Mitochondrial Stress as a Common Cause in Long COVID and Spike Protein-Related Damage

Long COVID, or post-acute sequelae of SARS-CoV-2 infection (PASC), continues to impact millions globally. Many patients experience persistent fatigue, brain fog, shortness of breath, or dysautonomia, sometimes for months after their initial infection [76]. These symptoms are often out of proportion to imaging or lab results, and frustratingly, many affected individuals appear "normal" on paper. Large epidemiologic studies have shown that this syndrome disproportionately affects women, racial minorities, and migrants, further highlighting disparities in both care and pathogenesis [77,78,79]. What is becoming clear is that we may be looking in the wrong places. Instead of lingering viral particles or structural damage, long COVID appears to be rooted in something more fundamental: a breakdown in cellular energy and immune balance, driven by mitochondrial dysfunction and oxidative stress.

From the earliest days of infection, SARS-CoV-2 exploits the host's mitochondria. Multiple viral proteins (ORF3a, ORF5, ORF6, ORF9c, ORF3c, ORF7b, ORF10, NSP4, NSP8, M, E proteins, and nucleocapsid) target distinct mitochondrial sites to destabilize homeostasis and blunt innate immunity and further impair respiration, induce mitophagy, elevate ROS, and promote immune evasion (see Table 2 for details) [73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100]. For example, ORF3a forms ion channels at the outer mitochondrial membrane to disturb calcium balance and trigger apoptosis, ORF5 downregulates MAVS-related signaling by limiting TBK1/IRF3 recruitment, while ORF6 alters the mitochondrial proteome while suppressing MAVS signaling [91,92]. ORF9b targets TOM70 on the outer mitochondrial membrane to silence MAVS signaling, blocking downstream IBK1/IRF3 activation and type I interferon production [93,94]. In contrast, E protein localizes mainly to ER/ERGIC/Golgi membranes, disrupting ER calcium stores and indirectly impairing ER–mitochondria calcium transfer, thereby contributing to mitochondrial dysfunction [80]. Together, these proteins drive excessive mitochondrial reactive oxygen species (mtROS) production [81,82,83,84,85,86,87,88,89]. Additionally, to increase mtROS in the acute phase of infection, calcium overload from ORF3a and E protein enhances reverse electron transport (RET) through Complex I, generating ROS bursts; in the chronic phase, proteins such as M (Complex I) and NSP6 (Complex V) inhibit the respiratory chain, sustaining electron leakage and oxidative stress [50,72] Together, these processes stabilize HIF-1α, enforce glycolytic reprogramming, and perpetuate inflammation. This increase in oxidative stress stabilizes hypoxia-inducible factor 1-alpha (HIF-1α), pushing cells away from oxidative phosphorylation (OXPHOS) and into glycolysis, a low-efficiency metabolic state more suited for acute stress and viral replication [90,93,94]. While this metabolic switch benefits the virus in the short term, it becomes maladaptive when sustained. The result is what many patients describe: a crushing lack of energy, poor stress tolerance, and brain fog that feels almost metabolic. This "glycolytic lock" mirrors what we see in other conditions like chronic fatigue syndrome or diabetic cardiomyopathy [19].

mtROS not only impair energy production but also damage mitochondrial DNA (mtDNA), leading to its leakage into the cytoplasm and bloodstream. These fragments act as danger-associated patterns (DAMPs) or pathogen-associated molecular patterns (PAMPs), activating innate immune sensors such as cGAS–STING, Toll-like receptor 9 (TLR9), and the NLRP3 inflammasome [81]. Even after the virus is cleared, this immune activation persists, with many long COVID patients showing elevated levels of IL-6, IL-1β, and type I interferons weeks or months post-infection, thus creating a self-perpetuating loop: mitochondrial dysfunction leads to ROS, which causes metabolic reprogramming, mtDNA leakage, innate immune activation, and then further mitochondrial injury. Additionally, mtROS enhances signaling through the MAVS pathway, promoting oligomerization and amplification of antiviral responses via IRF3 and NF-κB. Inadequate clearance of damaged mitochondria, particularly via defective mitophagy through the PINK1–Parkin pathway, perpetuates chronic inflammation and immune dysregulation. (Figure 1 and Figure 2).

