The trimeric S glycoprotein (1255 aminoacid {aa} residues) mediates viral entry. Its S1 subunit contains the receptor-binding domain (RBD), which binds to angiotensin-converting enzyme 2 (ACE2) on the host cells (14). The S2 subunit facilitates fusion between the viral envelope and the host cell membrane through conformational changes in heptad repeat (HR1 and HR2) regions, forming a fusogenic core (15). With only 20–27% sequence identity to other coronaviruses, the S protein is a key therapeutic target. Similar fusion mechanisms are seen in influenza (Hemagglutinin, HA), Ebola (Ebola virus glycoprotein), HIV (HIV glycoprotein 160, Env), and paramyxovirus (Hemagglutinin-neuraminidase, HN).

The N protein aids in viral genome packaging, replication, and immune evasion by disrupting interferon (IFN) responses. It is highly conserved and immunogenic (16), making it a viable diagnostic and therapeutic target. Monoclonal antibody CoV396 binds efficiently to its N-terminal domain (NTD) through hydrophobic interactions and hydrogen bonds (17). Inhibitors targeting N-NTD RNA binding and the C-terminal domain’s dimerization may have therapeutic potential.

The E protein (~75 aa) is a 8.5 kDa cationic viroporin involved in virus assembly, budding, release and endoplasmic reticulum–Golgi intermediate compartment (ERGIC) membrane channel formation (18). Its deletion reduces virulence, and mutations affecting ion channel activity reduce pathogenicity, making protein E a potential candidate for antiviral strategies and vaccine design.

M is the most abundant structural protein, critical for virion shape and assembly. It interacts with all other structural proteins (19) and impedes host immune responses by antagonistic interactions with IFNs and by inhibiting Nuclear Factor-Kappa B (NF-κB) signaling, lowering the production of COX-2, a key inflammatory protein. Glycosylation and interaction with IkB kinase beta (IKKβ), thereby inhibiting the growth of an IKK signalosome (20), lowers NF-κB activity, influences inflammation and aids in immune evasion. Its immunogenicity and capacity to elicit neutralizing antibodies and cytotoxic T-lymphocyte (CTL) responses (21), support its potential as a vaccine or therapeutic target. Recently, molecular dynamics simulations have identified potential drugs such as remdesivir, targeting the M protein besides RNA-dependent RNA polymerase (RdRp), though further validation is needed (22).

SARS-CoV-2 encodes 15 non-structural proteins (nsp1–nsp16 excluding nsp11) that play key roles in replication, transcription, and immune evasion and may serve as potential therapeutic targets ( Table 1 ). These proteins are encoded by open reading frame (ORF)1a/1b regions of the viral genome, and translated as polyprotein that is cleaved by viral proteases. nsp11 (13 aa) is the shortest peptide expressed at the end of ORF1a ( Figure 2 ).

nsp1 (Host Shutoff Factor) suppresses host gene expression via 40S ribosome binding, leading to mRNA degradation. This host shutoff mechanism inhibits antiviral responses (23). Drugs disrupting nsp1-ribosome interaction may restore host protein synthesis and innate immunity. nsp2 interacts with host proteins like prohibitin, impacting key mitochondrial functions, lipid homeostasis and innate immunity (24). Further studies are needed to assess its potential as a drug target. nsp3 (Papain-like protease, PLpro) has protease activity, cleaving the viral polyprotein to release individual nsps. It also deubiquitinates and deISGylates host proteins, subverting immune responses (25). PLpro inhibitors, such as GRL-0617, are being investigated for their antiviral effects. nsp4/6 remodel host membranes to form double-membrane vesicles (DMVs), which serve as replication organelles for the virus (26). Drugs that disrupt DMV formation could inhibit viral replication. nsp5 (Main protease, 3CL{chymotrypsin-like}pro/Mpro) cleaves viral polyproteins at 11 distinct sites, making it crucial for viral maturation (27). 3CLpro inhibitors, such as nirmatrelvir, have shown efficacy in reducing viral replication. nsp7/8 forms RNA primase complex and aids RdRp, facilitating viral genome replication (28). They also curb IL-8 activation and subsequent recruitment of neutrophils, facilitating viral replication (29). Drugs that interfere with nsp7/8 complex could inhibit replication. nsp9 binds single-stranded (ss) RNA, aiding viral RNA synthesis (30). Inhibitors that disrupt RNA binding may interfere with replication. nsp10 acts as a cofactor for nsp14/16, enhancing their exonuclease and methyltransferase activities (31, 32). Drugs targeting nsp10 interface could suppress multiple enzymatic functions. nsp11 suppresses host’s immunity by inhibiting IFN response (33). It also regulates endoribonuclease, essential for viral replication (34). nsp12 (RdRp) catalyzes RNA synthesis, using nsp7/8 as cofactors (35). RdRp is targeted by remdesivir/molnupiravir, disrupting viral RNA synthesis (36). nsp13 (helicase) unwinds RNA secondary structures during replication and transcription (37). Helicase inhibitors, such as bananins, have shown promise in preclinical studies (38). nsp14 has proofreading exonuclease activity, ensuring replication fidelity, and guanine-N7 methyltransferase activity for RNA capping (39). Inhibitors targeting nsp14’s exonuclease or methyltransferase domains may reduce viral viability (40). nsp15 (endoribonuclease, NendoU) cleaves viral and host RNA, and evades immune detection by degrading viral RNA intermediates (41). NendoU inhibitors could disrupt immune evasion and inhibit viral RNA synthesis. nsp16 (2′-o-methyltransferase) modifies viral RNA to mimic host mRNA, evading immune detection. Inhibitors of nsp16 methyltransferase activity could restore immune recognition (42).

