SARS-CoV-2 causes damage through a combination of direct viral destruction of cells and an overblown immune reaction that can be more harmful than the virus itself. The virus enters cells by latching onto a specific protein found on the surface of cells throughout the body, which explains why COVID-19 can affect far more than just the lungs. What begins as a respiratory infection can cascade into vascular injury, blood clotting, brain inflammation, kidney damage, and gut dysfunction, with some of these effects persisting for months or years after the initial illness.
How the Virus Gets Inside Cells
SARS-CoV-2 uses its spike protein to bind to a receptor called ACE2 on the surface of human cells. Once the spike protein locks onto ACE2, human enzymes called proteases cut the spike in a way that allows the virus to fuse with the cell membrane and inject its genetic material inside.1PubMed Central. Cell entry mechanisms of SARS-CoV-2 This is the gateway for every downstream effect of the disease.
ACE2 is not limited to the lungs. Early work on the original SARS virus showed that ACE2 is abundantly present on the surface of lung cells lining the air sacs and on cells lining the small intestine, as well as on blood vessel walls in every organ examined.2PubMed Central. Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus More detailed protein-level mapping confirmed ACE2 expression in the kidneys, heart muscle cells, gallbladder, placenta, eye, and male reproductive tract.3PubMed Central. The protein expression profile of ACE2 in human tissues This broad tissue distribution is why COVID-19 behaves as a multi-organ disease rather than a purely respiratory one. Wherever ACE2 sits on a cell surface, the virus has a potential way in.
ACE2 also has an important day job: it helps regulate blood pressure and protect blood vessels. When the virus binds to ACE2 and pulls it off the cell surface or reduces its availability, that protective function is impaired. The loss of ACE2 activity can contribute to blood vessel constriction and inflammation on its own, compounding the damage the virus is already doing directly.
The Immune System Fights Back, Sometimes Too Hard
A well-coordinated immune response clears the virus in most people within a couple of weeks. But in severe COVID-19, the immune system overshoots. The result is often described as a cytokine storm: an acute overproduction and uncontrolled release of inflammatory signaling molecules both in the lungs and throughout the bloodstream.4PubMed Central. COVID-19 infection: an overview on cytokine storm and related interventions Patients with severe disease show high levels of several pro-inflammatory cytokines, including IL-1, IL-6, TNF-α, and others, with some of these levels correlating directly with how sick the patient becomes.5PubMed Central. Cytokine Storm in COVID-19: Immunopathogenesis and Therapy
Part of the problem is that the virus actively sabotages the body’s early-warning system. One of the immune system’s first lines of defense involves proteins called type I interferons, which alert neighboring cells that a virus is present. SARS-CoV-2 carries several proteins that suppress this interferon signaling. Testing of 26 viral proteins found that four of them significantly blocked the interferon alarm, with two, nsp1 and ORF6, suppressing it by about 98% and 91% respectively.6Cell Reports. Evasion of Type I Interferon by SARS-CoV-2 By blinding the early immune response, the virus buys time to replicate. When the immune system finally catches on, it overcompensates with the inflammatory flood described above.
Another hallmark of severe COVID-19 is a sharp drop in T cells, the immune cells most important for clearing viral infections. T cells rarely carry ACE2, so the virus does not infect them directly. Instead, the inflammatory cytokine storm itself appears to suppress T-cell growth and trigger their self-destruction, partly through a shift toward more acidic conditions in the body during severe illness.7PubMed Central. SARS-CoV-2-associated lymphopenia: possible mechanisms and the role of CD147 Losing T cells at the moment you need them most is a significant reason why severe COVID-19 spirals.
Lung Damage and Respiratory Failure
The lungs bear the heaviest initial burden. In severe cases, the combination of viral destruction and immune overreaction produces a condition called acute respiratory distress syndrome, or ARDS. ARDS is one of the leading causes of death in hospitalized COVID-19 patients and is driven primarily by the cytokine storm damaging the delicate lining of the air sacs.4PubMed Central. COVID-19 infection: an overview on cytokine storm and related interventions
Under a microscope, the lung tissue in fatal COVID-19 cases shows a pattern called diffuse alveolar damage. The cells lining the air sacs and the tiny blood vessels around them are destroyed. A glassy layer called a hyaline membrane forms along the damaged surfaces, and blood clots develop inside the smallest capillaries.8PubMed Central. Pulmonary pathology of ARDS in COVID-19: A pathological review for clinicians These changes stiffen the lungs, prevent oxygen from crossing into the blood, and explain why patients with severe COVID-19 can deteriorate quickly even on supplemental oxygen.
