From Immune Evasion to Immunothrombosis: A Mechanistic Review of Innate Immunity in Severe COVID-19

1. SARS-CoV-2 Innate Immune Evasion

SARS-CoV-2 has evolved multiple immune evasion strategies that suppress early IFN signalling, predisposing patients to critical disease courses. 23 out of the 29 viral proteins are implicated in innate immune interference, and their interactions with host mechanisms can be seen in Figure 1.

These include: host PRR interference (13 proteins); viral RNA concealment (9 proteins); JAK-STAT signalling antagonization (8 proteins); antiviral proteins translation suppression (6 proteins); and inhibiting nuclear transport of immune signalling molecules (5 proteins) [1].

Specifically, NSP1 binds to the host 40S ribosomal subunit, inhibiting translation and antagonizing IFN signalling [2]. It also epigenetically represses antiviral gene expression through demethylation of histone H3K9 at key antiviral gene promoters, highlighting a previously unrecognized mechanism of host suppression [3]. NSP3, via its PLpro domain, not only processes viral polyproteins but also removes ubiquitin and ISG15 from host proteins, blunting antiviral signalling [4,5]. NSP13 suppresses IFN activation by targeting TBK1 for degradation, whereas NSP15 functions as an endoribonuclease that degrades viral dsRNA intermediates to evade PRR detection [6,7]. NSP8 interferes with IRF3 activation and nuclear translocation to supress IFN I and III; NSP8 also further suppress IFN I through inhibition of MDA5, a critical cytosolic sensor of viral dsRNA, by impairing TRIM4-mediated MDA5 K63-linked polyubiquitination [8,9]. NSP9 also suppresses IFN and inflammatory signalling by reducing RIG-I expression, NF-κB signalling, and TBK1 activity [10]. Finally, NSP14 reduces surface IFNAR expression, weakening IFN signal transduction [11].

Accessory proteins also contribute significantly. ORF6 inhibits nuclear translocation of STAT1/2 and suppresses IRF3 and NF-κB activation[12,13]. ORF7b blocks upstream IFN production and ORF8 disrupts IRF3 function and IFN signalling, robustly suppressing ISG transcription[14,15]. ORF3a inhibits STAT1 phosphorylation, reduces IFN signalling, and promotes inflammasome activation; ORF3b potently suppresses IFN induction through IRF3 suppression; while ORF3c localizes to mitochondria, promoting MAVS cleavage and reducing IFN-β production[16,17,18]. IFN signalling is further blocked by ORF9b disrupting MAVS signalling through TOM70 targeting, and by ORF9c, which impairs antigen presentation and inflammatory pathways[19,20]. ORF10s role currently remains unclear, however, it may modulate immune responses through STRING interaction[21]. Finally, structural M protein disrupts RIG-I/MDA5 signalling, reducing IFN-β promoter activation[22].

In addition to IFN evasion, SARS-CoV-2 modulates other innate immune pathways. The nucleocapsid protein dysregulates the NLRP3 inflammasome, promoting IL-1β and IL-18 secretion and pyroptosis, leading to inflammation rather than viral clearance[23]. NSP6 and ORF3a disrupt autophagy by inhibiting autophagosome maturation and lysosomal fusion, impairing antigen presentation[24,25]. NSP1 and ORF6 also appear to impair NK cell cytotoxicity by downregulating the NKG2D activating ligands on infected cells, reducing early viral clearance[26,27].

Host factors further influence the IFN response to SARS-CoV-2 infection. Genetic mutations in critical components of IFN signalling pathways, such as TLR7, IRF7, and IRF9, compromise IFN production[28,29]. Additionally, neutralizing autoantibodies against type I IFNs (found in a subset of severe COVID-19 cases) reduce functional IFN-α/ω levels, permitting uncontrolled viral replication and severe inflammation[30].