Translational studies reveal mitochondrial dysfunction across multiple organ systems in long COVID. In the kidney, suppression of OXPHOS-related genes in peripheral blood mononuclear cells (PBMCs) during acute infection predicted worse renal outcomes a year later [107]. In the endocrine pancreas, infected β-cells exhibit mitochondrial fragmentation and accumulation of NADH, mimicking the metabolic features of type 2 diabetes and potentially explaining the rise in post-COVID diabetes [19,108]. In the cardiopulmonary system, transgenic mouse models treated with mitochondrial-targeted antioxidants such as EUK-8 and mCAT demonstrated restored OXPHOS, reduced inflammation, and improved survival [81]. These findings strongly support the view that mitochondrial distress is not just a bystander in long COVID; it is central to its pathophysiology. Endothelial dysfunction also appears linked to mitochondrial stress, as excess ROS disrupts nitric oxide signaling, impairing vascular tone and contributing to orthostatic intolerance and post-exertional malaise [109,110].

Additionally, mtROS excess has been implicated in endothelitis, microthrombosis, and myocardial fibrosis [111]. Although COVID-19 and mRNA-associated myocarditis are poorly understood and complex phenomena, altered mitochondrial dynamics and increases in mtROS may play a role in myocardial injury. Huynh et al. demonstrated that the S1 unit of spike protein in vitro impaired mitochondrial dynamics in human cardiomyocytes, altering mitochondrial membrane potential, resulting in increases in myocardial calcium and excessive ROS production [112]. Increases in mtROS accumulation activate NLRP inflammasome, resulting in increased myocardial fibrosis [113].

In the liver, SARS-CoV-2 infects hepatocytes via ACE2 and TMPRSS2, including steatosis and persistent mitochondrial injury, even in those without prior liver disease [114]. This contributes to disease progression in patients with metabolic-associated steatohepatitis (MASH), especially in those with preexisting metabolic dysfunction. Persistent liver enzyme elevation, mitochondrial swelling, and altered redox signaling have been observed for up to 20 months post-infection, even in patients without prior liver disease [115,116,117]. Longitudinal studies showed elevated fibrosis indices and liver stiffness in long COVID cohorts, suggesting ongoing necroinflammation [114,118]. Parallel mechanisms appear in the nervous system [119,120]. Redox imbalance and immune dysregulation have been implicated in COVID-19-associated neuroinflammation, where mitochondrial dysfunction in neurons and glia fosters a pro-inflammatory state [120]. ROS-driven neuroinflammation and microglial activation, in part mediated by ACE2 depletion following viral entry, lead to mitochondrial injury. This injury is amplified by AngII/AT1R/Nox2-mediated ROS generation, compromising the blood–brain barrier and contributing to cognitive symptoms, anosmia, and neural apoptosis (Figure 3) [121,122].

The convergence of clinical, biochemical, and imaging data suggests that mitochondrial dysfunction is an upstream driver of persistent symptoms in long COVID. Redox-sensitive pathways regulate immune activation, vascular tone, and metabolic flexibility, all of which are commonly disrupted in post-COVID-19 syndromes.

The proposed mechanism, as synthesized across studies, involves acute viral injury triggering neutrophil activation and ROS production, followed by impaired resolution of oxidative stress in vulnerable individuals. This may be due to age-related reductions in endogenous antioxidant defenses, as noted by Laforge et al., who observed decreased SOD3 expression in elderly COVID-19 patients [123]. Continued ROS generation then perpetuates tissue injury, immune activation, and bioenergetic failure through a self-reinforcing cycle.

Several biomarkers support the central role of mitochondrial dysfunction in long COVID. Studies have identified elevated levels of peroxiredoxin-3 (PRDX3), malondialdehyde, 8-hydroxy-2'-deoxyguanosine, and nitric oxide metabolites in symptomatic patients, alongside reduced antioxidant enzymes such as superoxide dismutase (SOD) and glutathione peroxidase (GPx) [19,124,125]. These findings suggest sustained redox imbalance that correlates with persistent symptoms such as fatigue, dyspnea, and brain fog. Transcriptomic profiling has shown upregulation of genes involved in ROS generation, impaired mitophagy, and mitochondrial fragmentation. Circulating mtDNA, a potent immune activator, correlates with cardiovascular complications and may serve as a dynamic marker for mitochondrial stress. Magnetic Resonance Spectroscopy (MRS) has emerged as a non-invasive tool to quantify oxidative phosphorylation capacity, revealing prolonged phosphocreatine recovery and reduced ATP synthesis in long COVID patients. These findings not only correlate with symptom severity but are also partially reversible with targeted nutritional interventions.

