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Host Responses to SARS-CoV-2 with an Emphasis on Cytokines

Int. J. Mol. Sci. 2026, 27(2), 664; https://doi.org/10.3390/ijms27020664

by Hideki Hayashi^1,*

, Yoshinao Kubo²

and Yoshimasa Tanaka¹

Reviewer 1: Anonymous

Reviewer 2:

Alain E. Le Faou

Reviewer 3:

Caio Santos Bonilha

Int. J. Mol. Sci. 2026, 27(2), 664; https://doi.org/10.3390/ijms27020664

Submission received: 27 October 2025 / Revised: 31 December 2025 / Accepted: 3 January 2026 / Published: 9 January 2026

(This article belongs to the Special Issue Host-Virus Interaction)

Round 1

Reviewer 1 Report (Previous Reviewer 3)

Comments and Suggestions for Authors

The review article "Host Responses to SARS-CoV-2 with an Emphasis on Cytokines" is timely, well-researched, and focuses on the crucial role of the cytokine storm and interferon response in COVID-19 pathogenesis. The authors have included recent literature, which is commendable for a rapidly evolving field. Addressing the following points will ensure the review is fully comprehensive and structurally robust.

The paper needs a dedicated and detailed section on how the host cytokine response has evolved across the major SARS-CoV-2 Variants of Concern, specifically Alpha, Delta, and Omicron. For instance, did the generally lower severity of Omicron correlate with a distinct or more regulated interferon response compared to Delta? This discussion is crucial for an up-to-date review of the virus's biology.

The abstract mentions the aim to "elucidate strategies for managing SARS-CoV-2 infection." While cytokine biology is covered, the review should make a clearer, explicit connection to current and pipeline therapeutic strategies. Please expand the discussion to include the specific small-molecule drugs or biologics that target key cytokine axes (e.g., anti-IL-6, JAK inhibitors) and their success/failure in trials.
Given the inclusion of very recent references on Long COVID (e.g., Reference 117), the section covering this topic needs to be clearly demarcated and sufficiently detailed. The authors should explicitly discuss the persistent immune and cytokine dysregulation hypothesized to drive Post-Acute Sequelae of COVID-19. Is there a distinct "PASC cytokine signature," and how does it compare to the acute phase?
The opening statement in the Abstract ("Infectious diseases, particularly those caused by novel or unidentified pathogens...") is slightly too broad. As the review is singularly focused on SARS-CoV-2, consider refining this to immediately establish the COVID-19 pandemic as the context, thus making the scope sharper.
The manuscript would benefit greatly from a clear, high-quality schematic figure summarizing the primary cytokine axes discussed. This figure should illustrate the critical "bottleneck" where the balance between early Type I/III Interferon response and subsequent inflammatory cytokine production (IL-6, TNF-alpha, etc.) is lost, leading to immunopathology.
While the title uses "SARS-CoV-2," please ensure that whenever literature from the original 2003 SARS-CoV is used for comparative context, the distinction between the two viruses is consistently and clearly stated (e.g., "SARS-CoV-1 vs. SARS-CoV-2").

Author Response

Response to #1 Reviewer’s Comments

We sincerely appreciate your thoughtful and constructive comments on our manuscript (Manuscript ID: ijms‑3980956). In response, we have revised the manuscript accordingly, with all changes highlighted in red:

The paper needs a dedicated and detailed section on how the host cytokine response has evolved across the major SARS-CoV-2 Variants of Concern, specifically Alpha, Delta, and Omicron. For instance, did the generally lower severity of Omicron correlate with a distinct or more regulated interferon response compared to Delta? This discussion is crucial for an up-to-date review of the virus's biology.
Response: We agree with the comment and have revised the paragraph in the updated manuscript (lines 296–311) as follows.

Despite these host defenses, SARS-CoV-2 often achieves high viral titers, leading to elevated levels of proinflammatory cytokines such as TNF-α, IL-1β, IL-6, IL-10, and IFN-γ, alongside suppressed type I and III IFN responses. Since its emergence in Wuhan in December 2019, SARS-CoV-2 has continued to evolve to enhance its survival. Distinct from earlier major variants (Alpha, Beta, Gamma, and Delta), the most recent Omicron variant carries numerous mutations—particularly in the spike protein—that confer increased infectivity and immune evasion [93-96]. These mutations have shifted the primary target cells from the lung to the upper respiratory tract and attenuated host immune responses, resulting in generally milder clinical outcomes. Omicron variants preferentially utilize endocytosis-dependent entry rather than TMPRSS2-dependent cell surface fusion. Although attenuated, Omicron variants still retain fundamental pathogenic features, including lymphocytopenia affecting both T and B cell populations, as well as hyperactivation of monocytes, macrophages, and neutrophils. This dysregulated cytokine environment likely impairs the development of effective adaptive immunity, as timely and balanced cytokine signaling is essential for orchestrating an appropriate immune response.
The abstract mentions the aim to "elucidate strategies for managing SARS-CoV-2 infection." While cytokine biology is covered, the review should make a clearer, explicit connection to current and pipeline therapeutic strategies. Please expand the discussion to include the specific small-molecule drugs or biologics that target key cytokine axes (e.g., anti-IL-6, JAK inhibitors) and their success/failure in trials.
Response: In accordance with the reviewer’s suggestion, we have modified the paragraph in the revised manuscript (lines 467–491) as follows.

As illustrated in Figure 1, several viral components serve as targets for antiviral drug development. These include the inhibition of the interaction between the viral S protein and the host ACE2 receptor, as well as the inhibition of virus-specific proteases (PL^pro and 3CL^pro) and RdRP [114,115]. While monoclonal antibodies remain a prominent therapeutic modality, numerous small-molecule inhibitors have also been developed, often with the aid of artificial intelligence to optimize molecular design. To mitigate aberrant host immune responses, immunosuppressive agents targeting key cytokines and signaling pathways have been employed—(1) TNF-α, IL-1β, and IL-6 involved in amplification loops of inflammation; (2) TNF-α, IFN-γ, and IL-1β involved in cell death pathways; and (3) intracellular signaling molecules such as JAK kinases (Figure 2). These interventions aim to reduce the severity of cytokine storm and prevent downstream complications, and inhibition of IL-6, IL-1, and JAK kinases has generally shown clinical benefit in COVID-19 patients [114,115]. However, targeting TNF-α or IFN-γ does not consistently yield beneficial outcomes, as these cytokines possess strong immunostimulatory functions that contribute to viral clearance while also enhancing harmful inflammation, including PANoptosis. In addition, timely administration of type I and type III IFNs has been reported to be effective in clinical settings [116,117]. Compared to type I IFNs, type III IFNs (IFN-λs) exhibit more targeted activity, acting primarily on epithelial and endothelial cells at sites of infection, while inducing minimal pro-inflammatory responses. Finally, to manage thrombotic complications, anticoagulants or NET inhibitors may be considered, although their benefits are not universal [99,118]. NET production by activated neutrophils and subsequent NETosis can help trap viral particles and limit their spread. However, NETs can also promote thrombosis through platelet activation and contribute to the generation of autoantibodies harmful to the host, ultimately leading to clinical complications [119].
Given the inclusion of very recent references on Long COVID (e.g., Reference 117), the section covering this topic needs to be clearly demarcated and sufficiently detailed. The authors should explicitly discuss the persistent immune and cytokine dysregulation hypothesized to drive Post-Acute Sequelae of COVID-19. Is there a distinct "PASC cytokine signature," and how does it compare to the acute phase?
Response: We agree with the reviewer and have revised the corresponding paragraph in the updated manuscript (lines 518-532) as follows.

Following the resolution of the acute phase of the COVID‑19 pandemic, a substantial proportion of individuals continue to experience persistent symptoms—commonly referred to as “long COVID” or “PASC” (Post‑Acute Sequelae of COVID‑19)—that last for months or even years after the initial infection [130,131]. Although cytokine profiles in these patients do not markedly differ from those observed during the acute phase, their levels remain diminished yet persistently elevated, suggesting a smoldering inflammatory state [132]. Although the precise mechanisms underlying long COVID remain unclear, persistent viral reservoirs may continuously drive the production of inflammatory cytokines [133]. Recent studies further suggest that immune dysregulation—particularly the sustained activation of CD8⁺ T cells secreting high levels of IFN‑γ—contributes to contributes to ongoing respiratory inflammation [134,135]. These findings underscore the importance of regulating aberrantly activated or suppressed cytokine responses and dysfunctional immune cell populations. Such regulation is likely to be critical not only for mitigating acute disease severity but also for preventing or managing long-term sequelae.
The opening statement in the Abstract ("Infectious diseases, particularly those caused by novel or unidentified pathogens...") is slightly too broad. As the review is singularly focused on SARS-CoV-2, consider refining this to immediately establish the COVID-19 pandemic as the context, thus making the scope sharper.
Response: We agree with the reviewer and have modified this section in the revised manuscript (lines 10–14) as follows.