SARS-CoV-2 encodes several accessory proteins (e.g., ORF3a, ORF6, ORF7a, ORF8, ORF10), which are not required for replication but modulate host responses and pathogenesis ( Table 1 ) (43). ORF3a forms ion channels, induces apoptosis and inflammation and antagonizes IFNs. Ion channel blockers could inhibit its pathogenic effects (44). ORF6 interferes with nuclear import by binding to karyopherin/importin, suppressing IFN signaling (45). Inhibitors that restore nuclear transport could counteract ORF6 activity. ORF7a antagonizes IFN responses, promotes apoptosis of infected host cells (46, 47). It inhibits autophagosome-lysosome fusion, thereby promoting viral pathogenesis (48). Blocking ORF7a interactions with host proteins may reduce immune suppression. ORF8 downregulates major histocompatibility complex I (MHC-I), aiding the virus to evade cytotoxic T cells (49). ORF8 inhibitors could enhance immune clearance of infected cells (50). ORF9b suppresses interferon response, inhibiting antiviral signaling (51). ORF10 is poorly characterized and may influence ubiquitination pathways mediating proteosomal degradation (52). Further studies are required to identify specific therapeutic targets.

SARS-CoV-2 initiates infection at the nasal mucosa, where respiratory epithelial cells, particularly goblet and ciliated cells, express high levels of ACE2 and TMPRSS2 (53). The fusogenic S glycoprotein binds ACE 2 via RBD of the S1 subunit, facilitating viral attachment (54). Proteolytic activation/priming by host proteases, TMPRSS2 and furin at the S1/S2 and S2’ sites induces conformational change and enables membrane fusion and entry of viral RNA into the host cytoplasm (55). In the absence of TMPRSS2, alternative endocytic routes, such as clathrin-mediated endocytosis, allow internalization, although with reduced efficiency (56). Thus, individuals with diminished TMPRSS2 expression may still be susceptible to infection through endosome-dependent pathways (57). Experimental models reveal that loss or reduction of ACE2 worsens lung injury after viral infection, likely due to unchecked angiotensin II activity via angiotensin II type 1 receptor (AT1R), leading to inflammation, vasoconstriction and fibrosis (58, 59). Clinically, this RAAS imbalance correlates with severe COVID-19 outcomes, indicating that while ACE2 downregulation may limit viral entry, it risks exacerbating disease by disrupting homeostatic pathways (Wang X et al., 2025). Early viral replication in the nasopharynx contributes to high transmissibility. Mutation like D614G in the S protein enhances ACE2 binding affinity, facilitating more efficient mucosal colonization (60). Understanding these mechanisms has informed the development of entry inhibitors and monoclonal antibodies (61).

Once inside the cytoplasm, the viral positive-sense RNA (+ssRNA) serves directly as mRNA, initiating translation by hijacking the host’s ribosomes to produce viral proteins. ORF1a and ORF1b, comprising about 75% of the viral genome, are translated into polyproteins pp1a and pp1ab, which are cleaved by viral proteases, PLpro and 3CLpro (main protease, Mpro), into nsps that form the replication-transcription complex (RTC). The key components include nsp12 (RdRp) that synthesizes new viral RNA, nsp13 (helicase) that unwinds RNA, nsp14 (exonuclease) that ensures replication fidelity (28). Replication occurs within double-membrane vesicles (DMVs) derived from the ER (62, 63). Initially, RTC synthesizes negative-sense RNA (-ssRNA) as a template for generating multiple new genomic (+ssRNA) copies (64). Simultaneously, discontinuous transcription produces sub-genomic RNAs (sgRNAs), encoding structural proteins (S, M, E, N) and accessory proteins (65). The RNAs are translated to form components needed for new virions.

Structural proteins synthesized in the ER are transported to ERGIC wherein, N protein packages the new viral RNA into nucleocapsids (66). While S, M, and E proteins are embedded into the ERGIC membrane of budding virions that assemble within this compartment. Instead of using the classical secretory pathway, SARS-CoV-2 exits via lysosomal trafficking, helping it evade host immune detection (62). Fully assembled virions are released by exocytosis, allowing infection of neighboring cells.

The mucosal surfaces of the respiratory tract serve as the primary entry point and battleground for SARS-CoV-2. As the first line of host defense, the mucosal epithelium and associated immune components orchestrate a dynamic interplay with the virus, influencing disease outcomes and transmission. Understanding how SARS-CoV-2 exploits, modulates, and is countered at this critical barrier is essential to unraveling its pathogenesis and informing mucosal vaccine strategies. Herein, the specific molecular and immunological interactions between SARS-CoV-2 and the mucosal interface is explored, highlighting mechanisms of viral entry, immune evasion, and local immune responses.

