing body of physiological, transcriptomic, proteomic and metabolomic evidence indicates that some patients with Long COVID exhibit impaired oxidative phosphorylation, altered skeletal-muscle bioenergetics, increased reliance on glycolysis, abnormalities of tricarboxylic-acid-cycle metabolism, oxidative stress, altered amino-acid and lipid metabolism, and persistent activation of mitochondrial stress pathways. A 2026 multi-omic analysis integrating human and animal datasets reported sustained suppression of oxidative-phosphorylation programs and mitochondrial stress signatures extending into the post-acute period, with particularly prominent abnormalities in skeletal muscle.[1] A contemporaneous Nature Communications study provides important physiological evidence that skeletal-muscle abnormalities in Long COVID cannot be explained simply by physical deconditioning: muscle phenotypes and exercise responses differed from those produced by prolonged bed rest.[2]
The mitochondrial hypothesis is nevertheless more nuanced than the proposition that SARS-CoV-2 simply “damages mitochondria”. Mitochondrial dysfunction may arise secondarily from persistent inflammation, immune-cell metabolic reprogramming, endothelial dysfunction, impaired oxygen delivery, viral proteins or nucleic acids, altered redox state, autoimmunity, autonomic disturbance, nutritional or metabolic stress, and persistent viral reservoirs. Mitochondrial impairment may itself then become a feed-forward mechanism: defective oxidative phosphorylation increases reactive oxygen species and cellular stress, promotes compensatory glycolysis, alters innate immune signaling, and reduces energetic reserve. In skeletal muscle, this may contribute directly to reduced exercise capacity and post-exertional malaise; in the brain, it may impair cognitive and autonomic function; in the heart, it may reduce energetic reserve; and in immune cells, it may perpetuate abnormal inflammatory states.
The genomic basis remains incompletely defined. Because oxidative phosphorylation depends upon coordinated expression of the nuclear and mitochondrial genomes, Long COVID may involve disturbances of mitochondrial gene expression, mitochondrial quality control, mitophagy, nuclear-encoded respiratory-chain proteins, mitochondrial dynamics and epigenetic regulation rather than conventional single-gene mitochondrial disease. Host genetic susceptibility may influence the ability to resolve inflammation and restore metabolic homeostasis. The clinical implication is that mitochondrial dysfunction should be regarded as a candidate mechanistic endotype, rather than a universal explanation for Long COVID. Definitive progress will require longitudinal integration of genomic, metabolomic, proteomic, physiological and tissue-level measurements, together with intervention studies capable of demonstrating that correction of the metabolic abnormality improves clinical outcomes.
Introduction
Fatigue is among the most characteristic and disabling manifestations of Long COVID.
Yet “fatigue” is an imprecise clinical term.
It can denote:
- sleepiness;
- generalized weakness;
- impaired motivation;
- cognitive exhaustion;
- reduced exercise capacity;
- muscular fatigue;
- autonomic intolerance;
- or the distinctive delayed deterioration known as post-exertional malaise (PEM).
In Long COVID, several of these phenomena frequently coexist.
The central physiological question is therefore not simply why patients feel tired, but why apparently modest physical or cognitive demands can produce disproportionate and sometimes delayed deterioration.
One compelling explanation is a failure of bioenergetic reserve.
Every cellular function ultimately depends upon energy availability. Mitochondria generate most cellular ATP through oxidative phosphorylation (OXPHOS), while simultaneously regulating redox balance, calcium signaling, apoptosis, inflammatory pathways and cellular adaptation to stress.
Tissues with exceptionally high energetic requirements—including skeletal muscle, myocardium, brain and immune cells—should therefore be particularly vulnerable to persistent mitochondrial dysfunction.
This proposition has moved beyond theoretical speculation.
A 2025 systematic review of omics studies in Long COVID identified mitochondrial dysfunction among recurring biological findings across symptom phenotypes, while emphasising substantial heterogeneity among studies.[3] A 2026 multi-omic analysis subsequently reported persistent suppression of OXPHOS and mitochondrial stress signatures across several tissues and biological compartments.[1] And physiological studies of skeletal muscle indicate abnormalities that cannot be explained simply by inactivity or deconditioning.[2]
Taken together, these findings provide the basis for a coherent immunometabolic model of Long COVID.
I. Mitochondria as the Cellular Integrator
Mitochondria are traditionally described as the organelles responsible for ATP production.