The COVID-19 pandemic has profoundly affected societies around the world. Although the emergency phase of coronavirus disease 2019 (COVID-19) has ended, the threat it poses remains persistent. This review aims to clarify the mechanisms of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection to support effective management of the disease.
The manuscript would benefit greatly from a clear, high-quality schematic figure summarizing the primary cytokine axes discussed. This figure should illustrate the critical "bottleneck" where the balance between early Type I/III Interferon response and subsequent inflammatory cytokine production (IL-6, TNF-alpha, etc.) is lost, leading to immunopathology.
Response: We agree with the reviewer and have reorganized Section (i) “Possible Mechanisms of Cytokine Storm” into four subsections (1. Historical background; 2. Characteristics of SARS-CoV-2; 3. Host cells vs. SARS CoV 2 in the lung; 4. Extraordinary immune cell reactions). We have also added one new figure (Figure 4) and one table (Table 1) to better illustrate the immunopathology in the primary target site—the lung—where various cell types interact to counter SARS-CoV-2. The revised section (lines 176–294) is presented as follows.
Possible Mechanisms of Cytokine Storm
- Historical background
  Historically, the pathogenic secretion of cytokines by activated monocytes and T cells has been linked to toxic shock syndrome (TSS), which is triggered by staphylococcal toxins—classified as superantigens [34,35]. Excessive production of inflammatory cytokines, commonly referred to as a cytokine storm or cytokine release syndrome, is frequently induced by anti-CD3 antibody administration, allogeneic transplantation, chimeric antigen receptor (CAR) T cell therapy, or viral infections [29,36-38]. In severe cases of SARS-CoV-2 infection, cytokine storm is triggered, marked by elevated levels of IL-1β, IL-2, IL-4, IL-6, IL-10, TNF-α, IFN-γ, GM-CSF, MCP-1, CXCL10, and others, alongside deficiencies in type I and type III IFNs [28–30,39-45]. Although the precise mechanisms underlying cytokine storms remain incompletely understood, several contributing factors have been identified, including high viral loads, dysregulated cytokine signaling pathways, and extensive lytic cell death.
- Characteristics of SARS-CoV-2
  Compared to influenza virus, SARS-CoV-2 more readily induces cytokine storms while simultaneously suppressing type I and type III IFN responses [40]. Although these IFNs typically induce a broad spectrum of ISGs that facilitate viral clearance, SARS-CoV-2 encodes multiple proteins that antagonize this pathway at various levels (see Figure 3). For example, viral proteins NSP13, NSP12, NSP14, and NSP16—assisted by the cofactor NSP10—cap the 5′ ends of viral RNA to mimic host mRNA and evade recognition by RIG-I-like receptors (RLRs) [46-48]. NSP3, a papain-like protease with deubiquitinase activity, removes ISG15 modifications from MDA5, while NSP5 (3CLpro) cleaves RIG-I, disrupting signalosome assembly and TBK1 activation [49,50].
  
  NSP1 promotes the translation of viral positive-sense genomic RNA (+gRNA) while inhibiting host mRNA translation, targeting key components of IFN signaling such as TYK2 and STAT2 [51-53]. Additional viral proteins—including NSP9, NSP8, and NSP16—further suppress host protein synthesis by impairing signal recognition and mRNA splicing [51]. NSP6, in conjunction with NSP3 and NSP4, remodels the endoplasmic reticulum (ER) to form double-membrane vesicles (DMVs) that house the viral replication-transcription complex (RTC) and modulate autophagy [54-57]. NSP6 also inhibits phosphorylation of IRF3, STAT1, and STAT2, thereby attenuating IFN signaling [58]. The accessory protein ORF6 binds to the nuclear pore complex (NPC), blocking nuclear translocation of IRF3 and STAT1 [59-61]. Further suppression of ISG activity is mediated by NSP3, ORF7a, ORF3a, and the spike (S) protein [62-67].
  
  Host cells, however, deploy additional mechanisms beyond ISGs to eliminate invading viruses. Loss-of-function studies have identified host restriction factors such as DAXX and mucins [63,66,68], while gain-of-function experiments have revealed antiviral roles for host proteins including LY6E, CH25H, IFITMs, FAM64C, NCOA7, CD74, IFIT3, ZAP, OAS1, CNP, and tetherin, which act at various stages of the viral life cycle [62,66,69-76].
- Host cells vs SARS-CoV-2 in the lung
  As shown in Figure 4, in the lung—the primary target site of SARS-CoV-2—the virus efficiently infects alveolar epithelial cells that express ACE2 and TMPRSS2 [77–79]. It can also infect resident macrophages through ACE2-mediated entry [80,81]. Upon viral entry, intracellular signaling pathways are activated, leading to the production of type I and type III IFNs as well as various inflammatory cytokines (Figure 2). However, SARS-CoV -2 possesses multiple mechanisms to interfere with type I and III IFN production at several steps, enabling the virus to evade host antiviral responses (Figure 3). In many cases, sufficient amounts of type I and III IFNs are produced to activate their respective receptors and induce ISGs, thereby eliminating the virus. This is because nearly all cell types express receptors for type I IFNs, whereas expression of type III IFN receptors is largely restricted to epithelial cells such as alveolar cells [82]. Conversely, if the virus successfully replicates while suppressing IFN-mediated defences, the newly produced virions not only spread to neighbouring cells but also activate intracellular PRRs, and the damaged cells release DAMPs. Both PAMPs and DAMPs stimulate various PRRs located both on the cell surface and within the cytoplasm, triggering the production of inflammatory cytokines such as IL-1β, IL-6, TNF-α, type II IFN (IFN-γ), and IL-10, along with relatively weak type I and III IFN responses. Local immune cells—including DCs, monocytes, and macrophages expressing PRRs—respond to these cytokines and contribute to the development of adaptive immunity by instructing T and B cells, which ultimately eliminate viruses that evade the initial IFN mediated defence [83,84]. However, when these immune cells have already been activated by PAMPs and DAMPs, they may overreact to inflammatory cytokines, initiating a self-amplifying loop of cytokine production that culminates in a cytokine storm.
- Extraordinary immune cell reactions
  SARS-CoV-2 drives host cells, including immune cells, to produce extraordinarily high levels of inflammatory cytokines, likely due to its strong ability to suppress IFN signaling, resulting in high viral loads, robust PRR activation, and related downstream events. These excessively produced inflammatory cytokines damage and dysregulate immune cells, as summarized in Table 2. Notably, cytokines such as TNF-α, IL-1β, IL-6, IFN-γ, and IL-10 not only amplify the production of additional cytokines—including themselves—but also play critical roles in regulating immune cell differentiation and function, thereby exacerbating immune dysregulation in severe COVID-19 [83-88]. Aberrantly activated macrophages and monocytes are considered major sources of excessive cytokine production, while lymphocytopenia—affecting T cells, B cells, and NK cells—is frequently observed. Meanwhile, type I IFN production by plasmacytoid DCs (pDCs) is reported to be attenuated [89,90].
  
  Overproduced TNF-α and IL-1β exert priming effects by upregulating molecules involved in inflammation and cell death pathways, such as pyroptosis and PANoptosis, respectively [21,28]. Although these cytokines are required for proper DC maturation and for the activation of T cells and B cells, their excessive induction of cell death may contribute to dysregulated adaptive immunity. IL-6 further induces the expression of TNF-α, IFN-γ, and TGF-β, thereby amplifying inflammation and influencing T cell polarization [84-87]. IFN-γ, known to promote Th1 differentiation, activates various immune cells [84-86]. IL-10, on the other hand, is recognized as a key immunosuppressive cytokine predominantly secreted by Tregs [88,91]. Under certain conditions, however, it can also exert immunostimulatory effects on CD8⁺ T cells and B cells. A marked elevation of IL-10 is a hallmark of severe COVID-19, distinguishing it from other betacoronavirus infections such as SARS and MERS [91]. This elevation is not merely a compensatory response to suppress excessive inflammation; rather, its pleiotropic functions may interfere with the establishment of a properly regulated immune response. IL-10 also increases ACE2 expression, and a genetic risk factor has been identified: a polymorphism (rs13050728) dependent readthrough from IFNAR2 into the downstream IL-10 receptor gene, IL10RB, results in the formation of a hybrid receptor (CiDRE) that enhances IL-10 signaling while attenuating type I IFN signaling, thereby worsening COVID-19 severity [92]. Taken together, these findings suggest that extraordinarily high levels of inflammatory cytokines profoundly disrupt proper immune development.
  