The clotting in lung capillaries is not an incidental finding. It appears to be driven by a process called immunothrombosis, where the immune response itself triggers clot formation inside blood vessels. Inflammatory signals activate specialized white blood cells called neutrophils, which release web-like structures of DNA and proteins. These webs, known as neutrophil extracellular traps, snare platelets and clotting proteins, creating clots inside the lung’s smallest vessels.9PubMed Central. Mechanisms of immunothrombosis in COVID-19 This mechanism links the immune storm directly to the respiratory failure that kills.
Blood Clots and Vascular Injury
Clotting in COVID-19 is not limited to the lungs. The inflammatory environment creates a body-wide shift toward excess clot formation, predominantly affecting the smallest blood vessels throughout the body.10Thorax. COVID-19, immunothrombosis and venous thromboembolism: biological mechanisms This helps explain why severe COVID-19 patients develop problems in organs far from the lungs, including the kidneys, brain, and heart, all at once.
The complement system, a branch of immunity that normally helps clear pathogens, adds fuel to the fire. In COVID-19 patients, markers of complement activation are significantly elevated compared to uninfected controls. In mild and moderate disease, these markers tend to decline over time. In severe cases, they stay persistently high, suggesting ongoing, unchecked immune activation that feeds more vascular damage.11PubMed Central. Immunothrombosis and Complement Activation Contribute to Disease Severity and Adverse Outcome in COVID-19
Heart and Blood Vessel Effects
The heart can be harmed by COVID-19 through multiple pathways. Direct viral infection of heart muscle cells can trigger inflammation of the heart, a condition called myocarditis. But more commonly, the heart is damaged indirectly: a patient running a high fever with a racing heart needs more oxygen at precisely the moment their lungs are failing to deliver it. Meanwhile, cytokines released during the infection can destabilize pre-existing fatty plaques in the coronary arteries, raising the risk of heart attacks. The same cytokines activate the tiny blood vessels within the heart, causing direct injury to heart tissue.12PubMed Central. The Heart in COVID-19: Primary Target or Secondary Bystander?
Even after the acute infection resolves, cardiovascular risk appears to stay elevated for at least twelve months, regardless of whether someone had heart problems before getting sick.13PubMed Central. Clinical Implications of COVID-19-Related Endothelial Dysfunction This persistent risk likely reflects lasting damage to the endothelium, the thin layer of cells lining every blood vessel. Ongoing symptoms like chest pain, palpitations, and exercise intolerance after COVID-19 may be driven by myocardial injury, lingering cardiac inflammation, or systemic vascular damage that was initiated during the original infection.14PubMed Central. Possible Long-Term Cardiovascular Effects of COVID-19
How the Virus Reaches the Brain
Neurological symptoms in COVID-19 range from the familiar loss of smell to headaches, confusion, and a persistent cognitive difficulty commonly called brain fog. How the virus reaches the brain is still debated. The initial assumption was that the virus traveled along the olfactory nerve, the nerve responsible for smell, from the nasal cavity directly into the brain. More recent work suggests the virus may instead use a different nerve, the nervus terminalis, as a shortcut from the nose to the brain.15PubMed Central. The route of SARS-CoV-2 to brain infection: have we been barking up the wrong tree?
There is likely more than one route. Researchers examining brain tissue from people who died of COVID-19 found viral RNA in brain regions that have no direct nerve connection to the nose, such as the cerebellum. They also found viral spike protein in the cells lining blood vessels in the brain, suggesting the virus can cross from the bloodstream into the central nervous system through vessel walls.16Nature Neuroscience. Olfactory transmucosal SARS-CoV-2 invasion as a port of central nervous system entry in individuals with COVID-19 It is also possible that infected immune cells carry the virus across the blood-brain barrier, functioning as a kind of Trojan horse.
