Long COVID Progression- the Transitioning of Cytokine Dysregulation to Cellular Suicide

Dr Graham Exelby June 2025

Abstract

Long COVID is emerging as a complex neuroimmune–metabolic disorder marked by persistent inflammation, hypoxia, and mitochondrial dysfunction. This paper outlines the evolving pathophysiological landscape of Long COVID, from initial Toll-like receptor (TLR) activation and mast cell responses to chronic hypoxia-driven HIF-1α activation, immune polarization, and progressive cellular dysfunction.

Central to this process is the formation of a self-sustaining loop involving HIF-1α, DAMPs, TLR4, RAGE, NF-κB, and STAT3, resulting in endothelial damage, immune maladaptation, and impaired metabolic clearance. We explore the clinical implications of this transition, emphasizing potential therapeutic targets including telmisartan, nicotinamide, low-dose naltrexone, and manual lymphatic therapy. The need for tailored, mechanism-based interventions is underscored.

Introduction

When the SARS-CoV-2 pandemic first erupted in 2019, early breakthroughs in management came from researchers such as Malone et al 2021 (1), Afrin Weinstock and Molderings 2020 (2) and Mukherjee et al 2021 (3) where mast cell blockade with H1, H2 blockers and low dose naltrexone (LDN) were found to provide significantly reduced COVID severity and often provided relief in managing long term symptoms.

In these patients, if the infection was not overwhelming, were often controllable. But as time passed, these and patients receiving delayed attention have become harder to treat, and less responsive to the treatments utilized.   This has led to this hypothesis describing the progression from early antiviral innate immune activation through adaptive dysregulation, and finally toward a chronic neuroimmune–hypoxic–metabolic syndrome driven by hypoxia-driven HIF-1α and RAGE signalling.   This hypothesis is strongly supported by emerging evidence across immunology, metabolomics, and neurovascular pathology in Long COVID.

Note on Terminology: Cellular Suicide as Apoptotic and Regulated Cell Death

The term cellular suicide is used as a conceptual framework to describe the progressive cellular deterioration seen in Long COVID.  While evocative, it is grounded in the well-established biological process of apoptosis, a form of programmed cell death characterized by caspase activation, chromatin condensation, and mitochondrial membrane disruption.

However, in the context of chronic hypoxia, sustained oxidative stress, and unresolved inflammation—as driven by HIF-1α and RAGE/TLR4 signalling—this may evolve into mixed forms of regulated cell death, including ferroptosis and necroptosis. These forms of cell demise share common upstream triggers but diverge in execution, with implications for tissue damage, immune activation, and clinical sequelae. Therefore, 'cellular suicide' in Long COVID denotes this spectrum of programmed cell death mechanisms activated by a neuroimmune–metabolic collapse.

Initial Responses to SARS-CoV-2 Infection

During the acute phase, SARS-CoV-2 triggers Toll-Like Receptor (TLR) activation, especially TLR4, and downstream signalling via NFKB. This leads to microglial, astrocyte, and mast cell responses, releasing pro-inflammatory cytokines like IL-1β, IL-6, and TNF-α, as well as chemokines like CCL2.

The acute infection phase activates TLR3 (dsRNA), TLR7/8 (ssRNA), and TLR2/4 (via spike glycoprotein and viral envelope proteins), resulting in rapid NF-κB–mediated transcription of IL-6, TNF, and chemokines like CCL2/MCP-1.

Early activation of microglia, astrocytes, and mast cells in this phase is well documented and helps shape the cytokine and neuroinflammatory milieu.

Long COVID affects a significant proportion of individuals post-SARS-CoV-2 infection, with symptoms persisting for months or years.  Treatments like famotidine, which modulates TLR3 and indirectly affects NFKB/CCL2, can help manage these early responses, particularly in less severe cases, often supported by additional therapies like low-dose naltrexone (LDN).

Transition to Long COVID- Transition Phase: From Acute to Chronic – The Failure to Resolve

As time progressed, Long COVID patients often faced harder recovery, with research suggesting a shift to chronic inflammation and metabolic dysfunction. Chronic Long COVID patients show persistent IL-6, CCL2, IFN-γ, and TNF-α, often despite normalized viral load, implying a non-resolving innate immune activation.   Patient SPECT brain scans are beginning to show increasing hypoxia unresponsive to previously successful treatments.

Research indicates that Long COVID is characterized by persistent inflammation and metabolic imbalances, with a notable shift to pathways involving hypoxia-inducible factor-1α (HIF-1α).  HIF-1α is a master regulator activated under hypoxic conditions, which are common in severe COVID-19 and can persist in Long COVID.