  Figure 4. Schematic representation of immunological reactions to SARS-CoV-2 in the lung.
  
  Table 1. Major immunological effects of the inflammatory cytokines

While the title uses "SARS-CoV-2," please ensure that whenever literature from the original 2003 SARS-CoV is used for comparative context, the distinction between the two viruses is consistently and clearly stated (e.g., "SARS-CoV-1 vs. SARS-CoV-2").
Response: We added several references beyond those related to SARS-CoV-2 to provide essential background information and to explain the biological mechanisms underlying the phenomena observed in SARS-CoV-2 infection. We clarified in the text the distinctions between SARS‑CoV‑2 and SARS‑CoV‑1, as well as other viruses.

Reviewer 2 Report (New Reviewer)

Comments and Suggestions for Authors

The virology part is a perfect nonsense and there is no excuses as very good recent reviews are available. It justifies by itself the rejection of the paper.

More detailed: Please provide a satisfactory description of the Betacoronavirus pandemicum (SARS-Cov-2) replication based on sound scientific data.

Author Response

#2 Reviewer’s Comments and Suggestions for Authors

The virology part is a perfect nonsense and there is no excuses as very good recent reviews are available. It justifies by itself the rejection of the paper.

More detailed: Please provide a satisfactory description of the Betacoronavirus pandemicum (SARS-Cov-2) replication based on sound scientific data.

The main errors are associated with the mechanism of entry of the virus and the reconstitution of the viral particle. Among the sub-genomic RNA, their production is a very complex process producing mRNAs of different length corresponding to accessory proteins along with the structural ones using the same initial internal sequence of the (-) RNA which is not cleaved and double strand rNA are not formed at this stage (thus the drawing is not correct).
Response: We sincerely appreciate your thoughtful and constructive comments on our manuscript (Manuscript ID: ijms‑3980956). In accordance with your suggestions, we have revised Figure 1 and removed the depiction of dsRNA at the stage you indicated.

At the same time, we would like to clarify that multiple studies have demonstrated the presence of dsRNA intermediates generated during SARS‑CoV‑2 genome replication and transcription. For your reference, we provide the following papers:

Wang X, Zhu B. SARS‑CoV‑2 nsp15 preferentially degrades AU‑rich dsRNA via its dsRNA nickase activity. Nucleic Acids Res. 2024;52(9):5257–5272.
“It was suggested that the EndoU activity of coronavirus nsp15 mediates evasion of host cell double‑stranded (ds)RNA sensors by reducing dsRNA produced by viral genome replication and transcription.”

Li Y, et al. SARS‑CoV‑2 induces double‑stranded RNA‑mediated innate immune responses in respiratory epithelial‑derived cells and cardiomyocytes. Proc Natl Acad Sci U S A. 2021;118(16):e2022643118.
“Coronaviruses are adept at evading host antiviral pathways induced by viral double‑stranded RNA, including interferon signaling, OAS–RNase L, and PKR.”

Wickenhagen A, et al. A prenylated dsRNA sensor protects against severe COVID‑19. 2021;374(6567):eabj3624.
“Prenylated OAS1 colocalizes with viral dsRNA because SARS‑CoV‑2 replication uses dsRNA intermediates.”

We hope these references help clarify the scientific basis for the presence of dsRNA intermediates during SARS‑CoV‑2 replication.

The manuscript has been revised extensively in response to comments from all reviewers, and all modifications are highlighted in red in the revised version. We would be grateful if you could kindly re‑evaluate the updated manuscript.

Reviewer 3 Report (New Reviewer)

Comments and Suggestions for Authors

This manuscript provides a comprehensive and clearly presented overview of host responses to SARS-CoV-2 with a particular emphasis on cytokine biology. The authors synthesise current knowledge of viral sensing pathways, cytokine dynamics and mechanisms underlying hyperinflammation and they integrate these aspects with discussions of functional cytokine assessment and therapeutic approaches. The work is logically structured, well written and supported by informative figures which together offer a valuable resource for readers. I list below, however, some points that should be addressed to further strengthen the scientific clarity and conceptual breadth of the manuscript.

It would be helpful to specify which cell types are the predominant producers of the cytokines discussed throughout the text. For example, DCs are mentioned in the abstract but not revisited in the main body despite their central role in antiviral cytokine responses.
The abbreviation for NETs appears more than once in full form before being abbreviated. I recommend checking consistency for all abbreviations to ensure that each is introduced only once.
The manuscript discusses NETs only within the section on pathological consequences. Given that neutrophils sense SARS-CoV-2 and release traps early during infection and that trap-associated proteins can themselves amplify cytokine secretion, it would be appropriate to highlight their potential roles both as drivers of cytokine storm and as mediators of downstream tissue injury.
The manuscript could consider including comments on the contribution of non haematopoietic cells such as epithelial cells or endothelial cells to the cytokine milieu during SARS-CoV-2 infection, as these cells can dominate local cytokine production in the respiratory tract.
It may be helpful to refine the discussion of cytokine storm mechanisms by mentioning the interplay between cytokine driven feedback loops and cell intrinsic antiviral pathways, which contributes to the heterogeneity of patient responses.
The authors should comment on NET and NETosis-specific therapies, which are highly relevant to COVID-19 immunopathology and directly intersect with the cytokine-centred focus of the review. These two drug classes act through distinct mechanisms and differ markedly in their impact on SARS-CoV-2-specific immunity, with PAD4 inhibitors uniquely suppressing SARS-CoV-2-specific T cell responses (DOI 10.1016/j.mucimm.2025.04.006).

Author Response

Response to #3 Reviewer’s Comments

It would be helpful to specify which cell types are the predominant producers of the cytokines discussed throughout the text. For example, DCs are mentioned in the abstract but not revisited in the main body despite their central role in antiviral cytokine responses.
Response: We agree with the reviewer and have reorganized Section (i) “Possible Mechanisms of Cytokine Storm” into four subsections (1. Historical background; 2. Characteristics of SARS-CoV-2; 3. Host cells vs. SARS CoV 2 in the lung; 4. Extraordinary immune cell reactions). We have also added one new figure (Figure 4) and one table (Table 1) to better illustrate the immunopathology in the primary target site—the lung—where various cell types interact to counter SARS-CoV-2. The revised section (lines 176–294) is presented as follows.
Possible Mechanisms of Cytokine Storm
- Historical background
  Historically, the pathogenic secretion of cytokines by activated monocytes and T cells has been linked to toxic shock syndrome (TSS), which is triggered by staphylococcal toxins—classified as superantigens [34,35]. Excessive production of inflammatory cytokines, commonly referred to as a cytokine storm or cytokine release syndrome, is frequently induced by anti-CD3 antibody administration, allogeneic transplantation, chimeric antigen receptor (CAR) T cell therapy, or viral infections [29,36-38]. In severe cases of SARS-CoV-2 infection, cytokine storm is triggered, marked by elevated levels of IL-1β, IL-2, IL-4, IL-6, IL-10, TNF-α, IFN-γ, GM-CSF, MCP-1, CXCL10, and others, alongside deficiencies in type I and type III IFNs [28–30,39-45]. Although the precise mechanisms underlying cytokine storms remain incompletely understood, several contributing factors have been identified, including high viral loads, dysregulated cytokine signaling pathways, and extensive lytic cell death.
- Characteristics of SARS-CoV-2
  Compared to influenza virus, SARS-CoV-2 more readily induces cytokine storms while simultaneously suppressing type I and type III IFN responses [40]. Although these IFNs typically induce a broad spectrum of ISGs that facilitate viral clearance, SARS-CoV-2 encodes multiple proteins that antagonize this pathway at various levels (see Figure 3). For example, viral proteins NSP13, NSP12, NSP14, and NSP16—assisted by the cofactor NSP10—cap the 5′ ends of viral RNA to mimic host mRNA and evade recognition by RIG-I-like receptors (RLRs) [46-48]. NSP3, a papain-like protease with deubiquitinase activity, removes ISG15 modifications from MDA5, while NSP5 (3CLpro) cleaves RIG-I, disrupting signalosome assembly and TBK1 activation [49,50].
  