DNA methylation plays a pivotal role in regulating gene expression. It involves the addition of methyl groups to cytosine residues in CpG islands by DNA methyltransferases (DNMTs), leading to gene silencing. Specifically, methylation in the promoter region obstructs the binding of transcription factors resulting in transcriptional repression. SARS-CoV-2 infection alters host DNA methylation patterns, contributing to disease progression and severity (76). This suggests a potential risk factor for COVID-19 associated with the host epigenome. Recent studies have shown altered DNA methylation patterns in COVID-19 patients, with significant changes observed at 172 kidney-specific sites and 49 heart-specific sites within seven days of infection (77). Additionally, genome-wide DNA methylation studies in severe COVID-19 patients suggest accelerated biological aging compared to those with milder symptoms. Even patients with mild COVID-19 symptoms exhibited notable signs of increased aging compared to healthy individuals (78). Understanding methylation changes could pave the way for novel therapies, including DNA methylation inhibitors, to restore normal gene expression.

Histone modification serves as another critical mechanism of epigenetic regulation influencing the severity of COVID-19. Histone modifications regulate gene expression by altering chromatin structure. SARS-CoV-2 impacts histone acetylation, methylation, phosphorylation, ubiquitination and other modifications which influence the accessibility of DNA to transcription factors and other regulatory proteins, to modulate host immune responses (80). Dysregulated histone modifications enhance susceptibility to viral replication and severe inflammation.

miRNAs are small, non-coding RNAs, usually about 22 nucleotides long, that regulate gene expression after transcription by targeting complementary sequences on specific mRNAs, leading to their degradation or translational inhibition. SARS-CoV-2 disrupts host miRNA profiles, influencing immune responses and viral replication (95). Profiling miRNA expression may serve as a biomarker for disease severity and guide personalized treatments. Modulating miRNA expression offers a promising avenue for therapeutic interventions to enhance antiviral responses.

SARS-CoV-2 entry into mucosal epithelial cells relies on ACE2, whose expression is governed by both genetic and epigenetic factors (114). DNA methylation at the ACE2 promoter and enhancer regions inversely correlates with ACE2 expression in airway epithelial cells. It suppresses transcription, reducing receptor availability and viral entry but potentially impairing tissue homeostasis, especially within the pulmonary and renal systems (115, 116).

Age, sex, and comorbidities modulate ACE2 expression via methylation-dependent mechanisms, contributing to differential susceptibility across populations (117, 118). Gene expression profiling in humans and mouse models has shown consistently increased abundance of ACE2 mRNA in older males that correlated with higher viral loads and severe outcomes (119). These results highlight the intricate cross talk between genetic and epigenetic processes that regulate receptor abundance and thereby individual susceptibility to SARS‐CoV‐2 infection. ACE2 is also a critical regulator of the renin-angiotensin-aldosterone system (RAAS) which is important for the homeostasis of cardiovascular system and pulmonary function (115). Thus, excessive suppression risks promoting angiotensin II-mediated inflammation and fibrosis (58, 120). Similarly, TMPRSS2, a protease that primes the S protein for membrane fusion, is influenced by DNA methylation status. Alternative proteases like cathepsins and furin provide redundant entry routes, expanding viral tropism via miRNA-106a (121, 122). This epigenetically controlled redundancy underscores SARS-CoV-2’s adaptability in mucosal environments. Studies have shown that hypomethylation of ACE2 in nasal epithelium (especially in smokers and the elderly) enhances its transcription, potentially increasing susceptibility to infection (Corley & Ndhlovu, 2021). Conversely, hypermethylation may restrict entry in individuals with lower risk profiles. Similarly, epigenetic regulation of TMPRSS2 and FURIN via androgen-responsive enhancers or methylation-sensitive regions influences viral activation potential at mucosal surfaces.

SARS-CoV-2 rewires host defenses to facilitate their replication and survival by modifying chromatin structure, and gene accessibility (86). Viral tactics primarily target histone acetylation, methylation, and deacetylation, each of which has a unique function in immune suppression. Histone acetylation and methylation dynamically regulate chromatin accessibility, influencing antiviral gene expression. During infection, SARS-CoV-2 exploits host chromatin-modifying enzymes to suppress ISGs and PRRs (86, 123).

Peptidylarginine deiminases (PADs) catalyze the conversion of specific arginine residues on histone tails into citrulline (90). Hyperactivation of neutrophils in severe COVID-19 leads to formation of neutrophil extracellular traps (NETs), characterized by cell-free citrullinated histone H3 (Cit-H3), a product of PAD4 activity (124). This post-translational modification is typically initiated in response to intracellular calcium signaling and subsequent activation of neutrophils, positioning PADs as central mediators of NET-driven inflammation during SARS-CoV-2 infection (125). Agents like Cl-amidine that inhibit PAD4 can significantly reduce NET release in neutrophils from individuals infected with SARS-CoV-2 (126). PAD4-mediated histone citrullination weakens histone-DNA interactions, promotes chromatin decondensation, NETosis, and triggers inflammatory tissue damage and disease progression in critically ill patients (126, 127). The presence of Cit-H3 is strongly associated with increased counts of circulating platelets, leukocytes, granulocytes, and heightened levels of pro-inflammatory cytokines such as IL-8 (128). It remains unclear whether PAD4 is activated by the direct invasion of neutrophils by the virus or indirectly through the strong pro-inflammatory signals associated with cytokine storms that are common in severe COVID-19 cases (129).