The HIF-1α pathway becomes prominent, driven by hypoxia—a common feature in severe COVID-19 that can persist. HIF-1α, activated under low oxygen, promotes vascular proliferation, angiogenesis, and metabolic reprogramming, contributing to symptoms like fatigue and organ dysfunction.  The dominant chronic pathway became-  HIF-1α → DAMP–TLR4/RAGE → CCL2/NF-κB/STAT3.

HIF-1α is upregulated by SARS-CoV-2 proteins (e.g., ORF3a), enhancing viral replication and inflammation, and remains significant in Long COVID, impacting brain and heart function. Iosef et al 2023 (4) found that HIF-1α is associated with vascular proliferation and is most prominent in Long COVID, driving angiogenesis and impacting organ function like the brain and heart.

HIF-1α’s role is further supported by studies on acute COVID-19, such as "HIF-1α promotes SARS-CoV-2 infection and aggravates inflammatory responses to COVID-19" (Tian et al 2021 (5) , which showed that SARS-CoV-2 ORF3a induces mitochondrial damage and reactive oxygen species (Mito-ROS) production, promoting HIF-1α expression. This facilitates viral replication and cytokine production, and its persistence in Long COVID likely contributes to chronic symptoms like fatigue and post-exertional malaise.

Key Pathways Activated by HIF-1α

Hypoxia-inducible factor 1-alpha (HIF-1α) is a transcription factor stabilized in hypoxic, inflammatory, or redox-imbalanced conditions. In Long COVID, brainstem hypoperfusion, mitochondrial dysfunction, and sympathetic vasoconstriction converge to chronically activate HIF-1α.

HIF-1α regulates over 100 genes involved in oxygen delivery, metabolism, immune signalling, and cell survival, contributing to persistent pathophysiology.

1. Glycolytic Reprogramming and PDH Inhibition

• Target genes: LDHA, PDK1, HK1/2, ENO1, GLUT1 (SLC2A1)

• HIF-1α induces a metabolic shift toward anaerobic glycolysis, increasing lactate production and inhibiting mitochondrial pyruvate oxidation.

• Via PDK1 upregulation, HIF-1α inhibits pyruvate dehydrogenase (PDH), contributing to the suppressed TCA cycle observed in Long COVID and ME/CFS patients.

2. RAGE Ligand Amplification and Inflammation

• HIF-1α promotes transcription of HMGB1, S100A8/9, and AGE-receptor components, enhancing RAGE–NF-κB–CCL2 inflammatory signalling.

• This forms a self-sustaining feedforward loop: HIF-1α → RAGE ligands → NF-κB → more HIF-1α (via IL-1β and ROS)

3. Angiogenesis and Vascular Leak

• VEGF, ANGPTL4, EPO upregulation increases vascular permeability and dysfunctional neovascularization.

• VEGF-mediated angiogenesis in a hypoxic, pro-inflammatory environment leads to immature, leaky vessels, contributing to brain fog, oedema, and lymphatic drainage failure.

4. Erythropoiesis and Iron Dysregulation

• HIF-1α induces erythropoietin (EPO) and modulates hepcidin–ferroportin axis.

• In Long COVID, this may worsen iron sequestration and ferroptosis risk, especially under conditions of glutathione depletion and ROS accumulation.

5. Immune Polarization and Myeloid Skewing

• HIF-1α favours M1 macrophage and Th17 polarization; it suppresses Treg stability and promotes myeloid-derived suppressor cells (MDSCs) under chronic hypoxia.

• This helps explain sustained IL-6, TNF-α, and IL-1β activity in post-viral states.

6. Fibrosis and Extracellular Matrix Remodelling

• Activation of TGF-β, LOX, collagen genes (COL1A1/3A1), and MMPs promotes fibrosis in vasculature, lungs, and fascia.

• Fibrotic remodelling is seen in post-COVID lung disease, but similar pathways may underlie lymphatic scarring and impaired ECM drainage in PEM.

7. Mast Cell and Glial Priming

• HIF-1α augments histamine, tryptase, and VEGF-A release in mast cells.

• In glia, it enhances ROS, NF-κB, and TLR4 sensitization, supporting central sensitization and allodynia.

8. Autophagy, Mitochondrial Quality Control, and Cell Survival

• Via BNIP3, BNIP3L, and BCL2 family genes, HIF-1α alters mitochondrial autophagy and apoptosis thresholds.

• May contribute to persistent mitochondrial fragmentation, dysregulated mitophagy, and impaired energy metabolism observed in Long COVID patients.

Additional Context in Long COVID

CNS and ECM hypoxia likely perpetuates this via DAMP signalling.