  NSP1 promotes the translation of viral positive-sense genomic RNA (+gRNA) while inhibiting host mRNA translation, targeting key components of IFN signaling such as TYK2 and STAT2 [51-53]. Additional viral proteins—including NSP9, NSP8, and NSP16—further suppress host protein synthesis by impairing signal recognition and mRNA splicing [51]. NSP6, in conjunction with NSP3 and NSP4, remodels the endoplasmic reticulum (ER) to form double-membrane vesicles (DMVs) that house the viral replication-transcription complex (RTC) and modulate autophagy [54-57]. NSP6 also inhibits phosphorylation of IRF3, STAT1, and STAT2, thereby attenuating IFN signaling [58]. The accessory protein ORF6 binds to the nuclear pore complex (NPC), blocking nuclear translocation of IRF3 and STAT1 [59-61]. Further suppression of ISG activity is mediated by NSP3, ORF7a, ORF3a, and the spike (S) protein [62-67].
  
  Host cells, however, deploy additional mechanisms beyond ISGs to eliminate invading viruses. Loss-of-function studies have identified host restriction factors such as DAXX and mucins [63,66,68], while gain-of-function experiments have revealed antiviral roles for host proteins including LY6E, CH25H, IFITMs, FAM64C, NCOA7, CD74, IFIT3, ZAP, OAS1, CNP, and tetherin, which act at various stages of the viral life cycle [62,66,69-76].
- Host cells vs SARS-CoV-2 in the lung
  As shown in Figure 4, in the lung—the primary target site of SARS-CoV-2—the virus efficiently infects alveolar epithelial cells that express ACE2 and TMPRSS2 [77–79]. It can also infect resident macrophages through ACE2-mediated entry [80,81].. Upon viral entry, intracellular signaling pathways are activated, leading to the production of type I and type III IFNs as well as various inflammatory cytokines (Figure 2). However, SARS-CoV -2 possesses multiple mechanisms to interfere with type I and III IFN production at several steps, enabling the virus to evade host antiviral responses (Figure 3). In many cases, sufficient amounts of type I and III IFNs are produced to activate their respective receptors and induce ISGs, thereby eliminating the virus. This is because nearly all cell types express receptors for type I IFNs, whereas expression of type III IFN receptors is largely restricted to epithelial cells such as alveolar cells [82]. Conversely, if the virus successfully replicates while suppressing IFN-mediated defences, the newly produced virions not only spread to neighbouring cells but also activate intracellular PRRs, and the damaged cells release DAMPs. Both PAMPs and DAMPs stimulate various PRRs located both on the cell surface and within the cytoplasm, triggering the production of inflammatory cytokines such as IL-1β, IL-6, TNF-α, type II IFN (IFN-γ), and IL-10, along with relatively weak type I and III IFN responses. Local immune cells—including DCs, monocytes, and macrophages expressing PRRs—respond to these cytokines and contribute to the development of adaptive immunity by instructing T and B cells, which ultimately eliminate viruses that evade the initial IFN-mediated defence [83,84]. However, when these immune cells have already been activated by PAMPs and DAMPs, they may overreact to inflammatory cytokines, initiating a self-amplifying loop of cytokine production that culminates in a cytokine storm.
- Extraordinary immune cell reactions
  SARS-CoV-2 drives host cells, including immune cells, to produce extraordinarily high levels of inflammatory cytokines, likely due to its strong ability to suppress IFN signaling, resulting in high viral loads, robust PRR activation, and related downstream events. These excessively produced inflammatory cytokines damage and dysregulate immune cells, as summarized in Table 2. Notably, cytokines such as TNF-α, IL-1β, IL-6, IFN-γ, and IL-10 not only amplify the production of additional cytokines—including themselves—but also play critical roles in regulating immune cell differentiation and function, thereby exacerbating immune dysregulation in severe COVID-19 [83-88]. Aberrantly activated macrophages and monocytes are considered major sources of excessive cytokine production, while lymphocytopenia—affecting T cells, B cells, and NK cells—is frequently observed. Meanwhile, type I IFN production by plasmacytoid DCs (pDCs) is reported to be attenuated [89,90].
  
  Overproduced TNF-α and IL-1β exert priming effects by upregulating molecules involved in inflammation and cell death pathways, such as pyroptosis and PANoptosis, respectively [21,28]. Although these cytokines are required for proper DC maturation and for the activation of T cells and B cells, their excessive induction of cell death may contribute to dysregulated adaptive immunity. IL-6 further induces the expression of TNF-α, IFN-γ, and TGF-β, thereby amplifying inflammation and influencing T cell polarization [84-87]. IFN-γ, known to promote Th1 differentiation, activates various immune cells [84-86]. IL-10, on the other hand, is recognized as a key immunosuppressive cytokine predominantly secreted by Tregs [88,91]. Under certain conditions, however, it can also exert immunostimulatory effects on CD8⁺ T cells and B cells. A marked elevation of IL-10 is a hallmark of severe COVID-19, distinguishing it from other betacoronavirus infections such as SARS and MERS [91]. This elevation is not merely a compensatory response to suppress excessive inflammation; rather, its pleiotropic functions may interfere with the establishment of a properly regulated immune response. IL-10 also increases ACE2 expression, and a genetic risk factor has been identified: a polymorphism (rs13050728) dependent readthrough from IFNAR2 into the downstream IL-10 receptor gene, IL10RB, results in the formation of a hybrid receptor (CiDRE) that enhances IL-10 signaling while attenuating type I IFN signaling, thereby worsening COVID-19 severity [92]. Taken together, these findings suggest that extraordinarily high levels of inflammatory cytokines profoundly disrupt proper immune development.
  
  Figure 4. Schematic representation of immunological reactions to SARS-CoV-2 in the lung.
  
  Table 1. Major immunological effects of the inflammatory cytokines

The abbreviation for NETs appears more than once in full form before being abbreviated. I recommend checking consistency for all abbreviations to ensure that each is introduced only once.
Response: In accordance with the reviewer’s comments, we have corrected the usage of abbreviations throughout the manuscript
The manuscript discusses NETs only within the section on pathological consequences. Given that neutrophils sense SARS-CoV-2 and release traps early during infection and that trap-associated proteins can themselves amplify cytokine secretion, it would be appropriate to highlight their potential roles both as drivers of cytokine storm and as mediators of downstream tissue injury.
Response: We agree with the reviewer that the production of NETs and subsequent NETosis are important contributors to the immunopathogenesis of SARS‑CoV‑2. To maintain balance with other factors discussed in the sections (lines 312-327 and lines 486-491), we have expanded the description of NETs and cited additional references [118,119] as follows.

Lines 312-327: Inflammatory cell death—including PANoptosis and NETosis—represents a criti-cal pathological hallmark of severe COVID-19. This process involves widespread death of vascular endothelial and alveolar epithelial cells, accompanied by elevated cytokine release [28–30]. Microthrombi frequently contain abundant neutrophils undergoing NETosis, often in close association with platelets. An elevated neutrophil-to-lymphocyte ratio (NLR) and increased formation of neutrophil extracellular traps (NETs) have been linked to severe cases of COVID-19 [28-30, 97-100]. Neutrophils are activated through both PRR-dependent and PRR-independent pathways, and overactivated neutrophils produce NETs and undergo NETosis. These NETs activate platelets and, together with inflammatory cytokines, contribute to the induction of PANoptosis or cause damage to alveolar and endothelial cells, ultimately leading to dyspnea and thrombosis [97-100]. In addition, sera from COVID-19 patients contain pro-NETotic factors such as RANTES (CCL5) and platelet factor 4 (PF4), likely secreted by hyperactivated platelets and their precursor megakaryocytes, which are known to harbor SARS-CoV-2 [100]. Excessive platelet consumption during thrombogenesis may contribute to the development of thrombocytopenia in these patients.