That description is incomplete.
Mitochondria participate in:
- oxidative phosphorylation;
- fatty-acid β-oxidation;
- the tricarboxylic-acid (TCA) cycle;
- amino-acid metabolism;
- calcium buffering;
- reactive-oxygen-species signaling;
- apoptosis;
- innate immune signaling;
- cellular stress responses;
- steroid and haem synthesis;
- metabolic adaptation.
The respiratory chain consists of complexes I–IV, which transfer electrons from reduced substrates to molecular oxygen while generating a proton gradient across the inner mitochondrial membrane. Complex V, ATP synthase, then uses that electrochemical gradient to generate ATP.
The process can be simplified as:
substrates → NADH/FADH₂ → electron transport → proton gradient → ATP synthesis.
A defect anywhere along this chain can reduce energetic efficiency.
But the physiological consequences are not restricted to ATP deficiency.
Electron leakage can increase mitochondrial reactive oxygen species (ROS), which can alter proteins, lipids, DNA and signaling pathways.
Mitochondria consequently represent both:
energy-producing organelles
and
stress-sensing organelles.
This dual role makes them particularly important in Long COVID.
II. The Bioenergetic Hypothesis
The simplest mitochondrial model proposes:
SARS-CoV-2 infection
↓
mitochondrial stress
↓
impaired oxidative phosphorylation
↓
reduced ATP availability
↓
increased glycolytic compensation
↓
metabolic inflexibility
↓
exercise intolerance and fatigue.
The actual biology is more complicated.
The evidence increasingly suggests a dynamic network involving:
inflammation ↔ mitochondrial dysfunction ↔ oxidative stress ↔ metabolic reprogramming ↔ immune activation.
Each component can reinforce the others.
III. SARS-CoV-2 and Mitochondrial Biology
SARS-CoV-2 infection profoundly alters host-cell metabolism.
Viruses depend upon host cells for:
- nucleotides;
- amino acids;
- lipids;
- ATP;
- protein synthesis.
Viral infection therefore necessarily modifies cellular metabolism.
During acute infection, host cells can undergo metabolic reprogramming toward glycolysis, altered lipid synthesis and modified mitochondrial signaling.
Several SARS-CoV-2 proteins have been reported experimentally to interact with mitochondrial or mitochondrial-associated processes, including pathways governing:
- mitochondrial membrane potential;
- innate immune signaling;
- ROS;
- apoptosis;
- mitochondrial dynamics.
The key question for Long COVID is whether these acute perturbations are completely reversed after viral clearance.
Increasing evidence suggests that in at least some patients they are not.
IV. Persistent Mitochondrial Suppression
The 2026 multi-omic study by Tasoula and colleagues provides important recent evidence.[1]
The investigators integrated transcriptomic, proteomic and metabolomic datasets from human cohorts and SARS-CoV-2-infected hamsters.
Across multiple tissues they identified recurring signatures of:
- suppressed OXPHOS;
- mitochondrial stress;
- inflammatory signaling;
- altered metabolism.
Skeletal muscle was particularly striking.
In experimental animals, OXPHOS-related transcriptional suppression persisted well beyond the acute phase. Human skeletal-muscle datasets from patients with post-COVID chronic fatigue demonstrated related mitochondrial and muscle-function abnormalities.[1]
The significance lies in the convergence of independent biological measurements.
The hypothesis is no longer based solely on a single metabolite or enzyme.
Instead:
transcriptomics + proteomics + metabolomics + tissue physiology
are beginning to point in the same direction.
Nevertheless, heterogeneity among cohorts remains considerable, and the findings should not yet be interpreted as proof that mitochondrial dysfunction is present in every patient with Long COVID.
V. Skeletal Muscle as a Metabolic Organ
Skeletal muscle is one of the body’s largest metabolic tissues.
During exercise, ATP consumption rises dramatically.
ATP must be continuously regenerated through:
- phosphocreatine buffering;
- glycolysis;
- oxidative phosphorylation;
- fatty-acid oxidation.
At low workloads, these systems can compensate for one another.
At high or prolonged workloads, oxidative phosphorylation becomes increasingly important.
Consequently, a defect in mitochondrial oxidative capacity may be largely invisible at rest but become clinically apparent during exercise.
This provides a plausible explanation for an important characteristic of Long COVID:
Some patients can appear relatively well at rest yet become profoundly impaired after modest exertion.