Once inflammation reaches the brain, it can activate the brain’s resident immune cells, called microglia. Activated microglia release their own wave of inflammatory signals, which can disrupt learning, memory, and emotional regulation.17PubMed Central. Long Covid brain fog: a neuroinflammation phenomenon? The leading ideas for what causes brain fog include this neuroinflammation, the accumulation of abnormal tau protein (a hallmark of neurodegenerative diseases), and autoimmune reactions triggered by the virus’s presence in brain tissue.18PubMed. Brain Fog: a Narrative Review of the Most Common Mysterious Cognitive Disorder in COVID-19
Kidney and Gut Involvement
Acute kidney injury is a common complication in hospitalized COVID-19 patients. Post-mortem kidney samples show damage to the tubules, the structures responsible for filtering waste. There is often a mismatch: the visible tissue damage under a microscope can look relatively mild compared to how badly kidney function has actually declined, a pattern also seen in non-COVID severe infections.19Nature Reviews Nephrology. Pathophysiology of COVID-19-associated acute kidney injury A more severe kidney lesion called collapsing glomerulopathy has also been reported in some patients, possibly sharing mechanisms with the kidney disease seen in HIV infections.
In the gut, the virus enters intestinal lining cells through their ACE2 receptors. When those receptors are occupied or pulled from the surface, the intestinal barrier weakens. ACE2 in the gut normally helps regulate the composition of gut bacteria by supporting a specific amino acid transport system. When that system is disrupted, the balance of gut microbes shifts, which ramps up local and body-wide inflammatory responses.20PubMed Central. Pathophysiological mechanisms underlying gastrointestinal symptoms in patients with COVID-19 This gut disruption helps explain why diarrhea, nausea, and abdominal pain are common COVID-19 symptoms and why the gut may play a role in prolonged illness.
What Happens Inside Infected Cells
At the cellular level, SARS-CoV-2 essentially hijacks the cell’s internal machinery. The virus rearranges the cell’s internal membrane system, the endoplasmic reticulum, to build bubble-like structures called double membrane vesicles that serve as sheltered factories for viral replication.21PubMed Central. Coronavirus infection induces progressive restructuring of the endoplasmic reticulum involving the formation and degradation of double membrane vesicles The virus also disrupts degradation pathways the cell uses to clean up damaged components, and it alters the cell’s fat metabolism to supply raw materials for producing new viral particles.22PubMed Central. A portrait of the infected cell: how SARS-CoV-2 infection reshapes cellular processes and pathways
Mitochondria, the cell’s energy generators, are another target. Viral proteins cause the energy-production system to collapse, disrupt the normal splitting and joining of mitochondria, and throw off the balance of ions like calcium that mitochondria carefully manage. Viral particles found near the mitochondrial interior are thought to increase the production of damaging reactive oxygen molecules and compromise the integrity of the mitochondrial membrane, which can trigger cell death.23npj metabolic health and disease. Mitochondrial dysfunction in acute and post-acute phases of COVID-19 and risk of non-communicable diseases At the same time, the virus interferes with mitochondria’s role as an antiviral alarm system, essentially disabling a backup defense the cell would normally use to fight infection.24PubMed Central. Viral mitochondriopathy in COVID-19 This mitochondrial damage may persist well beyond the acute infection and contribute to the fatigue and exercise intolerance seen in long COVID.25PubMed Central. Mitochondrial dysfunction in long COVID: mechanisms, consequences, and potential therapeutic approaches
Why Some People Stay Sick for Months
Long COVID, the persistence of symptoms weeks to months after the initial illness, does not appear to have a single cause. Several biological mechanisms are under investigation, and they may overlap in different patients. One of the most striking findings is that fragments of SARS-CoV-2 RNA, and possibly replicating virus, can persist in tissues for remarkably long periods. One study detected viral spike protein RNA in gut tissue in all five participants tested, with some showing signs of actively replicating virus up to 676 days after their original infection.26PubMed Central. Tissue-based T cell activation and viral RNA persist for up to 2 years after SARS-CoV-2 infection These viral reservoirs could drive chronic inflammation and exhaust the T cells that are trying to clear them.27PubMed Central. Insights into Persistent SARS-CoV-2 Reservoirs in Chronic Long COVID