Shankar et al. conducted transcriptomic and proteomic profiling of individuals with long COVID and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), identifying convergent upregulation of genes related to ROS production, impaired mitophagy, and mitochondrial fragmentation [126]. These data support the hypothesis that mitochondrial redox dysfunction may be a shared driver of post-viral fatigue syndromes.

One of the most promising translational markers is mitochondrial DNA (mtDNA) damage. Semo et al. reported that individuals with PASC-related cardiovascular complications displayed evidence of sustained monocyte bioenergetic impairment and mtDNA fragmentation [127]. Circulating mtDNA acts as a damage-associated molecular pattern (DAMP), capable of activating innate immune sensors such as TLR9 and the cGAS–STING pathway, sustaining chronic inflammation long after viral clearance.

Magnetic resonance spectroscopy (MRS) has also emerged as a non-invasive technique to assess mitochondrial dysfunction. In a study by Chen et al., patients with post-COVID fatigue exhibited significantly delayed phosphocreatine recovery times (τPCr) and reduced maximal ATP synthetic capacity (Qmax) on skeletal muscle MRS, indicating impaired oxidative phosphorylation [128]. These MRS findings correlated with symptom severity and were partially reversible with personalized nutritional interventions.

Tsilingiris et al. reviewed the current literature on laboratory markers in long COVID. They highlighted alterations in multiple oxidative stress pathways, including reductions in reduced glutathione (GSH), increased lipid peroxidation, and elevated protein carbonylation [129]. These markers not only support the presence of mitochondrial dysfunction but may also serve as candidates for future diagnostic or prognostic algorithms.

Importantly, biomarkers such as MDA, d-ROMs, GSH/GSSG ratios, and mtDNA damage not only reflect disease severity but may be leveraged to stratify patients and monitor therapeutic response. Functional imaging modalities like MRS further enable real-time tracking of mitochondrial recovery and could be integrated into future clinical trials.

Therapies aimed at restoring mitochondrial function and redox balance are emerging as promising strategies. Mitochondria-targeted antioxidants such as MitoQ, EUK-8, and mCAT have shown preclinical benefits in reversing bioenergetic failure and reducing inflammation [19,81]. Over-the-counter agents such as coenzyme Q10 and α-lipoic acid may offer modest symptomatic relief by supporting mitochondrial respiration [130]. NAD⁺ precursors like nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN) support mitochondrial biogenesis and DNA repair through sirtuin and PARP pathways and are currently being evaluated in clinical trials, including NCT05703074 [19]. N-acetylcysteine (NAC), a glutathione precursor, may reduce neutrophil-driven oxidative injury and mitigate endothelial damage [131,132]. Metformin, via AMPK activation and inhibition of mitochondrial complex I, suppresses ROS production and reduces systemic inflammation, offering potential benefit in patients with concurrent metabolic disorders [133,134]. Precision nutrition based on MRS and biomarker profiling, including supplements like creatine, magnesium, and riboflavin, has shown promise in restoring mitochondrial function and alleviating fatigue [135].

Targeting redox imbalance and mitochondrial injury presents a rational therapeutic strategy in long COVID. Several antioxidants and metabolic modulators have shown promise in observational studies and early clinical trials.

Coenzyme Q10 (CoQ10) is a mitochondrial electron carrier and lipid-phase antioxidant that has been studied in post-viral fatigue syndromes. A review by Mantle et al. found improvements in fatigue scores and mitochondrial function parameters in ME/CFS and post-viral fatigue patients following CoQ10 supplementation [136]. Given its central role in ATP generation and ROS neutralization, CoQ10 represents a potentially safe and effective intervention in long COVID.

N-acetylcysteine (NAC), a precursor to intracellular glutathione, has both antioxidant and anti-inflammatory properties. In the context of COVID-19, NAC has been proposed to reduce neutrophil-driven ROS production and limit oxidative tissue damage. Laforge et al. suggested that NAC, particularly when combined with neutrophil elastase inhibitors like sivelestat, could attenuate reverse-transendothelial migration (rTEM) of neutrophils and thereby reduce ROS-induced endothelial injury and thrombosis [123].