VI. Exercise Physiology
Cardiopulmonary exercise testing (CPET) provides a window into this physiology.
Peak oxygen consumption (VO₂peak) reflects the integrated ability of the organism to:
- deliver oxygen;
- transport oxygen;
- extract oxygen;
- utilise oxygen within mitochondria.
The Fick principle can be expressed as:
VO₂ = cardiac output × arterial–venous oxygen difference.
Thus, a reduced VO₂peak does not automatically establish mitochondrial disease.
Possible causes include:
- cardiac dysfunction;
- pulmonary limitation;
- anaemia;
- autonomic dysfunction;
- impaired peripheral oxygen extraction;
- deconditioning;
- mitochondrial dysfunction.
The challenge is to determine which component is limiting performance in an individual patient.
VII. Long COVID Is Not Simply Deconditioning
This distinction is crucial.
Patients with chronic illness often become physically inactive.
Physical inactivity itself causes:
- muscle atrophy;
- reduced mitochondrial capacity;
- reduced aerobic fitness;
- altered fibre composition.
One might therefore argue that Long-COVID muscle abnormalities are simply consequences of inactivity.
Recent evidence argues against that being the complete explanation.
A 2026 Nature Communications study compared Long-COVID and ME/CFS patients with healthy individuals subjected to 60 days of strict bed rest.[2]
Bed rest produced predictable physiological adaptations, but the skeletal-muscle and exercise responses of Long-COVID patients differed from those induced by bed rest.
The investigators concluded that physical inactivity alone could not account for the reduced exercise capacity and muscle adaptations observed in Long COVID.[2]
This does not mean deconditioning is irrelevant.
Rather:
Deconditioning may contribute to Long-COVID exercise limitation without being sufficient to explain it.
That distinction is clinically important.
VIII. Skeletal-Muscle Fibre Remodeling
Muscle fibres differ metabolically.
Type I fibres are highly oxidative and resistant to fatigue.
Type II fibres are more glycolytic and suited to rapid force generation.
Recent skeletal-muscle studies have identified altered fibre characteristics in Long COVID, including a shift toward more glycolytic fibres and abnormalities in muscle metabolism.[2,4]
This provides a potential physiological bridge between molecular findings and symptoms.
If muscle becomes relatively more dependent on glycolysis:
ATP can still be generated rapidly
but
oxidative endurance may decline.
The patient may therefore tolerate brief activity while becoming markedly impaired by sustained activity.
IX. The Post-Exertional Phenotype
PEM is one of the most distinctive manifestations of Long COVID.
Its defining characteristic is not merely fatigue after exercise.
It is disproportionate, delayed worsening of symptoms after exertion.
Possible mechanisms include:
- impaired oxidative phosphorylation;
- abnormal lactate handling;
- autonomic dysfunction;
- impaired vascular regulation;
- immune activation;
- oxidative stress;
- abnormal skeletal-muscle metabolism.
A plausible model is:
exertion → increased ATP demand → inadequate oxidative reserve → compensatory glycolysis → metabolite accumulation and redox stress → immune/autonomic amplification → delayed symptom exacerbation.
The delay is important.
It suggests that the mechanism is not simply immediate ATP depletion.
Instead, exertion may initiate a cascade of downstream biological events.
X. Mitochondrial Reactive Oxygen Species
Mitochondrial ROS are not inherently pathological.
At physiological concentrations, they function as signaling molecules.
When excessive, however, ROS can oxidise:
- membrane lipids;
- respiratory-chain proteins;
- enzymes;
- DNA;
- mitochondrial DNA.
This can produce a vicious cycle:
respiratory dysfunction
→
electron leakage
→
ROS
→
mitochondrial damage
→
further respiratory dysfunction.
Such a feedback loop could help explain persistence after the initiating viral infection has resolved.
XI. Mitochondrial DNA
Mitochondria contain their own genome.
Mitochondrial DNA (mtDNA) encodes essential components of oxidative phosphorylation, while the vast majority of mitochondrial proteins are encoded by nuclear DNA.
This creates a unique biological dependency:
nuclear genome + mitochondrial genome → functional respiratory chain.
Damage or dysregulation in either system can affect mitochondrial performance.
Mitochondrial DNA is also biologically important as an immune signal.
When mitochondrial integrity is disrupted, mtDNA can enter the cytosol or extracellular environment and activate innate immune pathways.
