Submitted:
28 February 2025
Posted:
03 March 2025
You are already at the latest version
Abstract
The severe acquired respiratory coronavirus–2 (SARS–CoV-2) infection has initiated both acute and chronic COVID–19 disease between 2020 and 2023, currently evolving with other homologous prior coronavirus strains of the Nidoviridae order, which encompasses other prevalent alpha/ beta coronaviruses, but also the Middle East Respiratory Syndrome (MERS-CoV) and SARS-CoV-1, with recent SARS–CoV–2 variants, increasing demands for effective immunogens and therapeutic approaches that will reduce global disease burden and further infection from SARS–CoV-2 affected individuals that may experience post acute sequelae (PASC) or “Long COVID”. Following a worldwide programme of prophylactic vaccination, there is still a dilemma in the efforts to find prophylactic and early therapeutic approaches that would treat novel SARS-CoV-2 variants and prevent future epidemics or pandemics within host human and animal populations, where zoonotic or cross species transfer naturally occurs. Concerns about viral immune escape intersect at a specific point; a gained evolutionary ability of several viruses to co–infect and compete against previous scientific advances since 1796 that remain undetected or asymptomatic during the early stages of infection progressing to symptomatic and severe disease via the double methylation of the 5' end of eukaryotic DNA or RNA-based viral genomes, the 7-MeGpppA2’-O-Me cap, and its double methylation capping process is performed by the activated viral 2’ - O - Methyltransferase (MTase) enzyme, a complex of two viral non-structural proteins (NSPs) joined together through an activation process (NSP10/16) and by N7-Methyltransferase (N7-MTase/NSP14), respectively. Moreover, it was discovered that polymorphic viruses translate NSP1, which prevents the activation of various Pattern Recognition Receptors (PRRs), and consequently, detection of Pathogen-Associated Molecular Patterns (PAMPs) and Damage-Associated Molecular Patterns (DAMPs) alike. NSP1 also silences important interferon-encoding genes (INGs) and interferon-stimulated genes (ISGs), is signalled in a paracrine manner to neighbouring cells, and that induces the apoptosis of host cells, inducing an effect of “trace erase” effect and making the viral infection as immunologically “invisible” as possible during the initial, key stages of viral replication and distribution, all such mechanisms occurring independently of the viruses in cause. Another important viral NSP is NSP14, as it plays two functional roles that are independent of each other; to produce new viral genetic material for the purpose of maintaining the validity of the viral genome as well, and not just transfer a methyl group to the 5’ end of the viral genome. Other viral NSPs share a role with NSP1, 10, 14 and 16 in directly suppressing the activation of PRRs and ISGs, and all such viral proteins help the virus in its process of self-camouflaging against first- and second-line immunity, thereby often severely impacting the quality of the produced adaptive immune responses. The outcome of all such phenomena is the sharp decrease in the host Type I and Type III interferons' (IFNs) rate of synthesis by the host cells, that would usually occur and affect homeostatic cellular pathways, resulting in further viral replication and induced apoptosis. Nonetheless, effects of microbial immune evasion during the development of other viral or carcinogenic pathologies are not widely known. In short, polymorphic viruses developed a proportionate evolutionary response against developed adaptive immune responses, by currently relying on gaps mostly situated in the natural immune system in their process of molecular self-camouflaging. Scientists developed numerous approaches of early treatment that generally showed good success rates and fewer risks of adverse events, and the still early present stages of COVID-19 research should also be taken into consideration whilst filtering for the most appropriate solutions. For example, the administration of recombinant human interferons I and III into the nasal mucosa cellular layer, as key mediators of anti–viral activity, can simulate intracellular infection and stimulate cellular activity in a timely manner, training the innate and adaptive immune system cells to develop and appropriately stimulate an adequate immune response through B and T cells. Another example could involve the treatment of natural and adaptive lymphocytes with a low dose of IFNs I and possibly III, prior to their insertion into the host lymphatic system, possibly alongside additional recruitment of plasmacytoid dendritic cells (pDCs) as further interferon “factories”, all with the purpose of early infection management. It might be that focusing on directly offering the immune system the information about the genetics and protein structure of the pathogen, rather than training its first-line mechanisms to develop faster, excessively increases its specificity, making it reach a level that brings the virus the opportunity to evolve and escape previously-developed host immune mechanisms. It is until the scientific community realises this potentially crucial aspect that large proportions of the world population will probably continue to face serious epidemics and pandemics of respiratory diseases over the coming several decades, evidenced with dengue fever and more recently, monkeypox and possibly avian flu. Of note, it has been indicated that IFN I and / or III display significant immunising, early therapeutic and clinical disease onset-attenuating effects for many other microbial evoked diseases, as well as for a number of oncological diseases. Microbial agents could undergo loss-of-function research upon genes responsible for inducing clinical illness whilst keeping genes responsible for microbial reproduction and transmission at least generally as functional, CRISPR-Cas9 genome editing to have genes encoding proteins suppressive of the host interferon system eliminated prior to human genes encoding Pattern Recognition Receptor activator or agonist proteins, such as outer membrane proteins of Neisseria meningitidis, as well as Type I, Type III and possibly even Type IV Interferons and various ISGs inserted into the microbial genome. Such an approach would be based upon the model of editing genes of harmless bacteria to transform such them into “producers” and “distributors” of human insulin, and could turn several microbial agents into clinically harmless, transmissible “factories” for various key elements of the host interferon system, potentially placing such microbes into a reverse evolutionary path that would be deemed as “natural de-selection”, visibly reducing the average burden of disease and metabolic stresses, which in turn could gradually increase average human and animal lifespans worldwide.