2. Key Immune Cells in COVID-19 Pathogenesis

Airway epithelial cells are the main initial targets for SARS-CoV-2 and among the first to produce IFNs. However, often in severe disease, this response is notably delayed and insufficient to immediately control viral replication, preventing a robust antiviral state from establishing. During disease course, additional immune cells are activated through multiple complementary mechanisms. Below, the most relevant to pathogenesis are discussed.

Plasmacytoid Dendritic Cells (pDCs), often called “professional interferon-producing cells”, rapidly secrete large quantities of IFN-α/β upon viral detection, bridging innate and adaptive immunity by activating NK cells and T cells for virus clearance[31]. Notably, studies indicate pDCs detect SARS-CoV-2 more effectively by sensing infected cells, rather than free virus particles, through CD54-CD11a engagement between pDCs and infected cells[32]. Selective pressures have promoted some variants to limit this sensing, through reduced CD11a induction for Alpha, or perturbation of IFN production in the case of Delta and Omicron[32]. As pDCs are typically the largest producers of type I and III IFN during infection by a factor of 10–100, this lack of early pDC-driven IFN is a hallmark of severe COVID-19, and in such patients, a pronounced lack of functional pDCs in both blood and lung tissues is evident from disease onset[33,34,35,36,37,38]. This “pDC desert” may result from excessive recruitment into infected tissues alongside rapid, chronic activation, causing functional impairment, exhaustion and apoptosis. Resultingly, pDCs in the lungs of severe patients produce little to no IFN, contributing to a deficient antiviral response. Conversely, some studies caution that if pDCs persistently produce IFN, it might contribute late stage tissue damage, so balanced pDC response is key[39,40,41].

Alveolar macrophages (AMs) are tissue-resident cells that quietly maintain lung homeostasis by clearing debris and pathogens while preventing excessive inflammation. During early SARS-CoV-2 infection they engulf viral particles and secrete cytokines to recruit additional immune cells. In severe patients, viral propagation diminishes functional AMs and the remaining infected AMs upregulate IL1B, CCL4, CCL20, CXCL10 and CXCL11, which recruit massive numbers of blood monocytes (and T cells) to the lung for reinforcements[42]. Normally, these monocytes then differentiate into monocyte-derived macrophages (MDMs) with pro-inflammatory (M1) or anti-inflammatory (M2) signatures, dependent on cytokine environment, to balance the immune response[43]. SARS-CoV-2 however, induces a molecular shift in MDMs by promoting the uptake of viral RNA, triggering proinflammatory cytokine release and driving MDMs toward an M1-like phenotype whilst preventing reversion to an anti-inflammatory state[44]. In severe cases, this becomes a positive inflammatory feedback loop as incoming monocytes flood the alveolar space, differentiating into M1-like MDMs and secreting abundant IL-6, IL-8, TNF-α and other cytokines[45]. These cytokines majorly contribute to the cytokine storm, whilst the chemokines sustain lung inflammation through monocyte and neutrophil recruitment. Further, MDMs in the lungs of severe COVID-19 patients often express tissue-factor and contribute to immunothrombosis and fibrosis, linking the inflammatory response to some COVID-19 vascular complications[46,47].

Neutrophils are rapid responders that migrate to infection sites within minutes of trauma. However, in the lungs and alveolar space, efficient AM pathogen clearance restricts neutrophil recruitment to only periods of significant infection, preventing constant inflammation[48]. When recruited neutrophils clear pathogens through phagocytosis, inactivating them within phagolysosomes to minimize bystander damage. In contrast, excessive stimulation by PAMPs and DAMPs triggers neutrophils to unleash their full arsenal without restraint - NETs, granules, oxidants, and proteases – leading to lung injury and thrombosis. Specifically, uncontrolled degranulation and NET release damage the alveolar–capillary barrier via enzymes such as elastase and MPO, and cytokines like IL-8[49,50,51]. Furthermore, studies have found excessive NETs in the blood of severe COVID-19 patients forming thromboinflammatory clusters that contribute to microthrombi and organ damage[52,53]. Importantly, SARS-CoV-2 induces emergency granulopoiesis in severe disease, prematurely releasing immature neutrophils and granulocytic myeloid-derived suppressor cells (G-MDSCs)[54]. These left-shifted neutrophils exhibit enhanced degranulation and ROS production, and uncontrolled NET formation, whilst G-MDSCs are defined most notably by supressing T-cell proliferation and cytokine production, through secretion of molecules like arginase-1, ROS, and IL-10[54,55]. This creates a situation in which neutrophils exacerbate tissue-damaging inflammation while concurrently dampening adaptive immunity.