Thus:
mitochondrial injury → mtDNA release → innate immune activation → inflammation → further mitochondrial injury.
This provides a plausible mechanism for a self-reinforcing immunometabolic cycle.
XII. Genomics of Mitochondrial Dysfunction
The genomic dimension of Long-COVID mitochondrial dysfunction remains incompletely characterised.
There is little evidence that most Long-COVID patients have a conventional inherited mitochondrial disorder.
The more plausible hypothesis involves functional genomic reprogramming.
Potential mechanisms include:
- altered transcription of nuclear-encoded OXPHOS genes;
- altered mitochondrial gene expression;
- epigenetic modification;
- altered mitochondrial biogenesis;
- abnormal mitophagy;
- changes in transcription factors regulating metabolic state.
The 2026 multi-omic evidence is important in this context because persistent suppression of OXPHOS-related gene programs has been observed without requiring a classical inherited mitochondrial mutation.[1]
XIII. Nuclear–Mitochondrial Coordination
Mitochondrial respiration requires extraordinarily precise coordination between two genomes.
The nuclear genome encodes most respiratory-chain components.
The mitochondrial genome encodes selected essential subunits.
Successful oxidative phosphorylation therefore requires:
coordinated transcription + translation + mitochondrial import + assembly + membrane insertion.
Inflammatory or metabolic disruption at any stage could reduce respiratory efficiency.
This may be particularly relevant to persistent disease because recovery requires not simply elimination of the virus but restoration of an extraordinarily complex cellular system.
XIV. Mitochondrial Quality Control
Healthy mitochondria are continuously renewed.
Damaged organelles are removed through mitophagy.
New mitochondria are generated through mitochondrial biogenesis.
These processes are regulated by pathways involving:
- PGC-1α;
- AMPK;
- mTOR;
- SIRT proteins;
- NRF1/NRF2;
- TFAM.
Persistent inflammation can disrupt these pathways.
A Long-COVID patient might therefore have mitochondria that are not merely damaged but inadequately replaced.
The resulting state could be:
increased mitochondrial injury + impaired mitochondrial turnover = persistent bioenergetic deficiency.
XV. Metabolic Reprogramming
Cells possess metabolic flexibility.
When oxidative phosphorylation becomes inefficient, glycolysis can increase.
The advantage is speed.
The disadvantage is energetic efficiency.
Aerobic oxidation of glucose produces substantially more ATP per molecule of glucose than glycolysis alone.
Consequently:
OXPHOS ↓ → glycolysis ↑
may temporarily maintain cellular energy production but at greater substrate cost.
This may produce a state of metabolic inflexibility.
The 2026 multi-omic analysis identified persistent changes consistent with this phenomenon, including increased glycolytic programs and incomplete restoration of mitochondrial pathways in Long COVID.[1]
XVI. The Tricarboxylic-Acid Cycle
The TCA cycle is central to mitochondrial metabolism.
It converts carbon substrates into reducing equivalents that feed the respiratory chain.
Metabolomic studies of Long COVID have reported abnormalities involving TCA-cycle intermediates and glycolytic metabolites.[1,3]
Such findings are potentially important because they suggest that mitochondrial dysfunction is not simply a defect in the terminal respiratory chain.
The disturbance may involve substrate entry and carbon flux throughout the metabolic network.
Potential contributors include:
- pyruvate dehydrogenase regulation;
- fatty-acid oxidation;
- amino-acid metabolism;
- NAD⁺ availability;
- redox balance.
XVII. NAD⁺ and Cellular Redox State
NAD⁺ is essential for oxidative metabolism.
It accepts electrons during glycolysis and the TCA cycle and transfers reducing equivalents toward oxidative phosphorylation.
Inflammation and increased DNA repair can alter NAD⁺ metabolism.
The kynurenine pathway is particularly relevant because inflammation induces indoleamine 2,3-dioxygenase and can divert tryptophan metabolism toward kynurenine.
The 2026 multi-omic analysis identified persistent kynurenine abnormalities in post-COVID cohorts, linking immune activation with altered metabolism.[1]
A prolonged disturbance of NAD⁺ homeostasis could therefore contribute to impaired mitochondrial function.
This remains an active area of investigation.
XVIII. Lipid Metabolism
Mitochondria are also essential for fatty-acid oxidation.
Long-chain fatty acids enter mitochondria through the carnitine shuttle and undergo β-oxidation.