Keywords:
Introduction
- i)
- Overview to Interferon Cellular Types
- ii)
- Pathological context
| NCT Order | Disease status | NCT & Phase - Type I IFNs | NCT & Phase - Type III IFNs |
|---|---|---|---|
| I | COVID-19 | NCT04469491, Phase 2 (Oral/Nasal) | NCT04354259, Phase 2 (Pegylated, subcutaneous) |
| II | COVID-19 | NCT04469491, Phase 2 (Oral/Nasal) | NCT04967430, Phase 3 (Pegylated, subcutaneous) |
| III | COVID-19 | NCT04732949, Completed (Oral/Nasal) | NCT04534673, Phase 2 (Pegylated, subcutaneous) |
| IV | COVID-19 | NCT04350281, Phase 2 (Subcutaneous) | NCT04343976, Phase 2 (Pegylated, subcutaneous) |
| V | COVID-19 | NCT05381363, Phase 1/2 (Oral/Nasal) | NCT04727424, Phase 3 (Pegylated, subcutaneous) |
| VI | IAV infection | NCT00895947, Completed (Oral/Nasal) | Not available yet |
| VII | Hepatitis B/C | NCT00917358, Completed | NCT01204762, Completed (Pegylated, subcutaneous) |
| VIII | HIV Infection | NCT01295515, Completed | NCT01866930, Completed (Pegylated, subcutaneous) - HCV patients co-infected with HIV |
| IX | Cancer | NCT01462773, Completed | NCT04469491, Unknown status |
| X | Cancer | NCT00278174, Completed | Not available yet |

- iii)
- Limitations
Methodology
Discussion
- Important highlights of innate immune evasion

- 2.
- SARS-CoV-2 Mechanism of Cellular Action in Disease
- 3.
- Cellular Mechanism of IFN Action in Disease
Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Abbreviations
| SARS-CoV-2 | Severe Acute Respiratory Syndrome-Coronavirus 2 |
| COVID-19 | Coronavirus Infectious Disease 2019 |
| ECM | Extracellular Matrix |
| ACE2 | Angiotensin Convertase Enzyme 2 |
| IAV | Influenza A Virus |
| RSV | Respiratory Syncytial Virus |
| ICM | Intracellular Matrix |
| ORF | Open Reading Frame |
| NSP | Non-Structural Protein |
| IFN | Interferon |
| PAMP | Pathogen-Associated Molecular Pattern |
| PRR | Pattern Recognition Receptor |
| TLR | Toll-Like Receptor |
| MDA-5 | Melanoma-Differentiation Associated protein 5 |
| RIG-I | Retinoic acid-Inducible Gene I |
| ADAR | Adenosine Deaminase Acting on RNA / RNA-specific Adenosine Deaminase |
| ADAR1 | Adenosine Deaminase 1 |
| MyD88 | Myeloid-Differentiation primary response 88 |
| IKK | IkB Kinase |
| IFNAR | Interferon alpha/beta Receptor |
| IFNLR1 | Interferon lambda Receptor 1 |
| IL10R1 | Interleukin-10 Receptor 1 |
| STAT | Signal Transducer and Activator of Transcription |
| IRF | Interferon Regulatory Factor |
| NLRC | Nucleotide-binding oligomerization domain-Like Receptor C |
| NF-kB | Nuclear Factor-kappa-light-chain-enhancer of B-Lymphocytes |
| ISG | Interferon-Stimulated Gene |
| NK Cell | Natural Killer Cell |
| IFITM3 | Interferon-Induced Transmembrane Protein 3 |
| cGAS-STING | cyclic AMP-GMP Synthase - Stimulator of Interferon Genes |
| N7-MTase | C-terminal N7 Methyltransferase |
| ExoN | N-terminal 3’-5’ Exoribonuclease |
| IL | Interleukin |
| TNF | Tumour Necrosis Factor |
| TGF-α | Tumour Growth Factor-alpha |
| TGF-β | Transforming Growth Factor-beta |
| CRP | C-Reactive Protein |
| CCL | Chemokine (C-C motif) Ligand |
| CXCL | Chemokine (C-X-C motif) Ligand |
| CCR | Chemokine (C-C motif) Receptor |
| CXCR | Chemokine (C-X-C motif) Receptor |
| NK Cell | Natural Killer Cell |
| IMM | Inflammatory Monocyte and Macrophage |
| pDC | plasmacytoid Dendritic Cell |
| HLA | Human Leukocyte Antigen |
| MHC | Major Histocompatibility Complex |
| Th Lymphocyte | T-helper Lymphocyte |
| CTL | Cytotoxic T-Lymphocyte |
| CD | Cluster of Differentiation |
| LINE-1 | Long Interspersed Nuclear Element 1 |
| AIDS | Acute Immunodeficiency Syndrome |
| Ab | Antibody |
| Ig | Immunoglobulin |
| C5a | Complement component 5a |
| GRP78 | 78 kDa-Glucose-Regulated Protein |
| HSP | Heat-Shock Protein |
| ARS | Acute Radiation Syndrome |
| +ssRNA | positive-sense single-stranded Ribonucleic Acid |
| BMI | Body-Mass Index |
| IU | International Unit |
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