Lines 486-491: Finally, to manage thrombotic complications, anticoagulants or NET inhibitors may be considered, although their benefits are not universal [99,118]. NET production by acti-vated neutrophils and subsequent NETosis can help trap viral particles and limit their spread. However, NETs can also promote thrombosis through platelet activation and contribute to the generation of autoantibodies harmful to the host, ultimately leading to clinical complications [119].
The manuscript could consider including comments on the contribution of non haematopoietic cells such as epithelial cells or endothelial cells to the cytokine milieu during SARS-CoV-2 infection, as these cells can dominate local cytokine production in the respiratory tract.
Response: As noted in our response to Comment #1, we have added descriptions of alveolar cells and endothelial cells in the respiratory tract.
It may be helpful to refine the discussion of cytokine storm mechanisms by mentioning the interplay between cytokine driven feedback loops and cell intrinsic antiviral pathways, which contributes to the heterogeneity of patient responses.
Response: As stated in our response to Comment #1, we have incorporated additional explanations regarding feedback loops and the heterogeneity of patient responses in lines 176–294, with reference to Figure 4 and Table 1.
The authors should comment on NET and NETosis-specific therapies, which are highly relevant to COVID-19 immunopathology and directly intersect with the cytokine-centred focus of the review. These two drug classes act through distinct mechanisms and differ markedly in their impact on SARS-CoV-2-specific immunity, with PAD4 inhibitors uniquely suppressing SARS-CoV-2-specific T cell responses (DOI 10.1016/j.mucimm.2025.04.006).
Response: As noted in our response to Comment #3, we have expanded the description of NETs and included the reference concerning the PAD4 inhibitor [118] in detail in the revised manuscript.

Round 2

Reviewer 2 Report (New Reviewer)

Comments and Suggestions for Authors

I acknowledge the improvement of the text howeve Irhave a few remarks.

The official name of the SARS-Cov-2 should be indicated at least once: Betacoronavirus pandemicum even if the commonly used name is used throughout the text.

Why are CD8+ not considered and they are cited solely in table 1 where it is indicated they are activated.

A common shared opinion on viruses is, like indicated in this text (e.g. lines 87-88), that they govern their own evolution. It is certainly not the case!

Author Response

Response to #2 Reviewer’s comments

We sincerely appreciate your valuable comments on our manuscript (Manuscript ID: ijms-3980956). In response, we have revised the manuscript accordingly, with all changes highlighted in yellow:

I acknowledge the improvement of the text however, I have a few remarks.

The official name of the SARS-Cov-2 should be indicated at least once: Betacoronavirus pandemicum even if the commonly used name is used throughout the text.

Response: In accordance with the comment, we have added the official name, Betacoronavirus pandemicum in addition to the common name, SARS-CoV-2 in line 31 of the revised manuscript, as follows.

SARS-CoV-2, Betacoronavirus pandemicum is an enveloped, positive-sense, single-stranded RNA virus belonging to the Coronaviridae family [1–4].

Why are CD8+ not considered and they are cited solely in table 1 where it is indicated they are activated.

Response: In accordance with the comment, we have added the effects of TNF-α, IL-6, and IL-1β on CD8+T cells to Table 1 of the revised manuscript as follows.

TNF-α: Activation; Exhaustion of CD8⁺T cell
IL-6: Reduction of CD8⁺T cell cytotoxic function
IL-1β: Activation; Induction of Pyroptosis in CD8⁺T cell

A common shared opinion on viruses is, like indicated in this text (e.g. lines 87-88), that they govern their own evolution. It is certainly not the case!

Response: We appreciate the comment. To avoid any unintended teleological implications, we have revised the text to clarify that viral evolution is driven by host selection pressures rather than by virus-directed processes (lines 211-212, and lines 299-301) in the revised manuscript as follows.

Lines 211-212: Host cells, however, deploy additional mechanisms that contribute to the elimination of invading viruses.
Lines 299-301: SARS-CoV-2 has continued to evolve under strong host selection pressures, resulting in variants with increased fitness.

Finally, in accordance with your previous comments, we have refined the description of “1. The SARS-CoV-2 Life Cycle”, and revised Figure 1 for greater accuracy, as follows.

Line 41: cathepsin B/L for endolysosomal fusion
Lines 71-73: The +sgRNAs are translated into structural proteins (spike [S], envelope [E], membrane [M], and nucleocapsid [N] proteins) and interspersed accessory proteins (ORF3a ,6, 7a, etc.).

Reviewer 3 Report (New Reviewer)

Comments and Suggestions for Authors

All raised concerns have been satisfactorily addressed.

Author Response

Response to #3 Reviewer’s comment

Thank you for your kind acceptance of my response.

This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Lines 10–29 (Abstract): The abstract is relatively long and contains many details. We recommend shortening it to emphasize only the essential ideas and adding a concluding sentence that summarizes the main message of the paper. This change will give the reader a clearer overview from the abstract.

Lines 185–239 (Section Cytokine Storm): The section on the “cytokine storm” is very dense, addressing multiple aspects (systemic inflammation, platelet-involved coagulopathies, T cell dysfunction, etc.) in a single block. For a clearer structure, we suggest dividing this section into subsections or separate paragraphs, for example: (i) pro-inflammatory mechanisms of the “cytokine storm” and (ii) pathological consequences (coagulation disorders, immunological dysfunctions). This segmentation would facilitate reading and organize the ideas logically.

Lines 116–118 (Cell death pathways): The passage briefly mentions the pathways of lytic cell death – necrosis (MLKL-mediated), pyroptosis (GSDMD), and apoptosis (caspase-3) – all in a single sentence. To strengthen the explanation of the molecular mechanisms, I recommend either slightly expanding this section to briefly explain the role of each pathway in viral infection, or rewriting the sentence into two shorter sentences. This will give the reader a clearer understanding of how each type of cell death contributes to the host response.

Lines 237–241 (Cytokines and T cell differentiation): The text states that IL-6, IFN-γ, and IL-10 influence T cell differentiation and function, but the explanation remains general. I suggest clarifying the mechanism behind this—for example, briefly specify how each of these cytokines affects T cell subsets (such as Th1/Th2/Th17 polarization or regulatory T cell activity). This detail would strengthen the explanations in the text and give readers a deeper understanding of the molecular implications.

Lines 249–259 (Figure 3): Given the complexity of Figure 3 (which describes numerous viral evasion mechanisms of SARS-CoV-2 and host ISG genes with antiviral functions), it would be helpful to include an additional summary table. This table (complementary to Figure 3) could briefly summarize the main viral vs. host factors mentioned, along with their effects on the type I IFN pathway. Such a tabular presentation would improve readability, allowing readers to easily scan and compare key information in the figure.

Lines 202–204 (Comparison with other viral infections): The text provides a concise comparison between the host response to SARS-CoV-2 and to the influenza virus. I recommend expanding this comparison into a short paragraph dedicated to the host immune response in influenza infections (or other relevant viral infections). For example, you could mention the differences and similarities in the cytokine profile or immune escape mechanisms in influenza vs. SARS-CoV-2. This addition would provide broader context and highlight whether the mechanisms described are specific to SARS-CoV-2 or are also found in other viral infections.

Lines 387–396 (Interferon lambda as therapy): In the section on therapeutic approaches, I suggest introducing interferon lambda (IFN-λ) as a promising potential therapy against viral infections. IFN-λ (type III interferon) plays an important role in mucosal immunity and, according to recent studies, its administration in COVID-19 has demonstrated antiviral activity with a favorable safety profile. Mentioning IFN-λ as a therapeutic strategy under discussion (alongside existing ones) would complete the overview of interventions and align the text with current research directions in the field.

Lines 429–432 (Conclusion of the manuscript): The manuscript ends abruptly with a reference to “long COVID” syndrome, but without a well-defined concluding paragraph. For clarity and consistency, I recommend adding a short conclusion section. This should briefly reiterate the main ideas of the article and highlight any future prospects or recommendations resulting from the analysis. A concise conclusion will give the reader a sense of logical closure and tie all the ideas presented together in a coherent manner.

In conclusion, this manuscript provides a comprehensive and scientifically rigorous analysis of host-virus interactions, particularly focusing on SARS-CoV-2 and associated host immune responses. The article is highly relevant, well-written, and significantly contributes to our understanding of viral pathogenesis, immune modulation, and potential therapeutic interventions. However, minor revisions as suggested—particularly shortening the abstract, refining structural organization, incorporating comparative viral context, and adding brief mechanistic clarifications—would further enhance the manuscript’s clarity and readability. After addressing these recommendations, the manuscript would undoubtedly represent a valuable resource for researchers in virology, immunology, and clinical therapy, making it suitable for publication in International Journal of Molecular Sciences.