Disruption of this pathway would reduce the capacity to use fat as an energy source.
The consequence could be:
reduced metabolic flexibility + greater carbohydrate dependence + earlier exhaustion during prolonged exercise.
Multi-omic studies have identified abnormalities in lipid and fatty-acid pathways among subsets of patients with Long COVID.[3]
The challenge is determining whether these abnormalities are primary, secondary to inflammation, or consequences of reduced physical activity.
XIX. Immune Cells Are Metabolic Cells
One of the most important conceptual advances in modern immunology is that immune function is inseparable from cellular metabolism.
Activated immune cells alter their energy production.
For example:
- activated effector T cells increase glycolysis;
- regulatory cells rely relatively more heavily on oxidative metabolism;
- macrophage phenotypes are influenced by metabolic state.
Thus:
metabolism → immune phenotype
and
immune activation → metabolism.
This creates an immunometabolic feedback loop.
Persistent inflammatory signaling can therefore sustain mitochondrial dysfunction, while mitochondrial dysfunction can sustain inflammatory signaling.
XX. The Mitochondria–Immune Feedback Loop
A potentially central mechanism is:
SARS-CoV-2 infection
↓
immune activation
↓
mitochondrial stress
↓
ROS and altered metabolism
↓
innate immune signaling
↓
persistent inflammatory state
↓
further mitochondrial dysfunction.
This model helps explain how the disease might persist even after SARS-CoV-2 replication has largely ceased.
The host’s pathological state becomes partly self-sustaining.
XXI. Endothelial Function and Oxygen Delivery
Mitochondrial dysfunction cannot be considered in isolation from circulation.
A cell requires oxygen to perform oxidative phosphorylation.
Therefore:
oxygen delivery × mitochondrial utilisation
determines aerobic energy production.
Endothelial dysfunction, microvascular abnormalities and impaired oxygen extraction could all reduce effective oxygen availability at the cellular level.
This creates an important possibility:
Some Long-COVID patients may have normal arterial oxygen saturation yet impaired cellular oxygen utilisation.
This distinction could be particularly relevant to patients whose exercise intolerance seems disproportionate to conventional cardiopulmonary findings.
XXII. Autonomic Dysfunction and Metabolism
Autonomic dysfunction may compound metabolic impairment.
The autonomic nervous system regulates:
- heart rate;
- vascular tone;
- blood pressure;
- thermoregulation;
- gastrointestinal function;
- metabolic responses to exercise.
If autonomic regulation is impaired, the cardiovascular system may fail to appropriately match oxygen delivery to metabolic demand.
Thus:
autonomic dysfunction + vascular dysfunction + mitochondrial dysfunction
could produce substantially greater exercise intolerance than any single abnormality alone.
XXIII. The Brain
The brain consumes a disproportionate amount of the body’s energy.
Neurons depend heavily upon mitochondrial ATP production to maintain:
- ion gradients;
- synaptic transmission;
- neurotransmitter cycling;
- axonal transport.
Even modest reductions in energetic reserve could therefore affect:
- attention;
- processing speed;
- memory;
- executive function.
The 2026 multi-omic study reported persistent metabolic abnormalities in selected brain regions in experimental models, although translation from animal tissue to human cognitive Long COVID remains uncertain.[1]
The neurological consequences of Long COVID are therefore likely to reflect several interacting processes rather than mitochondrial dysfunction alone.
XXIV. The Heart
Cardiomyocytes have exceptionally high mitochondrial density.
Persistent mitochondrial stress could theoretically affect:
- myocardial energetics;
- contractile reserve;
- electrical stability;
- recovery after exercise.
However, this mechanism must be distinguished from myocarditis, ischemia, arrhythmia, autonomic dysfunction and other cardiovascular disorders.
The mitochondrial hypothesis should therefore complement—not replace—standard cardiovascular evaluation.
XXV. Kidney and Other High-Energy Organs
Mitochondrial metabolism is also essential to renal tubular transport.
The kidney consumes substantial amounts of ATP, particularly in the proximal tubule.
The 2026 multi-omic study identified persistent OXPHOS suppression in experimental renal tissue.[1]
Whether equivalent abnormalities occur consistently in human Long COVID remains unresolved.
The same principle may apply to other organs.
Long COVID could therefore represent a distributed bioenergetic disorder affecting different tissues to different degrees.
XXVI. Viral Persistence and Mitochondria
Persistent viral material provides another possible upstream mechanism.