The histone modifications modulate not only neutrophil responses but also suppress antiviral epithelial IFN responses and macrophage activation profiles. TRMs from COVID-19 lungs have been reported to exhibit altered chromatin landscapes, including reduced H3K4me3 at loci encoding IFN-γ and TNF, which correlate with T cell exhaustion and reduced effector functions (130). SARS-CoV-2 infection is associated with epigenetic silencing of IFN genes, especially IFNL1 and IFNB1, in mucosal epithelial and dendritic cells. Increased levels of repressive histone marks such as H3K27me3 and reduced activating marks (H3K4me3, H3K27ac that promote transcription of ISGs) at IFN loci have been detected in infected respiratory tissues, which correlates with blunted type I and III IFN responses (89, 91). This suppression delays or hinders antiviral signaling and supports viral replication during early infection stages.

Overall, the balance of histone acetylation and methylation shapes the landscape of antiviral gene expression at mucosal and systemic sites. Disruptions to this balance by the virus can weaken the host’s frontline defenses, promoting viral persistence and contributing to the severity of COVID-19. Understanding these epigenetic influences offers promising avenues for therapeutic intervention, such as using epigenetic modulators to restore proper immune gene expression and enhance viral clearance.

miRNAs and long non-coding RNAs (lncRNAs, RNA transcripts longer than 200 nucleotides that do not encode proteins), previously regarded as insignificant by-products of transcriptional noise, have been identified as vital regulators of immune responses, particularly at mucosal surfaces where SARS-CoV-2 initiates infection (131). miRNAs and lncRNAs orchestrate fine-tuned regulation of immune genes, affecting the fragile equilibrium between protective immunity and pathological inflammation at the mucosal sites during COVID-19 (131). In the respiratory mucosa, miRNAs are crucial in modulating key cytokine signaling pathways (132) and shaping other antiviral mechanisms (133). For instance, specific miRNAs can inhibit the synthesis of pro-inflammatory cytokines like IL-6 and TNF-α, thus averting excessive inflammation that may harm sensitive lung tissue (134). On the other hand, some miRNAs boost antiviral defenses by making IFNs and other antiviral factors more active (135). Crucially, miRNAs also control autophagy, a crucial antiviral mechanism that breaks down pathogens and damaged organelles (136). miRNAs limit viral replication in the airway and preserve cellular homeostasis by regulating genes linked to autophagy at several levels, including chromatin remodeling, transcriptional control, and post-transcriptional modification (115).

LncRNAs regulate chromatin remodeling and transcriptional landscapes. It has been discovered that lncRNAs affect the expression of important antiviral genes during COVID-19, including those related to the IFN response (137). To limit viral spread and augment the mucosal antiviral state, for example, some lncRNAs can upregulate the transcription of ISGs (87). Furthermore, lncRNAs are important for controlling inflammasome pathways, which are essential for identifying viral infections and triggering inflammation (115). lncRNAs can either enhance protective inflammation required for viral clearance or, if dysregulated, shift protective immunity towards pathological hyperinflammatory state, seen in severe COVID-19 cases by altering the expression or activity of inflammasome components (115, 138).

Together, the interplay between miRNAs and lncRNAs forms a complex regulatory network that shapes mucosal immunity. Their precise balance determines whether the immune response effectively contains the virus with minimal tissue damage or escalates into harmful inflammation. Understanding these non-coding RNA-mediated mechanisms opens new avenues for therapeutic interventions, such as designing RNA-based drugs to restore immune balance and reinforce mucosal defenses against SARS-CoV-2.

m6A methylation on host and viral RNAs modulates stability, translation, and immune recognition. Host methyltransferases (METTL3) and demethylases (ALKBH5) regulate these marks dynamically in response to infection (102, 103). Likewise, AMs show impaired antiviral gene expression due to m⁶A modifications of mRNA transcripts regulated by METTL3 and FTO enzymes, suggesting a role for RNA epitranscriptomics in dictating innate antiviral activity. SARS-CoV-2 alters their epigenetic programming to dampen their function. During SARS-CoV-2 infection, m⁶A dysregulation destabilizes IFN mRNAs or impairs ISG translation, weakening mucosal immunity (123, 139). m⁶A modifications are thus crucial for managing both host and viral RNA during SARS-CoV-2 infection (140). This occurs in mucous tissues like the respiratory tract, where the virus first enters and multiplies.

The initial stage of SARS-CoV-2 infection involves the binding of the trimeric S glycoprotein to the host receptor ACE2. This process can proceed via a late entry pathway involving receptor-mediated endocytosis or an early entry pathway through direct membrane fusion. Cathepsin proteases may potentially be responsible for the twofold cleavage of the S protein during receptor-mediated endocytosis (150). For direct fusion, the S protein requires two proteolytic cleavages - the first cleavage is mediated by furin protease during viral maturation while the second cleavage, essential for fusion, is facilitated by TMPRSS2 at the cell surface. Following entry, the viral genome dissociates from the nucleoprotein complex, and the genomic viral ribonucleoprotein complex enters the cytoplasm wherein the genomic RNA is translated into proteins by host ribosomes (151).

The translation of viral mRNAs into polypeptides depends on the cellular ribosomes. To prioritize its own replication, SARS-CoV-2 selectively hijacks host translation machinery by targeting eukaryotic initiation factors (eIF), preferentially promoting viral mRNA translation while suppressing host defenses by impairing host immune-related protein synthesis (152). This strategy ensures suppression of host antiviral defense mechanisms by suppressing or halting host translational processes, which prevent the production of proteins involved in the host’s innate immune responses. Moreover, in the context of an acute viral infection, host cells turn off the translation system as a whole stress response to infection stress (153). This interference maintains a balance, allowing efficient viral replication without completely halting host cell machinery, and ensuring immune evasion.