The gut appears to be a particularly important reservoir. Long-term disruption of the gut lining and its microbial balance, initially caused by viral infection, could sustain a smoldering immune response that produces symptoms throughout the body.28PubMed Central. Mechanisms of Gut-Related Viral Persistence in Long COVID
Autoimmunity is another leading hypothesis. Multiple studies have found new autoantibodies, immune proteins that mistakenly target the body’s own tissues, appearing after COVID-19 infection. A systematic review found that roughly seven in ten studies reported some association between autoantibodies and long COVID, although there was substantial variation in how the studies were designed and what they measured. Antibodies targeting certain receptors and signaling molecules have emerged as possible biomarkers for long COVID diagnosis and severity.29The Lancet Infectious Diseases. Autoantibodies and post-COVID-19 condition: a systematic review Whether these autoantibodies are a cause of long COVID or a consequence of the immune disruption the virus sets off remains an open and actively debated question.30PubMed. Autoimmunity in long COVID
Vascular damage offers a third thread. Persistent endothelial dysfunction, the ongoing injury to blood vessel linings, is proposed as a central driver of long COVID symptoms ranging from fatigue to cognitive problems.31PubMed Central. Vascular Pathogenesis in Acute and Long COVID: Current Insights and Therapeutic Outlook One measurable sign of this vascular injury is the presence of microclots, tiny abnormal blood clots circulating in the bloodstream. A recent study found that the total number of microclots was roughly twenty-fold higher in long COVID patients than in healthy people, and these microclots were structurally intertwined with the same neutrophil extracellular traps involved in acute COVID clotting.32PubMed Central. Circulating Microclots Are Structurally Associated With Neutrophil Extracellular Traps and Their Amounts Are Elevated in Long COVID Patients ACE2 deactivation and shedding from blood vessel surfaces may contribute to the formation and persistence of these microclots, creating a cycle of ongoing vascular injury.33PubMed Central. Persistent Vascular Complications in Long COVID: The Role of ACE2 Deactivation, Microclots, and Uniform Fibrosis
How Variants Changed the Disease
Not all versions of SARS-CoV-2 affect the body in the same way. The Omicron variant, which became dominant in late 2021, carries a large number of mutations in its spike protein. These mutations increased the spike’s binding affinity for ACE2 beyond what was seen in earlier variants like Beta and Delta.34PubMed Central. Change in binding affinity with ACE2 receptor in beta, delta and omicron SARS CoV2 variants That tighter binding contributed to Omicron’s dramatically increased transmissibility. At the same time, Omicron tends to replicate more efficiently in the upper airways and less efficiently deep in the lungs compared to Delta, which partly explains why Omicron infections are generally less likely to cause severe pneumonia, though population-level immunity from vaccines and prior infection also plays a significant role in that shift.35PubMed Central. A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies
The broader lesson from variant evolution is that the pathophysiology of COVID-19 is not fixed. Mutations alter how efficiently the virus enters cells, which tissues it prefers, and how well it evades immunity. These shifts mean that clinical patterns observed in 2020 with the original strain do not perfectly predict what a new variant will do. The underlying mechanisms, ACE2 entry, immune overreaction, vascular damage, remain the same, but the balance between them shifts with each major variant.
Autoimmune Connections and Autonomic Dysfunction
One of the more puzzling consequences of COVID-19 is its apparent ability to trigger autonomic dysfunction, a disruption of the involuntary nervous system that controls heart rate, blood pressure, and digestion. Symptoms like rapid heart rate on standing, dizziness, temperature regulation problems, and gastrointestinal issues have been reported in a subset of long COVID patients. Multiple autoantibodies have been identified in both COVID-related and non-COVID autonomic disorders, suggesting a possible shared autoimmune mechanism. The finding is not specific enough to prove causation on its own, but the consistency across studies is compelling.36PubMed Central. Autoimmunity in Long Covid and POTS
This overlap raises an uncomfortable possibility: for some people, SARS-CoV-2 does not just cause a transient illness but reprograms parts of the immune system in ways that produce ongoing autoimmune-like disease. Whether these autoantibodies will decline over time and symptoms will resolve, or whether some patients have been set on a trajectory toward chronic autoimmune illness, is one of the most important unanswered questions in long COVID research. The science is still catching up to the clinical reality that millions of people are living with.