If SARS-CoV-2 RNA or protein persists in tissues, it could continually stimulate innate immunity.
That inflammation could then impair mitochondrial function.
The sequence would be:
persistent viral antigen
→
innate immune activation
→
cytokines/ROS
→
mitochondrial dysfunction
→
metabolic failure.
Alternatively, viral proteins themselves may directly perturb mitochondrial pathways.
These mechanisms are not mutually exclusive.
XXVII. Viral Reactivation as a Secondary Metabolic Stressor
The recently emerging evidence of herpesvirus and other viral reactivation adds another dimension.
Latent-virus reactivation could increase inflammatory signaling and metabolic demand.
Thus:
SARS-CoV-2
→ immune dysregulation
→ latent-virus reactivation
→ secondary inflammatory activation
→ mitochondrial stress
may represent one pathway to persistent fatigue.
This provides a possible mechanistic bridge between the viral-reactivation and mitochondrial hypotheses.
Neither needs to be correct independently.
XXVIII. The Gut–Mitochondrial Axis
The intestinal microbiome produces metabolites capable of influencing mitochondrial function and immune signaling.
Microbial metabolites include:
- short-chain fatty acids;
- secondary bile acids;
- tryptophan derivatives.
Dysbiosis can therefore alter systemic metabolism.
If SARS-CoV-2 disrupts intestinal barrier integrity and microbial composition, altered microbial metabolites could influence:
immune function → mitochondrial metabolism → neurological function.
This creates another potential pathway connecting gastrointestinal and neurological manifestations of Long COVID.
XXIX. Clinical Course
The mitochondrial hypothesis also offers a framework for understanding different clinical trajectories.
Acute mitochondrial stress
During severe acute COVID-19, mitochondrial dysfunction may be profound but reversible.
Incomplete recovery
Some individuals may fail to restore mitochondrial homeostasis.
Chronic bioenergetic deficit
Persistent metabolic inefficiency develops.
Stress-sensitive disease
Patients function near the limit of their energetic reserve.
Post-exertional deterioration
Exertion exceeds the available metabolic reserve and triggers delayed physiological decompensation.
Recovery
Improvement may occur as mitochondrial turnover, immune resolution and metabolic flexibility recover.
This model predicts that recovery should be gradual rather than instantaneous.
XXX. Why Some Patients Recover and Others Do Not
A central unanswered question is why most people recover while others develop persistent disease.
Potential determinants include:
- viral burden;
- acute disease severity;
- age;
- metabolic health;
- obesity;
- diabetes;
- mitochondrial reserve;
- host genetics;
- immune phenotype;
- persistent viral reservoirs;
- autoimmunity;
- autonomic susceptibility.
A useful conceptual model is:
initial mitochondrial injury + host susceptibility − repair capacity = probability of persistent bioenergetic dysfunction.
This remains a hypothesis rather than a validated predictive equation.
XXXI. Genomic Susceptibility
Several categories of genes could influence mitochondrial recovery.
These include genes involved in:
- respiratory-chain assembly;
- mitochondrial biogenesis;
- antioxidant defense;
- mitophagy;
- autophagy;
- NAD⁺ metabolism;
- inflammatory signaling;
- interferon responses.
Importantly, susceptibility may arise from combinations of common variants rather than a single pathogenic mutation.
Long COVID may therefore involve a polygenic metabolic vulnerability.
The relevant phenotype would not be classical mitochondrial disease.
Instead, genetically determined differences in metabolic reserve could influence the response to viral and inflammatory stress.
XXXII. Epigenetic Metabolic Memory
Inflammation can alter cellular transcription without changing DNA sequence.
Epigenetic mechanisms can modify:
- chromatin accessibility;
- DNA methylation;
- histone modification;
- transcription-factor activity.
A prolonged inflammatory state could therefore create a form of metabolic memory.
The infection disappears.
The transcriptional program does not completely reset.
The cell remains metabolically altered.
This provides a potential explanation for persistent mitochondrial abnormalities months after the acute infection.
XXXIII. Mitochondrial Senescence
Persistent oxidative stress can promote cellular senescence.
Senescent cells undergo durable changes in:
- metabolism;
- proliferation;
- mitochondrial function;
- inflammatory signaling.
They can produce a senescence-associated secretory phenotype (SASP) containing inflammatory mediators.
The potential feedback loop is:
mitochondrial stress → cellular senescence → inflammatory signaling → further mitochondrial stress.