Efficient synthesis of viral proteins such as nsp1, inhibit host mRNA translation by binding to the ribosome. Additionally, SARS-CoV-2 disrupts normal cellular responses, such as phosphorylation of eIF and degradation of host mRNA (154). While many mechanisms remain under study, it is clear that SARS-CoV-2 employs host shutoff to evade immune responses and maintain viral replication. Additionally, the virus’s exoribonuclease (nsp14) proofreads its genome for replication fidelity, thereby reducing replication errors and making it more genetically stable (155).

More than 60% of the total mRNA detected in an infected cell can be viral-derived, reflecting the efficiency with which the virus usurps the cell, as determined by single-cell RNA sequencing of SARS-CoV-2-infected cells. Significant amounts of transcription of viral genomic RNA and sgRNA, collectively with the nsp1-mediated inhibition of host mRNA, result in this outcome. SARS-CoV-2 effectively suppresses IFN signaling to avoid early immune detection through nsp1- and ORF6-mediated inhibition of host mRNA translation that prevents IFN-stimulated genes (ISG) expression. Proteins like nsp10 and nsp14 repress RNA splicing and host mRNA translation, ensuring that viral proteins are preferentially produced.

SARS-CoV-2 employs multiple strategies to suppress IFN responses, thereby evading early immune detection to establish infection. The S protein triggers the onset of SARS-CoV-2 infection and immune evasion by activating NF-kB signaling cascade through Toll-like receptor 2 (TLR-2) in dendritic cells, epithelial cells, monocytes, and macrophages contributing to inflammation but dampening antiviral signaling. The virus masks or reduces the recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs), thereby interfering with IFN production (156). Although the virus suppresses IFN responses early in infection, it eventually causes cell death, allowing phagocytes to detect and remove infected cells. Despite the immune suppression, SARS-CoV-2’s aggressive replication contributes to cellular invasion and widespread infection (157, 158).

SARS-CoV-2 downregulates MHC-I expression, impairing CTL activation and CTL-mediated clearing of infected cells. The virus achieves this by blocking the karyopherin complex-dependent nuclear translocation of Nod-like receptor family caspase recruitment domain-containing 5 (NLRC5), a critical MHC-I transactivator and by suppressing IFN-induced STAT1 signaling which lowers the expression of the genes for NLRC5 and IFN regulatory factor (IRF)-1, thereby targeting the critical MHC-I transcriptional regulators, STAT1-IRF-NLRC5. Downregulation of MHC-I molecules, particularly by ORF8, hampers cytotoxic T cell recognition of infected cells at the mucosal interface, allowing the virus to persist and replicate (159).

A sizable structure known as the nuclear pore complex (NPC) connects the inner and outer membranes of the SARS-CoV-2 nuclear envelope to create an aqueous channel that controls nucleocytoplasmic trafficking. The nuclear transport receptors (importins and exportins) of the karyopherin protein family, which are in charge of transporting precisely tagged proteins between the nucleus and the cytoplasm, interact with the several protein subunits that make up the NPC, known as nucleoporins. SARS-CoV-2 disrupts the nuclear transport system, which is essential for host antiviral responses. By targeting the NPC and associated karyopherin transport proteins, the virus prevents or limits translocation of transcription factors critical for immune responses and impedes the export of host mRNA required for protein synthesis, impairing antiviral responses. ORF6 and ORF9b block nuclear translocation of transcription factors critical for IFN production. These manipulations provides SARS-CoV-2 with a selective advantage, enabling it to evade host defenses while continuing its replication (160).

Mutations in the S protein enhance immune escape by altering antibody recognition, without compromising ACE2 binding. Variants such as Alpha (B.1.1.7) that emerged in the UK in November 2020, Beta (B.1.351) first identified in South Africa, and Gamma (P.1) reported in Japan, harbor mutations like N501Y (161) and E484K (43) in the S protein’s RBD and NTD, reducing antibody neutralization and challenging vaccine efficacy. Omicron, the dominant strain of SARS-CoV-2 globally and has demonstrated a more rapid spread compared to earlier variants due to extensive mutations in the S protein, reducing antibody binding and vaccine effectiveness (162). These mutations enable the virus to evade immunity from prior infections or vaccinations.

SARS-CoV-2 has evolved sophisticated strategies to evade host immune surveillance, many of which are now recognized to operate through epigenetic mechanisms. Rather than relying solely on classical mechanisms such as antigenic drift or suppression of IFN pathways, SARS-CoV-2 actively manipulates the host’s epigenetic landscape to suppress antiviral responses, alter gene expression, and reprogram immune cell function. These virus-induced changes affect multiple levels of host transcriptional regulation ranging from chromatin accessibility and histone modifications to DNA methylation and non-coding (nc) RNA networks, and contribute substantially to immune escape and pathogenesis.