3. The “Cytokine Storm”

In patients where the immune response and IFN production are not sufficiently calibrated - such as with COVID-19 clinical risk factors like advanced age, obesity, lung disease, etc. - SARS-CoV-2 gains an early foothold that predisposes to life-threatening outcomes. During the initial “stealth” phase, infected cells produce minimal IFN while secreting proinflammatory chemokines, allowing unchecked viral replication[56].

By the time a substantial IFN response is mounted, the infection is often widespread. A late “compensatory” surge of IFNs may occur as accumulating viral RNA and cell damage eventually trigger PRRs. Paradoxically, IFNs that are protective when produced early can be detrimental if produced too late or excessively, with elevated systemic IFN during later stages of COVID-19 disease correlated with worsening disease outcomes[57]. Prolonged or high-dose IFN exposure can amplify inflammation and impede lung tissue-repair processes[58,59]. This weak initial IFN activity followed by an uncoordinated surge, leads to an overzealous innate response that spirals towards immunopathology. The innate immune system, now fully alarmed, releases torrents of cytokines into the lungs and circulation, creating a vicious cycle that recruits additional immune cells which then secrete more cytokines and increase the number of target cells for infection[60,61,62]. The lung becomes a battleground of uncontrolled inflammation, leading to diffuse alveolar damage, pneumonia, and ARDS[63]. In critical cases, inflammation spills over systemically, causing vasculature dysfunction, coagulopathy, and multi-organ exhaustion and injury.

NF-κB is a master transcription factor, orchestrating the expression of numerous inflammatory cytokines and mediators. It is maintained in an inactive state by IκB binding to its RHD, preventing its nuclear localization. During SARS-CoV-2 infection, however, NF-κB is markedly activated through multiple mechanisms, including TLR-mediated sensing of S protein (TLR2/4) and viral RNA (TLR3/7/8), cytosolic detection via RIG-I/MDA5, and TNF-α-driven amplification[64,65,66]. NSP3, NSP14, ORF3a, ORF6, and Nucleocapsid also show direct or indirect activation of NF-κB[17,67,68,69,70]. NF-κB is also additionally activated through cellular stress and ROS, a scenario especially pertinent in patients with pre-existing conditions where baseline oxidative stress and NF-κB activity are already elevated and thus one of the reasons such conditions are risk factors for severe disease[71,72]. Once within the nucleus, NF-κB drives the transcription of proinflammatory cytokines and chemokines (e.g. IL-1β, IL-6, TNF-α) that further launch their own signaling cascades. Moreover, its interplay with inflammatory pathways such as JAK-STAT and MAPK amplifies cytokine production. For example, NF-κB-driven IL-6 expression activates STAT3, further promoting additional proinflammatory mediator transcription, a key event in the progression toward cytokine storm[73]. High levels of NF-κB activity have been directly correlated with the severity of disease in COVID-19[74]. Concurrently, NF-κB also regulates the expression of cell survival, proliferation, and apoptosis inhibiting genes. While these functions are beneficial in mounting an effective immune response, their persistent activation can result in pathological cellular survival and prolonged inflammation. In COVID-19 patients, particularly those with pre-existing conditions or advanced age, the regulatory mechanisms that normally dampen NF-κB activity (re-synthesis of IκB proteins) may be compromised[75]. This imbalance predisposes to the uncontrolled and sustained inflammatory response observed in severe cases.