Metformin, while primarily used in diabetes management, has demonstrated the ability to reduce mitochondrial ROS production through AMPK activation and inhibition of mitochondrial complex I. In both ME/CFS and long COVID cohorts, metformin has been shown to suppress hyperactive T cell phenotypes and reduce systemic inflammation. Its metabolic effects may be particularly relevant in patients with concurrent metabolic syndrome or cardiovascular risk [137,138,139,140].

Nutraceutical approaches, including nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN), support NAD⁺ biosynthesis, which is critical for mitochondrial sirtuin activation and DNA repair. These compounds have shown potential to reverse mitochondrial dysfunction in preclinical models and are currently under investigation in long COVID [141].

Precision nutrition, guided by biomarker and MRS profiling, may also play a role. Chen et al. demonstrated that patients with impaired muscle oxidative capacity on MRS benefited from tailored nutritional interventions targeting mitochondrial cofactors, including creatine, magnesium, and riboflavin [128]. These interventions improved both MRS parameters and subjective fatigue scores.

Non-pharmacologic strategies such as light aerobic exercise, when timed appropriately, may also aid mitochondrial recovery. In one study, Nordic walking helped improve lactate handling and subjective energy levels, likely through enhanced mitochondrial capacity [142]. However, exertion must be carefully calibrated to avoid exacerbating symptoms during periods of active inflammation. This emphasizes the importance of identifying the right therapeutic window for rehabilitation, guided by clinical and metabolic markers. Therapeutic interventions are summarized in Table 3 and Figure 4.

The next step in translating this knowledge into clinical practice lies in identifying which patients have a mitochondrial-dominant phenotype. Emerging biomarkers may help. PBMC OXPHOS gene expression panels, such as those developed by Jayaraman and colleagues, could help stratify patients and monitor response [107]. Serum peroxiredoxin-3 (PRDX-3), a mitochondrial antioxidant enzyme, appears elevated in patients with long COVID-related fatigue and dizziness [19]. Circulating mtDNA levels, which correlate with mitochondrial stress and respond to antioxidant therapy, may serve as a dynamic, real-time marker for treatment efficacy [81]. These tools bring us closer to a precision medicine model where therapies are not just empiric but personalized.

Dysautonomia and brain fog affect many individuals with long COVID, possibly due to neuroinflammation [151]. Given the pathophysiologic role of dysfunctional mitochondria and mtROS in long COVID and perhaps post-vaccine syndromes, from a translational medicine standpoint, it is of importance to revisit the repurposing of agents with overlapping anti-inflammatory and antioxidant properties such as Ivermectin, Dimethyl sulfoxide (DMSO), and Methylene blue (Mb). Either indirectly via anti-inflammatory mechanisms or through direct effects on mitochondrial electron transport chain, these agents have an impact on mitochondrial function pathways and generation of reactive oxygen species [152,153]. When discussing the protective role of antioxidants, it is essential to consider that, depending on the clinical scenario, the timing of administration, the doses administered, and the patient's internal milieu, antioxidants can paradoxically induce oxidant stress [154,155].

The majority of evidence shows that ivermectin induces mitochondrial oxidant stress and increases reactive oxygen species [156,157]. The oxidant effect of ivermectin is not the case in all instances. For example, in a rat model of bleomycin-induced pulmonary fibrosis, Ivermectin resulted in a reduction in markers of oxidative stress [158,159]. Additionally, Ivermectin suppressed NLRP3, thus supporting the antioxidant and anti-inflammatory effects of Ivermectin [158]. In a rat model of methotrexate-induced liver injury, rats who received ivermectin demonstrated lower levels of malondialdehyde, presumably due to antioxidant and anti-inflammatory mechanisms [160]. In a rat model of transient cerebral ischemia, Seyyedabade et al. demonstrated that treatment with ivermectin resulted in a decrease in infarct size, lipid peroxidation, and myeloperoxidase [161]. De Melo et al. in a Syrian hamster model of SARS-CoV-2, Ivermectin prevented the development of anosmia and limited inflammation in the lungs of treated animals [162]. In a rat model of streptozotocin-induced Alzheimer's disease, ivermectin attenuated amyloid plaque buildup by inhibiting acetylcholinesterase [163]. Thus, preclinical evidence supports the possibility that ivermectin may be an ideal candidate drug in reducing neuroinflammation in patients with long COVID.