The immune evasion by SARS-CoV-2 is not merely a matter of viral stealth but rather a targeted, epigenetically regulated process. Epigenetic modifications at mucosal surfaces orchestrate the interplay between viral entry, innate immune alertness, and adaptive responses during SARS-CoV-2 infection. By manipulating host chromatin structure, ncRNA networks, and epigenetic enzymes, the virus enhances its replication potential and attenuates early antiviral responses, particularly in the respiratory tract, and thus, rewires the host transcriptional landscape to its advantage. Understanding these interactions underscores the potential of epigenetic therapeutic strategies or adjuvants aimed at restoring immune competence (such as mucosal IFN responses) or limit receptor expression to mitigate early viral spread, thereby offering insights into the long-term immunological consequences of COVID-19. However, viral immuno-epigenetic strategies might differ or be particularly potent in the mucosal environment compared to systemic responses due to tissue-specific potency of immuno-epigenetic strategies in the mucosal environment during SARS-CoV-2 infection.

The mucosal surfaces of the respiratory tract, the primary entry point and early battleground for SARS-CoV-2, are a focal point for the virus’s immuno-epigenetic strategies. Compared to systemic tissues, the mucosal environment exhibits a unique immune architecture dominated by epithelial-immune crosstalk, tissue-resident lymphocytes, and a tolerogenic milieu, which the virus exploits through targeted epigenetic reprogramming. Recent studies demonstrate that epigenetic suppression of type III interferon (IFN-λ) responses in airway epithelial cells is more pronounced than in peripheral immune cells, a process associated with increased H3K27me3 and promoter DNA methylation at IFNL1 and IFNL2 loci (178). This selective silencing impairs localized antiviral defenses without triggering strong systemic cytokinemia, allowing early viral propagation while avoiding early immune detection.

Moreover, nasal and bronchial epithelial cells display distinct chromatin accessibility profiles compared to peripheral blood mononuclear cells (PBMCs), following SARS-CoV-2 infection inducing chromatin remodeling at mucosa-specific regulatory elements (167). Mucosal macrophages and dendritic cells, already epigenetically tuned for tolerance and low inflammatory thresholds, undergo further repression of pro-inflammatory genes encoding TNF and IL-12 via increased H3K9me2 and recruitment of HDACs, enabling the virus to suppress early local innate immune responses (80). Importantly, ncRNAs such as miR-146a and miR-155, which are differentially expressed in the respiratory epithelium, target TLR and NF-κB signaling more robustly in mucosal settings, contributing to dampened antigen presentation and costimulatory signaling in dendritic cells (132).

In contrast, systemic immune responses typically display delayed but hyperinflammatory responses, a second wave of cytokine production that reflects systemic spillover, often exacerbated by a lack of early mucosal containment. The failure of early mucosal IFN responses, driven by epigenetic suppression, may thus underlie the progression from asymptomatic to severe disease (179). These findings suggest that SARS-CoV-2 has evolved epigenetic evasion strategies that are fine-tuned to the immune context of mucosal surfaces because of tolerogenic immune tone, specialized cytokine profile, and epigenetic plasticity of resident cells in the mucosal environment, prioritizing stealth over systemic disruption during early infection. Understanding this tissue-specific epigenetic plasticity may inform the development of mucosal-targeted antivirals and epigenetic adjuvants to bolster frontline defenses.

Studies indicate that SARS-CoV-2 infection induces long-lasting epigenetic reprogramming in monocytes, AMs, and mucosal epithelial cells, favoring a pro-inflammatory phenotype. For instance, genomic and epigenomic profiling of COVID-19 survivors has revealed persistent open chromatin states at IL-1β, TNF, and CXCL10 loci, marked by sustained H3K4me3 and H3K27ac, supporting continued cytokine expression even in the absence of active infection (180). This may underpin chronic symptoms such as fatigue, dyspnea, and cough.

c. Such reprogramming is supported by elevated chromatin accessibility at key pro-inflammatory loci and persistent STAT1 and NF-κB activation (181). While protective initially, this maladaptive training may promote low-grade chronic inflammation and exaggerated responses to commensals or allergens, contributing to respiratory and gastrointestinal symptoms.

Sustained DNA methylation at effector gene loci such as IFN-γ, GZMB and enhancer repression through H3K9me3 deposition have been reported in mucosal CD8⁺ and CD4⁺ T cells from long COVID patients (182). This epigenetic scarring resembles exhausted T cell profiles seen in chronic viral infections and may impair adaptive responses and barrier surveillance.

In bronchial and intestinal epithelial cells, SARS-CoV-2 has been shown to modulate DNA methylation and histone acetylation of genes regulating tight junctions such as CLDN1, OCLN, mucins, and anti-inflammatory mediators like IL-10 (80). Prolonged silencing of these genes can compromise epithelial regeneration, perpetuating barrier disruption and microbial translocation.

Persistent alteration in miRNAs such as miR-21, miR-146a and lncRNAs (NEAT1, MALAT1) modulates the JAK/STAT and TLR signaling pathways, influencing inflammatory gene expression and immune cell function post-infection (86). Additionally, m⁶A RNA methylation of key transcripts may control their stability and translation, skewing mucosal immune responses (183).

Collectively, these findings underscore that epigenetic rewiring at mucosal surfaces is not merely a byproduct of infection but a central mechanism in the persistence of inflammation and immune dysfunction in long COVID. Understanding these processes offers a basis for biomarker discovery and opens avenues for epigenetic therapies aimed at restoring mucosal immune balance.

Traditional views conceptualized immune activation as a binary response to viral antigens. However, SARS-CoV-2 has demonstrated how the timing, magnitude, and tissue specificity of immune responses are epigenetically programmed. Chromatin accessibility, DNA methylation, and histone modifications dynamically influence the expression of PRRs, type I/III IFNs, and antiviral effectors, shaping outcomes ranging from asymptomatic infection to severe COVID-19 (184).