Author Response

Reviewer #1

Thank you for your valuable comments. We have revised our manuscript in accordance with your suggestions.

Regarding the specific comments:

We fully agree with your suggestion. Accordingly, we have shortened the abstract and added a concluding sentence as follows.

Abstract: Infectious diseases, particularly those caused by novel or unidentified pathogens, represent a substantial threat to global public health. Drawing on insights gained from the COVID-19 pandemic, this review aims to elucidate strategies for managing emerging infectious diseases. A central focus is the host cellular response to viral infections, with particular emphasis on the role of cytokines. Cytokines play a dual role in antiviral defense: they contribute to the inhibition of viral replication and facilitate the clearance of pathogens, yet dysregulated cytokine responses can result in severe immunopathology. Type I interferons (e.g., IFN-α and IFN-β), type II IFN (IFN-γ), and other cytokines are pivotal in activating intracellular antiviral mechanisms and in orchestrating the recruitment of immune cells through extracellular signaling. Effective immune responses to viral infections are governed not only by primary immune cells—such as dendritic cells, T lymphocytes, and B lymphocytes—but also by the local cytokine milieu shaped by infected and neighboring cells. Given the presence of endogenous inhibitors and autoantibodies in vivo, it is essential to evaluate the functional activity of cytokines in clinical samples. We propose a novel approach to quantify biologically active cytokine levels and to modulate immune cell functions that are dysregulated, either through excessive activation or suppression.

We agree with your suggestion and have divided this section into the following subsections:

Cytokine storm

Possible Mechanisms of Cytokine Storm

Although the precise mechanisms underlying cytokine storms remain incompletely understood, several contributing factors have been identified, including high viral loads, dysregulated cytokine signaling pathways, and extensive lytic cell death. Aberrantly activated macrophages and monocytes are considered major sources of excessive cytokine production. Notably, cytokines such as IL-6, IFN-γ, and IL-10 play critical roles in regulating T cell differentiation and function, thereby exacerbating immune dysregulation in severe COVID-19 cases [45-48]. Upon activation by specific antigens and co-stimulatory signals, naïve T helper cells are primarily polarized toward the Th1 lineage under the influence of IFN-γ and IL-12, while Th2 differentiation is concurrently suppressed [46]. However, IFN-γ can also promote the differentiation of certain Th2 subsets. In the presence of IL-6, IL-23, and TGF-β, T helper cells are skewed toward a Th17 phenotype, enhancing inflammatory responses. In contrast, TGF-β alone promotes the development of regulatory T cells (Tregs) [47]. IL-6 further induces the expression of IFN-γ and TGF-β, thereby influencing T cell polarization. IL-10, predominantly secreted by Tregs, functions to suppress excessive inflammation, although it can also exert immunostimulatory effects under certain conditions [48]. A marked elevation of IL-10 is a hallmark of severe COVID-19, distinguishing it from other beta-coronavirus infections such as SARS and MERS [48], and may interfere with the establishment of a properly regulated immune response.

Compared to influenza virus, SARS-CoV-2 more readily induces cytokine storms while simultaneously suppressing type I and type III interferon (IFN) responses [36]. Although these IFNs typically induce a broad spectrum of interferon-stimulated genes (ISGs) that facilitate viral clearance, SARS-CoV-2 encodes multiple proteins that antagonize this pathway at various levels (see Figure 3). For example, viral proteins NSP13, NSP12, NSP14, and NSP16—assisted by the cofactor NSP10—cap the 5′ ends of viral RNA to mimic host mRNA and evade recognition by RIG-I-like receptors (RLRs) [49-51]. NSP3, a papain-like protease with deubiquitinase activity, removes ISG15 modifications from MDA5, while NSP5 (3CLpro) cleaves RIG-I, disrupting signalosome assembly and TBK1 activation [52,53].

NSP1 promotes the translation of viral positive-sense genomic RNA (+gRNA) while inhibiting host mRNA translation, targeting key components of IFN signaling such as TYK2 and STAT2 [54-56]. Additional viral proteins—including NSP9, NSP8, and NSP16—further suppress host protein synthesis by impairing signal recognition and mRNA splicing [54]. NSP6, in conjunction with NSP3 and NSP4, remodels the endoplasmic reticulum (ER) to form double-membrane vesicles (DMVs) that house the viral replication-transcription complex (RTC) and modulate autophagy [57-60]. NSP6 also inhibits phosphorylation of IRF3, STAT1, and STAT2, thereby attenuating IFN signaling [61]. The accessory protein ORF6 binds to the nuclear pore complex (NPC), blocking nuclear translocation of IRF3 and STAT1 [61-64]. Further suppression of ISG activity is mediated by NSP3, ORF7a, ORF3a, and the spike (S) protein [65-70].

Loss-of-function studies have identified host restriction factors such as DAXX and mucins [71], while gain-of-function experiments have revealed antiviral roles for host proteins including LY6E, CH25H, IFITMs, FAM64C, NCOA7, CD74, IFIT3, ZAP, OAS1, CNP, and tetherin, which act at various stages of the viral life cycle [10,65,68–70,72-79].

Despite these host defenses, SARS-CoV-2 often achieves high viral titers, leading to elevated levels of proinflammatory cytokines such as TNF-α, IL-1β, IL-6, IL-10, and IFN-γ, alongside suppressed type I and III IFN responses [32–41]. Patients typically exhibit lymphocytopenia affecting both T and B cell populations, as well as hyperactivation of macrophages and monocytes. This dysregulated cytokine environment likely impairs the development of effective adaptive immunity, as timely and balanced cytokine signaling is essential for orchestrating an appropriate immune response.

Pathological Consequences

Inflammatory cell death—including PANoptosis—represents a critical pathological hallmark of severe COVID-19. This process involves widespread death of vascular endothelial and alveolar epithelial cells, accompanied by elevated cytokine release [32–44]. Microthrombi frequently contain abundant neutrophils undergoing NETosis, a form of cell death characterized by the release of neutrophil extracellular traps (NETs), often in close association with platelets [42,43]. Sera from COVID-19 patients contain pro-NETotic factors such as RANTES (CCL5) and platelet factor 4 (PF4), likely secreted by hyperactivated platelets and their precursor megakaryocytes, which are known to harbor SARS-CoV-2 [44]. Excessive platelet consumption during thrombogenesis may contribute to the development of thrombocytopenia in these patients.

Experimental evidence has demonstrated that combined stimulation with TNF-α and IFN-γ induces PANoptosis in human bone marrow-derived macrophages (BMDMs) in vitro, as well as in the pulmonary and intestinal tissues of transgenic mice expressing human ACE2. Notably, administration of neutralizing antibodies against TNF-α and IFN-γ significantly reduced SARS-CoV-2-associated mortality in vivo [32]. These findings provide mechanistic insight into the interplay between cytokine storms, inflammatory cell death, and coagulopathy, and support the potential therapeutic value of targeted anti-inflammatory interventions.

The current presentation of the manuscript, in which figure legends are not clearly separated from the main text, may cause confusion. Please note that Lines 116–118 (Cell Death Pathways) are part of the legend for Figure 2, not the main text. As the cell death pathways are described in detail in the main text—specifically, necroptosis (Lines 152–156), pyroptosis (Lines 165–167), and apoptosis and necroptosis (Lines 173–176) in the original manuscript—we have only briefly mentioned them in the figure legend.

For clarity, we have tentatively enclosed the figures along with their legends, and the list of abbreviations has been moved to Table 1 (lines 477-517 in the revised manuscript). The publisher will ensure that figure legends and main text are clearly separated in the final version.

Table 1. Abbreviations

Figure 1

ACE2, angiotensin-converting enzyme 2; TMPRSS, transmembrane protease serine 2; +gRNA, positive-sense single-stranded genomic RNA; −sgRNA, negative-sense subgenomic RNA; ORFs, open reading frames; NSPs, non-structural proteins; PL^pro, papain-like protease; 3CL^pro, 3-chymotrypsin-like protease; S, spike; E, envelope; M, membrane; N, nucleocapsid; DMV, double-membrane vesicle; RTC, replication and transcription complex; RdRP, RNA-dependent RNA polymerase; ERGIC, endoplasmic reticulum–Golgi intermediate compartment; TLR, Toll-like receptor; RLR, RIG-I-like receptor; NLRP, NOD-like receptor with pyrin domain; AIM2, absent in melanoma 2; ZBP1, Z-DNA-binding protein 1; dsRNA, double-stranded RNA.