Mb possesses a net positive charge and unique hydrophilic and lipophilic properties, enabling it to penetrate and accumulate in mitochondrial membranes [164,165]. Mb can function as an alternative electron transporter in the mitochondrial transport chain (MTC), receiving electrons from NADPH and can bypass complex I-III, transporting electrons directly to cytochrome C [166]. This mechanism may restore function to a damaged MTC and restore ATP production [166]. Additionally, Mb is a powerful redox agent and can function as a free radical scavenger and antioxidant [164]. Mb has also demonstrated in vitro virucidal activity against SARS-CoV-2 and H1N1 influenza viruses [167]. In a clinically relevant rat model of sepsis, Mb demonstrated a reduction in plasma levels of inflammatory cytokines IL-6 and IL-1ß and TNF-α in rats treated with Mb [168]. In a murine model of skeletal ageing, Mb inhibited skeletal bone loss [164]. This effect was mainly mediated by Mb antioxidant properties [164]. Due to these properties, Mb has demonstrated effectiveness in reducing cellular damage in a variety of animal models of neurodegenerative and metabolic disorders [169,170,171].

DMSO at low doses acts as a powerful free radical scavenger and also increases the activity of antioxidant enzyme systems [172,173]. DMSO inhibits the activation of NLRP3 inflammasome and suppresses the release of proinflammatory cytokines [174]. Due to DMSO's antioxidant and anti-inflammatory properties, DMSO has demonstrated neuroprotective effects in models of neuroinflammation and ischemia [175]. In a rat model of traumatic brain injury, administration of DMSO attenuated oxidant injury and improved cognitive function [172].

Thus, ivermectin, Mb, and DMSO, via their pleiotropic effects on inflammatory and oxidant pathways, should be considered in the treatment of long COVID in general and symptoms such as brain fog and dysautonomia commonly encountered in this condition. Figure 5.

In post-acute COVID-19 syndrome (PACS), as well as post-acute COVID-19 vaccination syndrome (PACVS), reduced energy levels, post-exertional malaise (PEM), and brain fog are common issues, affecting large percentages of those affected by either condition. Chronic fatigue syndrome affects 45% (95% CI: 34%–57%) of PAC patients and 69% of PACVS patients [176]. PEM affects 55% (95% CI: 38%–71%) of PAC patients, and 71% of PACVS patients experience "exercise intolerance", the closest surveyed condition to PEM.

Mechanistically, it is known that the spike protein, a common element in both COVID-19 infection and vaccination, can interfere with mitochondrial function and decrease energy production [112]. Spike protein administration is used in the development of animal models for COVID-19-induced brain fog [177].

Apart from COVID-19 or COVID-19 vaccination-related symptoms, reductions in mitochondrial function due to genetic factors or exogenous agents can recreate the clinical presentation of fatigue [178,179], PEM, and/or brain fog.

Brain fog affects 20% (95% CI: 11%–34%) of PACS patients [180] and 63% of PACVS patients [176]. Brain fog is also associated with mitochondrial dysfunction [181] and is inducible in animal models through spike protein administration [177], as well as other agents that affect the mitochondria, including chemotherapy agents [182] and thiamine deficiency [183].

PEM also shows a high association with mitochondrial dysfunction in PACS patients [184], and the fatigue phenotype can be reliably induced by agents damaging mitochondrial function [178]. In short, mitochondrial dysfunction is a primary driver of the chronic sequelae of COVID-19 or COVID-19 vaccination. After infection, mitochondrial energy production is compromised [93,185,186]. Typically, loss of mitochondrial membrane potential is a signal for recycling of the mitochondria via mitophagy [187], but SARS-CoV-2 spike protein appears to inhibit this process via release of reactive oxygen species (ROS) [188], and possible downregulation of TOM20, which is associated with reduced mitophagy [112,188]. This creates a challenge of lower energy production until the issues can be resolved. One therapeutic strategy may be to upregulate the rate of autophagy through fasting or exogenous compounds [189]. Upregulating mitophagy may merely provide temporary relief, as any new mitochondria produced through mitochondrial biogenesis will be exposed to the circulating spike as well. Spike protein is observed in those with PACS [190,191,192,193,194] as well as PACVS [195], though the association has not been observed in some studies and may only be present for a subset of those with PACS [196].

As such, several therapeutic modalities for PACS and PACVS attempt to limit the damage induced by the spike protein and increase its degradation [189,197,198,199,200]. Besides autophagy [189], spike protein degradation may be induced through proteolytic enzymes [197], including nattokinase [201,202], which has been observed to degrade spike protein [201] and even dissolve microclots [202].