SARS-CoV-2 infection induces persistent epigenetic changes in mucosal epithelial and immune cells, extending well into convalescence. This has shifted focus from short-lived transcriptional responses to long-term epigenetic memory, including trained immunity in myeloid cells and exhaustion signatures in T cells. These durable alterations provide a mechanistic basis for long COVID, especially in individuals experiencing sustained inflammation or immune dysregulation (185).

Emerging research has revealed that mucosal tissues such as the respiratory and gastrointestinal tracts harbor unique epigenetic landscapes, which modulate their immunological responsiveness to SARS-CoV-2. IFN-λ genes, mucin production, and epithelial barrier function are under the control of site-specific histone modifications and chromatin remodeling complexes, highlighting the need for mucosa-specific therapeutic strategies (6).

Beyond classic immune evasion strategies, SARS-CoV-2 encodes proteins that directly interfere with host epigenetic machinery, including HDACs, chromatin remodelers, and RNA modification enzymes, to suppress antigen presentation and IFN signaling (90). This expands our understanding of how viruses subvert host immunity at the transcriptional and epigenomic level, rather than relying solely on structural protein variation.

The realization that key immune genes are epigenetically regulated has spurred interest in targeting epigenetic modifiers such as HDAC inhibitors, bromodomain inhibitors, methyltransferase blockers, to restore antiviral immunity and resolve chronic inflammation. This marks a conceptual shift from antiviral drugs targeting viral enzymes alone to host-directed therapies that reprogram the immune system’s epigenetic state (143).

These conceptual advances redefine the immune response to SARS-CoV-2 not as a linear cascade, but as a multilayered, plastic, and dynamically regulated system with epigenetic mechanisms at its core. This shift compels the integration of epigenomic profiling into infectious disease research and opens new avenues for diagnostic biomarkers, precision immunotherapies, and long COVID management strategies.

Histone mimicry involves the structural and functional resemblance of viral proteins to host histones. This mimicry allows the virus to exploit host cellular machinery, disrupting normal regulatory processes such as transcription and chromatin remodeling (176). Certain SARS-CoV-2 proteins, particularly the E protein and nsps (such as nsp5), have regions that structurally mimic the tails of histones. These regions can interact with bromodomain-containing proteins (BRDs), which are essential for recognizing acetylated histones and facilitating transcriptional activation. By mimicking histone tails, SARS-CoV-2 proteins can competitively bind to bromodomains (e.g., BRD2 and BRD4) that are critical for recognizing acetylated lysine’s on histones, facilitating the recruitment of transcriptional co-activators and RNA polymerase II. The viral proteins’ mimicry of histone tails allows them to bind to these bromodomains, effectively blocking their interaction with true histones and hindering the transcriptional machinery’s access to DNA, necessary for the expression of host genes, including those involved in immune responses (189). Binding of viral proteins to host transcription factors and chromatin remodeling complexes disrupts the activation of interferon-stimulated genes (ISGs). This impairs the host’s ability to mount an effective antiviral response, making it easier for the virus to replicate and spread. By affecting histone acetylation and methylation patterns, SARS-CoV-2 can change the chromatin structure of infected cells, leading to transcriptional silencing of genes critical for immune surveillance and response.

The disruption of normal transcriptional regulation can lead to a dysregulated immune response, contributing to cytokine storms—a severe overproduction of pro-inflammatory cytokines ( Figure 4 ). This phenomenon is observed in severe COVID-19 cases and results in extensive tissue damage and respiratory complications. The virus’s ability to inhibit ISGs through histone mimicry allows it to evade the innate immune response, prolonging the infection and increasing the risk of severe outcomes.

The effects of histone mimicry are not limited to immediate viral replication. Prolonged interaction with viral proteins can lead to lasting epigenetic changes in host cells, potentially affecting gene expression patterns even after the virus has been cleared. This may contribute to long-term complications associated with COVID-19 (80). Dysregulation of histone modification processes can lead to chronic conditions, including cardiovascular diseases, diabetes, and other metabolic disorders, which are observed more frequently in COVID-19 survivors. Understanding the mechanisms of histone mimicry by SARS-CoV-2 may open avenues for novel therapeutic strategies. Inhibitors that disrupt the interaction between viral proteins and host epigenetic machinery could potentially restore normal immune function and improve outcomes in infected patients (190). Agents that modify histone acetylation or methylation patterns could be explored to counteract the effects of viral hijacking of host transcriptional regulation. Such treatments could help re-establish normal immune responses and reduce the severity of inflammation.

By mimicking histones, SARS-CoV-2 proteins can inhibit the expression of type I and type III IFNs, which are crucial for orchestrating the immune response against viral infections. The suppression of IFN signaling leads to decreased activation of ISGs that would normally enhance the antiviral state of the cell. Histone mimicry may also impact the expression of various pro-inflammatory cytokines and chemokines (191). Disruption in the expression of these molecules can result in an inadequate immune response, allowing the virus to establish a stronger foothold in the host.

The interactions between viral proteins and host chromatin-remodeling factors can lead to long-lasting changes in the epigenetic landscape of infected cells. For instance, aberrant histone modifications could silence genes that are critical for immune surveillance long after the virus is cleared, potentially contributing to chronic conditions like post-viral syndrome or long COVID (80). Research suggests that the dysregulation of histone modification enzymes, such as DNMT1, during SARS-CoV-2 infection can lead to an increased risk of comorbidities (192). These epigenetic changes have been linked to increased risks of cardiovascular diseases, atherosclerosis, metabolic disorders such as diabetes, and liver dysfunction in COVID-19 survivors.