IL-1β and TNF-α are among the first cytokines released following NF-κB activation and play pivotal roles in inflammatory responses. Monocytes and macrophages predominantly produce IL-1β in a two-step process: NF-κB induced transcription of pro-IL-1β and NLRP3 as a first step, if cellular stress is then detected, NLRP3 inflammasome assembles and activates caspase-1 which cleaves pro-IL-1β into its mature, secreted form[76]. Caspase-1 is also responsible for plasma membrane rupture during pyroptosis, via GSDMD and NINJ1, allowing cytokine secretion, and contributing to pathological inflammation[76]. Once released, IL-1β binds to IL-1R1 and culminates in further NF-κB and MAPK pathway activation. In COVID-19, excessive IL-1β signaling triggers endothelial activation and dysfunction, inducing tissue factor expression and initiating the extrinsic coagulation cascade with subsequent thrombin generation and fibrin deposition[77]. Concurrent suppression of anticoagulant pathways and increased PAI-1 production shift the balance toward a prothrombotic state, driving hypercoagulation and, in severe cases, disseminated intravascular coagulation (DIC), increasing morbidity and mortality[78]. In a complementary manner, TNF-α, rapidly produced by macrophages, T cells, B cells, and dendritic cells, signals to also activate both NF-κB and MAPK pathways[76]. In particular, TNFR1 recruits TRADD and TRAF2, leading to the activation of TAK1 and downstream inflammatory cascades. TNF-α also enhances IL-1β signaling and vice versa, contributing to cytokine cross-talk that fuels the storm[78]. In the pulmonary system, TNF-α drives tissue injury by promoting bronchial constriction, increasing endothelial permeability, and stimulating epithelial cells to release inflammatory mediators such as GM-CSF and IL-8[79]. TNF-α neutrophil activation results in degranulation and protease release, further degrading lung architecture and function.

IL-6 has emerged as another critical cytokine in COVID-19. Studies consistently demonstrate markedly elevated levels in critically ill patients that strongly predict respiratory failure and mechanical ventilation requirements[78]. Following NF-κB activation, monocytes, macrophages, and dendritic cells rapidly secrete IL-6, which when bound to its receptor, recruits gp130, initiating the JAK/STAT3 pathway[78]. Activated STAT3 translocates to the nucleus to regulate proinflammatory and prothrombotic gene expression. Through STAT3 activation, IL-6 drives Th17 differentiation, promotes B cell maturation, enhances cytotoxic T cell responses, and increases neutrophil recruitment, whilst suppressing regT cell generation, skewing the immune balance toward uncontrolled inflammation[78]. STAT3 also upregulates acute-phase proteins (CRP, fibrinogen) in hepatocytes, increasing blood viscosity, enhancing platelet activation and increasing expression of adhesion molecules and tissue factor, further tipping the hemostatic balance toward a prothrombotic state[80]. Such mechanisms link IL-6 to the COVID-19 hypercoagulable state. Moreover, IL-6 trans-signaling in endothelial cells is particularly pathogenic, as it induces the release of IL-8 and MCP-1, which recruits proinflammatory neutrophils and macrophages, and stimulates VEGF secretion, which disrupts tight junction proteins to increase endothelial permeability[78].

These processes in severe COVID-19 are highly interconnected, unfolding concurrently as delayed IFN responses enable unchecked viral replication, subsequently triggering dysregulated cytokine production via pathways such as NF-κB, MAPK, and JAK-STAT. A self-amplifying cycle is created, driving systemic inflammation, coagulopathy, and multi-organ injury. Importantly, this highlights just a fraction of the many molecules and pathways involved in the complex pathophysiology of cytokine storm. This hyperinflammatory state is tightly linked with the next topic, coagulopathy via the thromboinflammatory cycle.

4. Immunothrombosis: Intersection of Inflammation and Coagulation

A striking feature of COVID-19 is coagulopathy with microthrombosis in the microvasculature of various organs, particularly lungs. Figure 2 represents and discusses a simplified normal interaction of complement and coagulation pathways in heathy individuals, whilst the below text discusses in detail how these pathways are perturbed in COVID-19 infection.