Evidence for senescence-related pathways has been reported in Long COVID, although their precise causal role remains under investigation.[3]
XXXIV. A Unified Bioenergetic Model
The emerging evidence permits a more comprehensive model:
SARS-CoV-2 infection
↓
viral replication and host metabolic reprogramming
↓
mitochondrial stress
↓
oxidative-phosphorylation suppression
↓
ROS / altered redox state
↓
innate immune activation
↓
persistent inflammation
↓
endothelial + autonomic dysfunction
↓
impaired oxygen delivery/utilisation
↓
skeletal-muscle metabolic dysfunction
↓
reduced energetic reserve
↓
post-exertional malaise
↓
repeated metabolic stress
↓
further inflammatory and mitochondrial activation.
This represents a feed-forward system, not a single lesion.
XXXV. Why Fatigue May Be a System-Level Phenomenon
The term “mitochondrial fatigue” risks oversimplification.
Fatigue is unlikely to arise from skeletal-muscle mitochondria alone.
A more complete formulation is:
central nervous system energy demand
skeletal-muscle oxidative capacity
cardiovascular oxygen delivery
microvascular perfusion
autonomic regulation
immune-metabolic state
=
functional energetic capacity.
Long COVID may reduce several components simultaneously.
This explains why fatigue can be profound despite relatively normal conventional laboratory investigations.
XXXVI. Diagnostic Implications
Mitochondrial dysfunction currently lacks a validated clinical biomarker specific to Long COVID.
Potential research biomarkers include:
- lactate;
- pyruvate;
- acylcarnitines;
- TCA-cycle intermediates;
- NAD⁺/NADH-related measures;
- FGF21;
- GDF15;
- mitochondrial proteins;
- mtDNA;
- metabolomic signatures;
- muscle OXPHOS measurements.
None should currently be regarded as diagnostic in isolation.
A clinically useful biomarker must demonstrate:
specificity + reproducibility + correlation with physiological impairment + longitudinal responsiveness.
XXXVII. Therapeutic Implications
If mitochondrial dysfunction contributes causally to Long COVID, several therapeutic approaches become theoretically relevant.
Potential strategies include:
- correction of nutritional deficiencies;
- treatment of insulin resistance and metabolic disease;
- restoration of sleep;
- management of autonomic dysfunction;
- reduction of persistent inflammatory drivers;
- treatment of viral persistence where demonstrated;
- interventions targeting mitochondrial redox balance;
- agents affecting NAD⁺ metabolism;
- mitochondrial biogenesis pathways.
However, evidence for disease-modifying mitochondrial therapy remains insufficient.
This distinction is essential.
Biological plausibility is not therapeutic efficacy.
XXXVIII. The Exercise-Treatment Paradox
One of the most difficult clinical implications concerns exercise.
If deconditioning contributes to reduced capacity, progressive rehabilitation might help.
But if exertion provokes pathological PEM, aggressive graded exercise may worsen symptoms.
The correct physiological approach is therefore likely to distinguish:
restorative activity within the patient’s metabolic envelope
from
repeated exertional stress that exceeds physiological reserve.
The recent physiological evidence showing that Long-COVID muscle abnormalities differ from ordinary bed-rest adaptation reinforces the importance of this distinction.[2]
XXXIX. What Would Prove the Mitochondrial Hypothesis?
A convincing causal demonstration would require several observations.
First
Mitochondrial abnormalities should precede or closely track symptom development.
Second
The magnitude of mitochondrial impairment should correlate with physiological disability.
Third
The abnormalities should be tissue-specific in biologically plausible ways.
Fourth
They should distinguish Long COVID from ordinary deconditioning.
Fifth
Correcting the mitochondrial abnormality should improve physiological function.
Sixth
Clinical improvement should accompany restoration of metabolic homeostasis.
The final criterion is crucial.
A biomarker that merely accompanies disease is not necessarily a therapeutic target.
XL. Research Priorities
Future Long-COVID cohorts should integrate:
Genomics
- whole-genome sequencing;
- mtDNA sequencing;
- HLA typing;
- epigenomics.
Transcriptomics
- nuclear OXPHOS genes;
- mitochondrial transcripts;
- inflammatory pathways;
- metabolic regulators.
Proteomics
- respiratory-chain proteins;
- mitochondrial stress proteins;
- inflammatory mediators.