Viroporin proteins, such as ORF3a and ORF8a, not only disrupt cellular ionic balance but also play a role in activating the NLRP3 inflammasome (193). This activation leads to a cascade of inflammatory cytokines, contributing to the hyperinflammatory state seen in severe COVID-19 cases. The mimicry of histone proteins may further exacerbate this by interfering with the normal resolution of inflammation (191).

SARS-CoV-2 utilizes histone mimicry as a sophisticated mechanism to manipulate host cellular processes, particularly in modulating immune responses and altering gene expression. This strategy not only facilitates viral replication but also contributes to the pathogenesis of severe COVID-19 outcomes and long-term health issues. Continued exploration of these interactions will be crucial for developing effective therapeutic strategies and understanding the broader implications of viral infections on host epigenetics. Understanding the mechanism of histone mimicry provides potential therapeutic avenues. Small molecules that inhibit the interaction between viral proteins and host bromodomain proteins could restore normal transcriptional regulation and enhance the antiviral response.

Nsp5’s interaction with HDAC2 inhibits the deacetylation of histones, which normally regulates the expression of antiviral genes. The blockage of HDAC2 by Nsp5 not only impairs interferon production but may also lead to an accumulation of acetylated histones, creating a feedback loop that further disrupts gene expression. ORF3b’s inhibition of type I interferons, coupled with its shorter variant in SARS-CoV-2, further enhances the virus’s ability to evade immune detection (194). This protein may also utilize histone mimicry to block the action of transcription factors that would normally promote antiviral responses.

Agents that modulate histone acetylation and methylation, such as HDAC inhibitors, may be repurposed to counteract the effects of SARS-CoV-2. These therapies could help reinstate proper immune signaling pathways and mitigate the long-term effects of infection. Further research is needed to explore the specific interactions between viral proteins and host epigenetic regulators. Identifying key viral-host interactions can inform the development of targeted therapies that could prevent COVID-19.

The virus’s interaction with DNMT1 and histone modification enzymes may create an “epigenetic memory,” perpetuating the dysregulated expression of immune-related genes. This may explain prolonged symptoms and susceptibility to reinfections.

Understanding SARS-CoV-2’s RNA synthesis has been critical in developing antiviral drugs. Remdesivir, for example, targets RdRp (nsp12), preventing the virus from copying its RNA (196). Molnupiravir introduces mutations into the viral genome, leading to non-functional viruses (197, 198), while Paxlovid (Nirmatrelvir + Ritonavir) inhibits Mpro (nsp5, the main protease), blocking viral protein processing (199). These treatments, along with vaccines, have played a crucial role in reducing the severity and spread of COVID-19. The virus’s ability to efficiently replicate and evade immune defenses underscores the need for continued research to develop more effective antiviral strategies.

An array of epigenetic-like mechanisms utilized by SARS-CoV-2 for its replication may be targeted by therapeutic drugs. These include m6A inhibitors that inhibit host methyltransferases involved in m6A modification and may thereby reduce viral RNA stability and replication (200). RNA G-Quadruplex (RG4) stabilizers have been reported to attenuate SARS-CoV-2 infection in pseudovirus cell systems and mouse models (201). Hence, compounds that disrupt G-quadruplex structures in the viral genome may impair its replication machinery. Host-driven RNA editing can be enhanced by RNA editing modulators that may introduce lethal mutations into the viral genome, reducing its infectivity (202). nsp5, a viral protease, interacts with and impairs HDAC2 function, preventing its nuclear localization. HDAC2 is crucial for regulating ISG expression and the interferon response (203). Inhibition of HDAC2 by nsp5 dampens antiviral gene activation, enhancing viral replication. RNA Pol II dysregulation via methylphosphate capping enzyme (MEPCE) has been found to attenuate host’s antiviral response. The interaction between Nsp8 and MEPCE disrupts transcription elongation mediated by RNA Pol II, impairing the expression of antiviral genes (187). Viroporins such as ORF3a and ORF8a activate the NLRP3 inflammasome, triggering a cytokine storm (204). This hyperinflammatory state is exacerbated by epigenetic silencing of genes that resolve inflammation. The ORF3b protein in SARS-CoV-2 enhances its ability to inhibit interferon responses, silencing ISG expression through epigenetic mechanisms (205). This suppression contributes to immune evasion and viral persistence.

Epigenetic modifications may be harnessed as potential therapeutic targets to combat SARS-CoV-2 infection. For instance, bromodomain inhibitors targeting BRD2/4 have been reported to prevent viral proteins from disrupting host transcription, thereby restoring normal immune responses (203, 206). Further, epigenetic enzyme modulators such as HDAC inhibitors may counteract the effects of nsp5, reactivating silenced antiviral genes (207). Likewise, DNMT1 inhibitors may mitigate aberrant DNA methylation patterns induced during infection (86). Further, epi-drugs targeting NLRP3 inflammasome activation may reduce cytokine storm and associated tissue damage (208). The potential of epigenetic-based therapies in managing COVID-19 underscores the growing need for further research into their efficacy and safety in combating SARS-CoV-2 infection.