Although coagulopathy occurs in various severe infections such as bacterial sepsis, viral hemorrhagic fevers, and influenza, CAC predominantly exhibits a thrombotic rather than hemorrhagic profile, though bleeding complications may still occur[81]. CAC is notably identifiable through elevations in D-dimer and fibrinogen, mild thrombocytopenia, and generally normal clotting times[82]. Elevated D-dimer (>0.5–1.0 μg/mL) correlate with poorer outcomes, with rising levels during hospitalization linked to increased mortality. Beyond microvascular thrombosis, CAC also predisposes patients to macrovascular complications such as deep vein thrombosis, pulmonary embolism, and stroke[83]. This distinct profile likely reflects a multifactorial pathogenesis involving direct viral injury, heightened inflammation, complement activation, platelet hyperreactivity, and NETosis.

Endothelial viral infection leads to endotheliitis and a loss of its inherent antithrombotic functions[84]. Endothelial cell damage reduces protective molecules like thrombomodulin and heparin sulfate, which inhibit clotting, while increasing prothrombotic factors such as vWF and P-selectin[85,86]. Although autopsy studies demonstrate widespread endothelial inflammation in COVID-19, direct evidence of active viral replication within endothelial cells remains limited and controversial[87,88,89,90]. Thus, vascular injury likely results from indirect immune-mediated responses or initial viral entry without full replication.

Such endothelial dysfunction creates a localized environment favouring thrombosis over bleeding, contributing to the overall hypercoagulable state observed in COVID-19.

Immunologically, CAC is driven by several mechanisms. Pro-inflammatory cytokines (IL-6, TNF-α) stimulate hepatic fibrinogen synthesis and upregulate TF expression on endothelial cells and monocytes[91]. This activity triggers the extrinsic coagulation cascade and subsequent thrombin generation. Elevated IL-6 correlates with increased fibrinogen, vWF, factor VIII, and D-dimer, whilst TNF-α and IL-1β suppress natural anticoagulants like thrombomodulin and the EPCR[92,93,94]. Neutrophils also contribute through NET release, trapping platelets and clotting factors to form thrombi; their presence in lung tissues and blood of COVID-19 patients strongly correlates with thrombotic events[52,95].

Complement activation also plays a critical role, detectable in early or mild disease and correlating with severity[96]. Mechanistically, SARS-CoV-2 triggers aberrant activation of the lectin and alternative pathways, generating potent anaphylatoxins that amplify cytokine release and promote leukocyte recruitment, intensifying pulmonary and systemic inflammation[97]. This dysregulated response also promotes the formation of the membrane attack complex, contributing to the endothelial injury and microvascular thrombosis in severe COVID-19 cases[97]. Evidence further suggests that SARS-CoV-2 may directly interact with complement components, leading to the formation of persistent immune complexes and sustained complement activation during infection and up to a year following[98,99]. Additionally, impaired regulation of complement-mediated clearance mechanisms may contribute to autoinflammatory responses and has been implicated in the pathogenesis of Post-Acute Sequelae of SARS-CoV-2 infection (PASC) and multisystem inflammatory syndrome in children (MIS-C) [100,101,102].

Immunothrombosis significantly contributes to organ damage in severe COVID-19. Autopsy studies revealed widespread microvascular thrombi in pulmonary alveolar capillaries, which are strongly implicated in ARDS development and impaired gas exchange[103]. Similarly, microthrombi in coronary microcirculation have been linked to myocardial injury and dysfunction, presenting as arrhythmias or heart failure[104]. Renal involvement often involves thrombotic obstruction of small vessels and proximale tubale dysfunction, resulting kidney damage[105,106]. In the cerebral circulation, immunothrombosis is associated with an increased stroke risk in critical patients[107]. Collectively, these findings illustrate the crucial interplay between immune responses and coagulation pathways in driving both localized thrombosis and multi-organ dysfunction during severe COVID-19.