• HIF-1α also interacts with viral sensing via TLR3/TLR4, amplifying cytokine cascades.

• It is further stabilized by succinate (via SDH inhibition) and ROS/NADPH oxidase activity—both commonly upregulated in hypoxic neurovascular environments.

• In intracranial venous congestion, e.g., jugular or vertebral reflux, HIF-1α can be regionally activated in brainstem nuclei, particularly the nucleus tractus solitarius (NTS) and locus coeruleus, perpetuating autonomic dysregulation and arteriolar constriction.

  
  

Involvement of DAMPs, TLR4, RAGE, and Related Pathways 

The hypothesis about the role of DAMPs, TLR4, RAGE, NFKB, CCL2, and STAT3 is well-supported by recent findings. Damage-associated molecular patterns (DAMPs), such as S100A8/A9, are released during SARS-CoV-2 infection and can sustain inflammation. A key study, "Long COVID pro-inflammatory TLR4/RAGE loop" (Holms 2022 (6)) , describes a pro-inflammatory feedback loop established during acute COVID-19 that persists in Long COVID. This loop involves SARS-CoV-2 Spike-protein hyper-activating TLR4 and the cell-membrane expressed Receptor for Advanced Glycation End-products (mRAGE), leading to chronic stimulation by S100A8/A9.

This chronic stimulation induces the expression of IL-1β, IL-6, and TNF-α via NFKB and STAT3 signalling. Specifically, secreted IL-1β binds to IL-1R and signals via NFKB to increase mRAGE and TLR4 expression, while secreted IL-6 binds to IL-6R and signals via STAT3 and C/EBPβ for more S100A8/A9 expression, creating a self-sustaining inflammatory cycle.

TLR4 is upregulated in Long COVID neutrophils, and NFKB is depressed in neutrophil extracellular trap formation compared to severe acute COVID-19, indicating a shift in immune dynamics. STAT3’s involvement is linked to IL-6 signalling, affecting targets like angiopoietin and FLT1, with downstream effects on angiogenesis and cell survival, further supports this hypothesis.

Metabolic and Hypoxic Components

The focus on hypoxia as a primary issue is critical. HIF-1α activation under hypoxic conditions leads to metabolic reprogramming, increasing glycolysis and decreasing oxidative phosphorylation (OXPHOS), as noted in studies on immune cell metabolic changes in Long COVID.

This shift results in the accumulation of metabolic "trash," such as hypoxic endproducts, in the extracellular matrix (ECM) and mitochondria, contributing to the difficulty in recovery. This metabolic dysfunction is evident in studies like "Metabolic Profile of Patients with Long COVID: A Cross-Sectional Study" (Menezes et al 2023 (7) , which found imbalances in metabolic parameters in Long COVID patients.

Summary Table: Key Pathways in Long COVID

Pathway/Molecule	Role in Long COVID	Evidence
HIF-1α	Drives vascular proliferation, angiogenesis, and metabolic reprogramming under hypoxia	Upregulated in plasma proteome, impacts brain/heart function (4)
DAMPs (e.g., S100A8/A9)	Sustains inflammation via TLR4/RAGE loop	Chronic stimulation noted in TLR4/RAGE loop studies (6)
TLR4	Hyper-activated by Spike-protein, part of pro-inflammatory loop	Upregulated in neutrophils, sustains IL-1β/IL-6 production (6)
RAGE	Hyper-activated by Spike-protein, amplifies TLR4 signalling	Part of feedback loop, increases mRAGE via NFKB (6)
NFKB	Mediates pro-inflammatory cytokine production, depressed in neutrophil traps	Signals for mRAGE/TLR4 expression, key in inflammation (6)
CCL2	Likely involved in immune cell recruitment, related to CCL5 elevation	Indirect evidence via related chemokines in inflammation (4)
STAT3	Signals via IL-6 for S100A8/A9 expression, affects angiogenesis	Part of TLR4/RAGE loop, linked to IL-6 signalling (6)

Emerging Risk of Malignancy in Long COVID

There is growing clinical concern that persistent dysregulation of the CCL2–STAT3 axis, in conjunction with reduced activity of natural killer (NK) cells, may foster an immune-permissive environment for malignant transformation. While formal epidemiological data remain limited, frontline observations are identifying patterns of unexpected or early-onset malignancies—particularly in patients with chronic Long COVID. Mechanistically, the chronic activation of IL-6/STAT3 signalling promotes survival, angiogenesis, and immune evasion, while impaired NK cell cytotoxicity compromises tumour immunosurveillance.

