Exploring the Role of MicroRNAs in SARS-CoV-2 Pathogenesis


This article provides an in-depth analysis of the role of microRNAs (miRNAs), particularly those encoded by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in the pathogenesis of COVID-19. It reviews recent studies elucidating the mechanisms of viral miRNA (v-miRNA) generation and their potential impact on disease progression, focusing on the interaction between these v-miRNAs and the human host’s cellular machinery.

Introduction to SARS-CoV-2 and its Impact on Human Health

SARS-CoV-2, an RNA virus, has been the causative agent of the global COVID-19 pandemic. This virus is part of the coronavirus family, known for primarily targeting the human respiratory system. The severity of COVID-19 varies significantly, influenced by the viral strain, patient age, comorbidities, and vaccination status.

The Concept of Viral miRNAs

Recent studies have emphasized the significance of miRNAs in viral pathogenesis. MiRNAs, typically small non-coding RNAs, regulate gene expression at the post-transcriptional level. Viruses such as SARS-CoV, HIV, and Ebola have been shown to produce v-miRNAs. These v-miRNAs are generated via the host’s Drosha and Dicer machinery, playing a pivotal role in modulating gene expression.

TABLE 1 – The Intriguing Concept of Viral miRNAs: Tiny Regulators with Big Impact

In the intricate dance between viruses and their hosts, a fascinating element has emerged: viral miRNAs (v-miRNAs). These tiny, non-coding RNA molecules, typically 21-23 nucleotides long, wield surprising power in shaping the course of viral infection. While initially thought to be solely the domain of our own cells, v-miRNAs have become a hot topic in viral research, revealing their crucial roles in viral pathogenesis.

What are miRNAs?

Before delving into the world of v-miRNAs, let’s rewind a bit and understand their cellular counterparts: miRNAs. These endogenous, non-coding RNAs act as master regulators of gene expression. They bind to messenger RNAs (mRNAs), the blueprints for proteins, and either block their translation or mark them for degradation. This allows miRNAs to fine-tune the levels of various proteins within a cell, influencing a multitude of cellular processes.

Viral Hijackers: How Viruses Exploit the miRNA Machinery

Viruses, being cunning opportunists, have evolved ways to exploit the host’s miRNA machinery for their own benefit. They encode v-miRNAs within their genomes, which are then processed by the host’s Drosha and Dicer enzymes into mature, functional molecules. These v-miRNAs then join the cellular orchestra of miRNA activity, targeting and regulating host genes in ways that favor viral replication and spread.

The Multifaceted Roles of v-miRNAs in Viral Pathogenesis:

The impact of v-miRNAs on viral infection is multifaceted and far-reaching. Here are some key ways they contribute to viral success:

  • Immune evasion: v-miRNAs can suppress the host’s immune response by targeting genes involved in antigen presentation, cytokine production, and T-cell activation. This allows the virus to evade detection and elimination by the immune system.
  • Cell cycle manipulation: v-miRNAs can promote cell proliferation by targeting genes that control cell cycle progression. This creates a larger pool of host cells for the virus to hijack for its replication machinery.
  • Apoptosis inhibition: v-miRNAs can inhibit apoptosis, programmed cell death, in infected cells. This allows the virus to continue replicating and spreading within the host.
  • Vascular permeability enhancement: v-miRNAs can increase the permeability of blood vessels, facilitating viral dissemination throughout the body.

Examples of v-miRNAs in Action:

Several well-studied viruses showcase the diverse roles v-miRNAs play in their life cycles:

  • SARS-CoV: The v-miRNA miR-142-3p downregulates genes involved in the host’s antiviral response, promoting viral replication.
  • HIV-1: The v-miRNA Tat-miR-214 targets a protein that inhibits viral gene expression, allowing HIV to produce more viral proteins.
  • Ebola virus: The v-miR-101 targets genes involved in the host’s immune response and cell death pathways, facilitating viral spread.

The Future of v-miRNA Research:

The study of v-miRNAs is a rapidly evolving field, and its implications are vast. Understanding how v-miRNAs modulate viral pathogenesis could pave the way for novel antiviral therapies. By targeting specific v-miRNAs or their processing machinery, researchers hope to develop strategies that disarm viruses and prevent them from hijacking our cellular machinery.

Discovery of miRNAs in Coronaviruses

The discovery of v-miRNAs in coronaviruses has been a groundbreaking development. Morales et al. identified three novel smRNAs in SARS-CoV-infected mouse lungs. Subsequent bioinformatic analyses have suggested the presence of miRNAs in SARS-CoV-2, potentially influencing the virus’s pathogenesis.

Identification of SARS-CoV-2 Encoded miRNAs

Singh et al.’s study was instrumental in identifying specific miRNA sequences in SARS-CoV-2 infected cells. This included the discovery of CoV2-miR-O7a.1 and CoV2-miR-O7a.2, mapping to the beginning of ORF7a. The involvement of Dicer in their generation and their presence in nasopharyngeal swabs of COVID-19 patients were notable findings.

Clinical Significance of SARS-CoV-2 Encoded smRNAs

The sequencing of RNA from nasopharyngeal swabs of COVID-19 patients has shed light on the transcriptome complexity of SARS-CoV-2. A significant discovery was the presence of the CoV2-miR-O8 sequence, derived from the ORF8 region of the virus. This smRNA showed characteristics of a typical microRNA, suggesting a potential role in modulating host-virus interactions.