Metabolomics
- glycolysis;
- TCA cycle;
- fatty-acid oxidation;
- amino-acid metabolism;
- NAD⁺ pathways;
- redox metabolites.
Physiology
- CPET;
- muscle spectroscopy;
- oxygen extraction;
- endothelial function;
- autonomic testing.
Tissue studies
- skeletal-muscle biopsy when clinically justified;
- mitochondrial ultrastructure;
- respiratory-chain activity;
- mitochondrial DNA integrity.
Such integration could finally determine whether mitochondrial dysfunction represents:
cause → consequence → amplifier → biomarker
or some combination thereof.
XLI. Conclusions
The mitochondrial hypothesis has emerged as one of the most compelling explanations for the profound fatigue and exercise intolerance experienced by many patients with Long COVID.
The evidence, however, supports a more sophisticated proposition than the simple assertion that SARS-CoV-2 “damages mitochondria”.
The emerging model is one of persistent immunometabolic dysregulation.
Acute SARS-CoV-2 infection may initiate mitochondrial stress. In susceptible individuals, inflammatory signaling, oxidative stress, persistent antigen, viral reactivation, endothelial dysfunction, autonomic disturbance and metabolic reprogramming may prevent complete restoration of mitochondrial homeostasis.
The consequence is a reduction in bioenergetic reserve.
At rest, this reduction may remain clinically subtle.
Under exertion, however, the deficit becomes apparent.
The patient crosses the threshold at which metabolic demand exceeds physiological reserve.
The result is exercise intolerance.
And in some patients, the subsequent inflammatory, autonomic and metabolic cascade produces delayed post-exertional malaise.
The recent evidence is particularly persuasive because the mitochondrial hypothesis is increasingly supported at several biological levels simultaneously. Multi-omic studies demonstrate persistent suppression of OXPHOS and mitochondrial stress pathways; metabolomic investigations identify altered substrate utilisation; skeletal-muscle studies demonstrate metabolic and structural abnormalities; and physiological experiments indicate that these abnormalities cannot be explained simply by inactivity.[1–3]
Yet important uncertainties remain.
Mitochondrial dysfunction is unlikely to be universal.
It may represent one of several Long-COVID endotypes.
Some patients may have predominantly vascular disease; others autonomic dysfunction, persistent viral antigen, immune dysregulation, autoimmunity or combinations of these mechanisms.
The most productive conceptual model is therefore not:
Long COVID is a mitochondrial disease.
It is:
In a subset of patients, SARS-CoV-2 initiates a persistent immunometabolic state in which impaired mitochondrial function reduces bioenergetic reserve and contributes to fatigue, post-exertional malaise and multisystem physiological dysfunction.
This hypothesis is biologically coherent, experimentally testable and increasingly supported by convergent evidence.
The decisive next step is not another descriptive metabolomic study.
It is intervention.
If restoration of mitochondrial function produces restoration of physiological capacity and relief of symptoms, the mitochondrial hypothesis will move from association toward causality.
Until then, mitochondrial dysfunction should be regarded as a major candidate mechanism and potentially important therapeutic endotype of Long COVID, rather than a universal explanation for the disease.
Numbered References
- Tasoula A, Arif S, Waisberg E, et al. Multi-omics analysis of long COVID (post-COVID-19 condition) reveals persistent mitochondrial dysfunction, suppressed oxidative phosphorylation, and immune dysregulation. Front Immunol. 2026;17:1776555. Published May 21, 2026.
- Skeletal muscle properties in long COVID and ME/CFS differ from those induced by bed rest. Nat Commun. 2026. The study compared Long-COVID and ME/CFS skeletal-muscle and exercise physiology with healthy participants exposed to 60 days of bed rest and found that inactivity alone did not account for the observed abnormalities.
- The Omics Landscape of Long COVID—A Comprehensive Systematic Review to Advance Biomarker, Target and Drug Discovery. Allergy. 2025. Systematic review of 29 human omics studies identifying recurring mitochondrial, metabolic, immune, vascular and tissue abnormalities while emphasising substantial cross-study heterogeneity.
- Appelman B, Charlton BT, Goulding RP, et al. Muscle abnormalities worsen after post-exertional malaise in long COVID. Nat Commun. 2024;15:17.
- Klein J, Wood J, Jaycox JR, et al. Distinguishing features of long COVID identified through immune profiling. Nature. 2023;623:139–148.
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