This constellation mirrors the microenvironment seen in virally driven lymphomas, glial neoplasms, and epithelial dysplasia, raising important concerns about immune senescence and silent oncogenesis. Further research must evaluate whether Long COVID patients, particularly those with low CD56/CD57 counts or elevated CCL2/STAT3 biomarkers, are at increased oncologic risk.

Therapeutic Implications and Future Directions

Controlling these pathways requires a multifaceted approach. Breaking the TLR4/RAGE loop might involve modulating TLR4 or RAGE signalling where LDN and Nicotinamide Riboside is currently being investigated.   The potential use of the anti-hypertensive Telmisartan holds great promise in the hypoxic brainstems.  Addressing metabolic dysfunction usually starts with nicotinamide to improve pyruvate dehydrogenase dysfunction, while the various amino acid changes observed may require targeted metabolic management, an area being developed by molecular biologist Dr Valerio Vittone.   The changes seen here can often be seen in reduction of PEM.    Manual lymphatic therapy offers a non-pharmacological option to reduce tissue hypoxia and metabolic waste.

However, the complexity of Long COVID means that treatments must be personalized, and more clinical trials are needed to match interventions to underlying mechanisms.

Conclusion

Long COVID represents a maladaptive and evolving disease state that transitions from initial viral immune activation to a chronic, neuroimmune–metabolic disorder. At its core is a sustained hypoxic response driven by HIF-1α, which alters mitochondrial metabolism, upregulates inflammatory signaling, and reprograms cellular survival pathways. This chronic activation propagates through a RAGE–TLR4–NF-κB–STAT3 feedback loop, impairing vascular and neurological regulation, perpetuating tissue injury, and leading to progressive dysfunction across multiple systems.

The resultant clinical picture—marked by fatigue, post-exertional malaise, dysautonomia, cognitive impairment, and now increasingly malignancy risk—demands proactive intervention. Therapies that target upstream immune signaling (e.g., LDN, antihistamines), correct metabolic dysfunction (e.g., nicotinamide, magnesium, targeted amino acid therapy), and improve perfusion and glymphatic clearance (e.g., telmisartan, manual lymphatic therapy) offer promising avenues to halt or reverse disease progression.

Importantly, the emergence of oncogenic signalling through persistent CCL2–STAT3 activation, compounded by natural killer cell dysfunction, highlights a deeper threat that may extend Long COVID’s impact far beyond chronic inflammation. This risk must be addressed both clinically and in research to safeguard patients from long-term immunologic sequelae.

A precision medicine approach, rooted in immunometabolic correction and vigilant monitoring of neurovascular, immune, and oncogenic markers, will be essential to improving outcomes. Long COVID is not a benign post-viral state—it is a progressive pathophysiological continuum requiring tailored, stage-specific intervention.

References

1. Afrin, Lawrence; Weinstock, Leonard; Molderings, Gerhard. Covid-19 Hyperinflammation and post-Covid 19 may be rooted in Mast Cell Activation Syndrome. 2020: International Journal of Infectious Diseases 100, 327-332.

2. Malone,R. et al. Covid-19: Famotidine,Histamine,Mast Cells and Mechanisms. 2021. Frontiers in Pharmacology, https://www.frontiersin.org/articles/10.3389/fphar.2021.633680/full

3. Mukherjee, R. et al. Famotidine inhibits toll-like receptor 3-mediated inflammatory signaling in SARS-CoV-2 infection. 2021. JBC Research Article. https://www.sciencedirect.com/science/article/pii/S0021925821007250

4. Iosef, C., Knauer, M.J., Nicholson, M. et al. Plasma proteome of Long-COVID patients indicates HIF-mediated vasculo-proliferative disease with impact on brain and heart function. J Transl Med 21, 377 (2023). https://doi.org/10.1186/s12967-023-04149-9

5. Tian, M., Liu, W., Li, X. et al. HIF-1α promotes SARS-CoV-2 infection and aggravates inflammatory responses to COVID-19. Sig Transduct Target Ther 6, 308 (2021). https://doi.org/10.1038/s41392-021-00726-w

6. Holms,R. Long COVID (PASC) Is Maintained by a Self-Sustaining Pro-Inflammatory TLR4/RAGE-Loop of S100A8/A9> TLR4/RAGE Signalling, Inducing Chronic Expression of IL-1b, IL-6 and TNFa: Anti-Inflammatory Ezrin Peptides as Potential Therapy. Immuno. 2022. DOI:10.3390/immuno2030033

7. Menezes DC, Lima PDL, Lima IC, et al. Metabolic Profile of Patients with Long COVID: A Cross-Sectional Study. Nutrients. 2023;15(5):1197. Published 2023 Feb 27. doi:10.3390/nu15051197