Figure 2

PRRs, pattern recognition receptors; PAMPs, pathogen-associated molecular patterns; DAMPs, damage-associated molecular patterns; ROS, reactive oxygen species; MyD88, myeloid differentiation primary-response gene 88; IRAK, IL-1 receptor-associated kinases; TRIF, TIR domain-containing adaptor-inducing IFN-β; RIPK, receptor-interacting serine/threonine-protein kinase; TRAF, TNF receptor-associated factor; TAK1, transforming growth factor-β-activated kinase 1; TBK1, TANK-binding kinase 1; IKK, IκB kinase; IκB, inhibitor of NF-κB; NF-κB, nuclear factor kappa B; IRF, interferon regulatory factor; ISGs, interferon-stimulated genes; MLKL, mixed lineage kinase domain-like pseudokinase; MAVS, mitochondrial antiviral-signaling protein; ASC, apoptosis-associated speck-like protein containing a CARD; FADD, Fas-associated protein with death domain; GSDMD, gasdermin D; STING, stimulator of interferon genes.

Figure 3

MDA5, melanoma differentiation-associated protein 5; RIG-I, retinoic acid-inducible gene I; IFNAR, interferon-α/β receptor; JAK1, Janus kinase 1; TYK2, tyrosine kinase 2; STAT, signal transducer and activator of transcription; DAXX, death domain-associated protein 6; ZAP, zinc finger antiviral protein; BST2/tetherin, bone marrow stromal antigen 2; IFITMs, interferon-induced transmembrane proteins; CH25H, cholesterol 25-hydroxylase; NCOA7, nuclear receptor coactivator 7; LY6E, lymphocyte antigen 6 complex locus E; OAS1, 2′,5′-oligoadenylate synthetase 1; CD74, invariant chain; FAM46C/TENT5C, terminal nucleotidyltransferase 5C; IFIT3, interferon-induced protein with tetratricopeptide repeats 3; CNP, 2′′,3′′-cyclic nucleotide 3′′ phosphodiesterase.

Figure 4

IFNAR1, interferon-α/β receptor subunit 1; IL1R1, interleukin-1 receptor type 1; IL1RAP/IL1R2, IL-1 receptor accessory protein; IL-1RA, IL-1 receptor antagonist; sIL1R1, soluble IL-1 receptor type 1; sIL1RAP, soluble IL-1 receptor accessory protein; IL-18BP, IL-18 binding protein; IL18R1, IL-18 receptor type 1; IL18RAP, IL-18 receptor accessory protein; IL6RA, IL-6 receptor α-subunit; gp130, glycoprotein 130; sIL6RA, soluble IL-6 receptor α-subunit; sgp130, soluble glycoprotein 130; SHP2, Src homology 2-containing protein tyrosine phosphatase 2; Grb2, growth factor receptor-bound protein 2; PI3K, phosphatidylinositol 3′-kinase.

Figure 5

cIAP, cellular inhibitor of apoptosis ; LUBAC, linear ubiquitin chain assembly complex; FLIP, FLICE (FADD-like IL-1β-converting enzyme)-inhibitory protein; κB, nuclear factor kappa B responsive element; Min. minimal.

Figure 6

IFNGR1, IFN-γ receptor 1; IFNGR2, IFN-γ receptor 2; IFNAR1, IFN-α/β receptor subunit 1; IFNAR2, IFN-α/β receptor subunit 2; EX, extracellular domain; TM, transmembrane domain; IN, intracellular domain; JAK1, Janus kinase 1; TYK2, tyrosine kinase 2; STAT1/2, signal transducer and activator of transcription 1/2; IRF9, IFN regulatory factor 9; ISRE, interferon-stimulated response element, Nluc, NanoLuc luciferase.

Figure 7

IL2RA, IL-2 receptor subunit α; IL2RB, IL-2 receptor subunit β; IL2RG, IL-2 receptor subunit γ.

Figure 8

GRkSB-043, HEK293Tcells stably expresses ISRE-driven IL-2, an anti-CD3εscFv-TM, and B7-1, along with chimeric receptors designed to detect IFN-γ; scFv-TM, single-chain variable fragment fused to a transmembrane domain; HLA, human leukocytic antigen; Pmin, minimal promoter; TCR, T cell receptor.

Figure 9

ZZ-TM, a transmembrane-anchored ZZ affibody that binds to the Fc region of antibodies; TGF-β, transforming growth factor-β.

We have accepted your suggestion and incorporated the following sentences into lines 174–185 of the revised manuscript.

Upon activation by specific antigens and co-stimulatory signals, naïve T helper cells are primarily polarized toward the Th1 lineage under the influence of IFN-γ and IL-12, while Th2 differentiation is concurrently suppressed [46]. However, IFN-γ can also promote the differentiation of certain Th2 subsets. In the presence of IL-6, IL-23, and TGF-β, T helper cells are skewed toward a Th17 phenotype, enhancing inflammatory responses. In contrast, TGF-β alone promotes the development of regulatory T cells (Tregs) [47]. IL-6 further induces the expression of IFN-γ and TGF-β, thereby influencing T cell polarization. IL-10, predominantly secreted by Tregs, functions to suppress excessive inflammation, although it can also exert immunostimulatory effects under certain conditions [48]. A marked elevation of IL-10 is a hallmark of severe COVID-19, distinguishing it from other beta-coronavirus infections such as SARS and MERS [48], and may interfere with the establishment of a properly regulated immune response.

We would like to use Figure 3 as it is, because it effectively illustrates the interference between SARS-CoV-2 and the type I IFN pathway. These interactions cannot be adequately represented in a table format. I apologize again for the poor separation between the figure legend and the main text, which may have contributed to the impression that Figure 3 is overly complex.

We acknowledge the importance of analyzing the differences and similarities in cytokine profiles and immune escape mechanisms between influenza and SARS-CoV-2. However, due to time constraints, we are unable to conduct an in-depth analysis of these aspects in this review. Instead, we hope that our presentation will encourage further analysis and discussion on this topic.

We appreciate your valuable suggestion. In response, we have incorporated two additional sentences (highlighted in yellow) into lines 368-371 of the revised manuscript, as shown below.

In addition, timely administration of type I and type III IFNs has been reported to be effective in clinical settings [95]. Compared to type I IFNs, type III IFNs exhibit more targeted activity, acting primarily on epithelial and endothelial cells at sites of infection, while inducing minimal pro-inflammatory responses.

We appreciate your insightful suggestions. Accordingly, we have added two Figures (Figures 8 and 9) describing approaches that may be applicable for enhancing the function of impaired CD8⁺ T cells or suppressing excessive pro-inflammatory cytokine production (lines 391-412 in the revised manuscript). In addition, a concluding paragraph (highlighted in yellow) is also incorporated in lines 462-469 of the revised manuscript, as shown below.

Finally, we propose a potential strategy to regulate dysregulated T cells, macrophages, and monocytes through the use of IFN-γ-responsive chimeric receptors (Figure 6). As illustrated in Figure 8, we established a HEK293T cell line, GRkSB-043, which stably expresses ISRE-driven IL-2, an anti-CD3ε scFv fused to a transmembrane domain (scFv-TM), and the co-stimulatory molecule B7-1, in addition to IFN-γ-detecting chimeric receptors [91]. GRkSB-043 cells can be loaded with SARS-CoV-2 antigens presented on human leukocytic antigen (HLA) class I molecules via viral infection, transfection with viral cDNA, or peptide pulsing. The resulting peptide–HLA complexes activate CD8⁺ T cells bearing virus-specific T cell receptors (TCRs), leading to IFN-γ secretion. This IFN-γ then activates ISRE-mediated expression of IL-2, anti-CD3ε scFv-TM, and B7-1 in GRkSB-043 cells. These molecules promote T cell proliferation and activation through IL2R, the TCR complex, and CD28 co-stimulatory signaling, respectively.

In parallel, this system can be adapted to suppress aberrantly activated macrophages and monocytes. We developed a HEK293T cell line expressing ZZ-TM, a transmembrane-anchored ZZ affibody that binds to the Fc region of antibodies [91]. By targeting surface markers such as CD68 or CD14 on macrophages and monocytes, respectively, these HEK293T cells can be directed to the target cells using anti-CD68 or anti-CD14 antibodies. When engineered to co-express IFN-γ-detecting chimeric receptors along with ISRE-driven TGF-β (transforming growth factor-β) and IL-10, these cells become responsive to IFN-γ secreted by the dysregulated macrophages or monocytes. Upon activation, they produce immunosuppressive cytokines (TGF-β and IL-10) in an ISRE-dependent manner, potentially suppressing the hyperactivated immune cells.