CoV2-miR-O8 and Host RNA Interactions

Fossat et al.’s research provided insights into the interactions between CoV2-miR-O8 and human RNA sequences. Their findings suggested that SARS-CoV-2 might utilize this v-miRNA to manipulate host cellular pathways, potentially influencing the immune response to the infection.

Predictive Analysis of CoV2-miR-O8 Targets

Bioinformatic predictions have indicated that CoV2-miR-O8 could regulate a wide range of human mRNAs. The analysis suggested a significant correlation between the predicted targets of CoV2-miR-O8 and genes regulated during COVID-19 infection, particularly those involved in the type I interferon signaling pathway.


The present study delves into a patient-based examination of SARS-CoV-2 encoded small RNAs (smRNAs) in nasopharyngeal swabs from individuals afflicted with COVID-19. Employing smRNA sequencing (smRNAseq), the research has successfully identified a specific and conserved smRNA sequence labeled as CoV2-miR-O8. This sequence, significantly, distinguishes itself by not being expressed by other coronaviruses while being consistently preserved in all known SARS-CoV-2 variants.

Importantly, CoV2-miR-O8 exhibits a higher representation in nasopharyngeal samples from COVID-19 patients compared to other smRNA sequences initially defined in cell culture studies. This finding underscores the importance of conducting studies in infected individuals to provide an accurate profile of the existence and abundance of small viral-encoded RNAs, which have been previously predicted primarily through bioinformatics or cell culture experiments.

Furthermore, the study demonstrates that CoV2-miR-O8 can be detected using reverse transcription polymerase chain reaction (RT-PCR) assays in nasopharyngeal swabs from COVID-19 patients. Nevertheless, it is crucial to emphasize that further investigations are needed to comprehend the extent to which the detection of CoV2-miR-O8 correlates with active infection, disease severity, and recovery.

Moreover, its presence is notably higher in these samples compared to miR-O7a.1, highlighting the importance of studying the levels and potential RNA targets of viral microRNAs (v-miRNAs) in patient samples rather than solely relying on cell culture studies. It is also worth considering that variations in RNA purification and detection methods may influence the relative detection of different microRNAs. Moreover, the study raises the question of whether the detection of CoV2-miR-O8 or other v-miRNAs could offer improved sensitivity or specificity for determining the stage of infection compared to existing diagnostic assays.

While this study provides compelling evidence for the existence of SARS-CoV-2 encoded small RNAs in patient samples, it has not directly addressed potential correlations between the expression of such sequences and the clinical severity of infection. Therefore, there is an urgent need for clinical trials aimed at exploring the association between CoV2-miR-O8 and other virally encoded microRNAs and various clinical features of acute COVID-19 infection, as well as the post-acute sequelae of SARS-CoV-2 infection (PASC).

CoV2-miR-O8 possesses several characteristics consistent with those of a v-miRNA, including its generation by Dicer and Drosha, interaction with Argonaute, and predictions of targeting specific human RNAs. The notable disparity in the abundance of either the 5p or 3p arms of the predicted hairpins for CoV2-miR-O8 and other hairpin sequences observed across all patient samples suggests an asymmetric degradation pattern of the passenger or * strand, strongly indicative of Argonaute-mediated generation.

However, it is essential to acknowledge the possibility that other sequence features or biophysical properties may also contribute to the presence and asymmetric stability of these hairpin arms. Furthermore, it is conceivable that the binding of Argonaute to virally encoded hairpin structures could mediate an antiviral defense mechanism. The significant differences in the abundance of v-miRNAs between cell culture and patient samples underscore the need for careful consideration when interpreting their potential pathogenic significance.

An intriguing finding from the research is the existence of chimeric sequences that contain both CoV2-miR-O8 and human microRNA sequences. These findings stem from CLEAR-CLIP experiments conducted by Fossat et al. in two different types of SARS-CoV-2-infected cells, providing more direct evidence of an association between these RNAs. However, the exact nature of this association remains elusive.

It is unclear whether this is a result of an interaction between mammalian miRNA sequences and the SARS-CoV-2 RNA encoding CoV2-miR-O8, or if CoV2-miR-O8 serves as a decoy for these microRNAs. Notably, the study mentions that the suppression of interacting human microRNAs (miR-30a and miR-27a) has been observed in other viral infections, suggesting a plausible decoy function for CoV2-miR-O8. However, it is also plausible that host antiviral responses might account for these interactions or that CoV2-miR-O8 interacts with long non-coding RNAs (lncRNAs).

In conclusion, this study provides valuable insights into the presence and characteristics of CoV2-miR-O8, a specific smRNA encoded by SARS-CoV-2, in nasopharyngeal swabs of COVID-19 patients. It highlights the need for further research to investigate the clinical relevance of these findings, potential diagnostic applications, and the intricate interactions between viral and host-encoded microRNAs in the context of SARS-CoV-2 infection.

This work paves the way for a deeper understanding of the role of v-miRNAs in COVID-19 pathogenesis and host-virus interactions, ultimately contributing to the development of more effective diagnostic and therapeutic strategies for combating the ongoing pandemic.

reference link : https://doi.org/10.1016/j.isci.2023.108719


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