Conclusion and Future Perspective

Cellular responses to viral infection, while essential for pathogen clearance, can sometimes result in unintended systemic damage. In this review, we have discussed the early stages of the host–virus interaction, including the development of cytokine storm. To evaluate functional cytokine activity, we propose a novel method utilizing chimeric receptors composed of extracellular domains of interest fused to the transmembrane and intracellular regions of IFNAR1/2. This approach may be applicable for enhancing the function of impaired CD8⁺ T cells or suppressing excessive pro-inflammatory cytokine production.

Following the resolution of the acute phase of the COVID-19 pandemic, a substantial proportion of individuals continue to experience persistent symptoms—commonly referred to as “long COVID”—lasting for months or even years after viral clearance [106]. Although the precise mechanisms underlying long COVID remain unclear, recent studies suggest that immune dysregulation, particularly involving IFN-γ, may contribute to sustained respiratory inflammation [107,108]. These findings underscore the importance of regulating aberrantly activated or suppressed cytokine responses and dysfunctional immune cell populations. Such regulation is likely to be critical not only for mitigating acute disease severity but also for preventing or managing long-term sequelae.

Reviewer 2 Report

Comments and Suggestions for Authors

Authors performed an interesting work to explore the host responses to virus infection. The authors cited a wide range of literature to illustrate how host immune responses can be modulated to enhance vaccine efficacy and to develop preventive strategies against hyper inflammatory conditions such as cytokine storm. It is a great review for readers to understand how the body react after the virus infection. Some minor concern needs to address before accept for publication.

I think the annotations of each Figure can be simplified, and if the authors want to explain more about each Figure it can be explained in the body of the text.
There are so many abbreviations in the text. I think the authors can add the “abbreviations section” in the text.
Please standardize the writing in the text, such as line 402 (TNFα). and harmonize the font formatting in each Figure.

Author Response

Thank you for your valuable comments. We have revised our manuscript in accordance with your suggestions.

Regarding the specific comments:

I think the annotations of each Figure can be simplified, and if the authors want to explain more about each Figure it can be explained in the body of the text.
There are so many abbreviations in the text. I think the authors can add the “abbreviations section” in the text.

We agree with your suggestions. To improve clarity and simplify the figure legends, we have relocated the abbreviations to Table 1, as shown below.

Table 1. Abbreviations

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

IL2RA, IL-2 receptor subunit α; IL2RB, IL-2 receptor subunit β; IL2RG, IL-2 receptor subunit γ.

Figure 8

Figure 9

ZZ-TM, a transmembrane-anchored ZZ affibody that binds to the Fc region of antibodies; TGF-β, transforming growth factor-β.

Please standardize the writing in the text, such as line 402 (TNFα). and harmonize the font formatting in each Figure.

In accordance with your suggestions, we have standardized and harmonized the font formatting throughout the revised manuscript. These changes are highlighted in yellow (lines 289 and 366) in the revised version.

Reviewer 3 Report

Comments and Suggestions for Authors

Dear Author's

The title of the article should be specific to reflect the content and objective of the article. Hence, revise accordingly. The present title is looks general. I found role of cytokines on virus in host and mechanisms were drawn for COVID. So focus on the tile and modify to catch readers.

The key words should be specific.

What is the significant new insights delivered in this article, though there were so many articles related to COVID exist in the same way. Hence, It is important to up to date in depth review and you should tell where the lacking information's were included and how discussed. Project this way in each and every section of the article.

Please elaborate cytokine based therapeutic interventions in chronological order and its advancement, possibly a table. Discuss and conclude.

Correlate the host defense mechanism functionalities among vaccinated/ booster and unvaccinated. Is the there any difference in virus clearance ? Discuss and conclude.

Author Response

Thank you for your valuable comments. We have revised our manuscript in accordance with your suggestions.

Regarding the specific comments:

The title of the article should be specific to reflect the content and objective of the article. Hence, revise accordingly. The present title is looks general. I found role of cytokines on virus in host and mechanisms were drawn for COVID. So focus on the tile and modify to catch readers.

We agree with your recommendation and have revised the manuscript title to “Host Responses to SARS-CoV-2 Infection.”

The key words should be specific.

According to your suggestion, we have specified the key words, as follows.

SARS-CoV-2 infection; host reactions; interferon α and β; interferon γ; cytokines; vaccine; cytokine storm.

What is the significant new insights delivered in this article, though there were so many articles related to COVID exist in the same way. Hence, It is important to up to date in depth review and you should tell where the lacking information's were included and how discussed. Project this way in each and every section of the article.

We agree with your suggestions. To better highlight the significant new insights, we have added a paragraph in Section 5, “Therapeutic and Preventive Approaches” (lines 391–412, highlighted in yellow), along with two new figures (Figures 8 and 9) in the revised manuscript, to distinguish our article from previous publications. In addition, both the “Abstract” and Section 6, “Conclusion and Future Perspective,” have been revised accordingly, as shown below.

Abstract: Infectious diseases, particularly those caused by novel or unidentified pathogens, represent a substantial threat to global public health. Drawing on insights gained from the COVID-19 pandemic, this review aims to elucidate strategies for managing emerging infectious diseases. A central focus is the host cellular response to viral infections, with particular emphasis on the role of cytokines. Cytokines play a dual role in antiviral defense: they contribute to the inhibition of viral replication and facilitate the clearance of pathogens, yet dysregulated cytokine responses can result in severe immunopathology. Type I interferons (e.g., IFN-α and IFN-β), type II IFN (IFN-γ), and other cytokines are pivotal in activating intracellular antiviral mechanisms and in orchestrating the recruitment of immune cells through extracellular signaling. Effective immune responses to viral infections are governed not only by primary immune cells—such as dendritic cells, T lymphocytes, and B lymphocytes—but also by the local cytokine milieu shaped by infected and neighboring cells. Given the presence of endogenous inhibitors and autoantibodies in vivo, it is essential to evaluate the functional activity of cytokines in clinical samples. We propose a novel approach to quantify biologically active cytokine levels and to modulate immune cell functions that are dysregulated, either through excessive activation or suppression.

Therapeutic and Preventive Approaches

Conclusion and Future Perspective

Legends for Figures

Figure 8. Activation of CD8⁺ T Cells by GRkSB-043 Cells. The HEK293T cell line GRkSB-043 stably expresses ISRE-driven IL-2, an anti-CD3ε single-chain variable fragment fused to a transmembrane domain (scFv-TM), and the co-stimulatory molecule B7-1, along with chimeric receptors designed to detect IFN-γ. When GRkSB-043 cells are loaded with SARS-CoV-2 antigens presented on HLA class I molecules, they activate CD8⁺ T cells bearing T cell receptors (TCRs) specific to these viral antigens, leading to the secretion of IFN-γ. In turn, IFN-γ stimulates ISRE-mediated expression of IL-2, anti-CD3ε scFv-TM, and B7-1 in GRkSB-043 cells, thereby promoting T cell proliferation and activation.

Figure 9 Suppression of aberrantly activated macrophages or monocytes by engineered HEK293T Cells. HEK293T cells engineered to express ZZ-TM and IFN-γ-sensing chimeric receptors are designed to produce ISRE-driven TGF-β and IL-10. Upon sensing elevated levels of IFN-γ, these cells upregulate the expression of TGF-β and IL-10 through ISRE activation. By targeting aberrantly activated macrophages or monocytes via surface-bound anti-CD68 or anti-CD14 antibodies, respectively, the engineered HEK293T cells may selectively suppress these dysregulated immune cells.

Please elaborate cytokine based therapeutic interventions in chronological order and its advancement, possibly a table. Discuss and conclude.

We appreciate your feedback. We have incorporated potential therapeutic interventions using our newly developed method in the revised Figures 8 and 9.

Correlate the host defense mechanism functionalities among vaccinated/ booster and unvaccinated. Is the there any difference in virus clearance ? Discuss and conclude.

We believe that vaccination contributed to viral clearance. However, due to time constraints, we were unable to conduct an extensive analysis comparing vaccinated, booster-vaccinated, and unvaccinated individuals in this manuscript. We hope that this presentation will stimulate further discussion on this topic.

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