Identification and characterization of virus-encoded circular RNAs in host cells

Roles of circRNAs in viral pathogenesis

Circular RNAs (circRNAs) are a class of non-coding RNAs with a covalently closed circular structure, lacking 5'-caps or 3'-poly(A) tails. They are relatively conserved, highly stable, and often exhibit tissue- or cell-specific production in eukaryotic cells. Based on the advances in sequencing technologies and bioinformatics, multiple reports have suggested that viruses and other microorganisms may encode circRNA-like molecules, providing new insights into the physiological and pathological roles of circRNAs. The innate immune system functions as the body's primary defense mechanism against viral infections. It detects pathogen-associated molecular patterns (PAMPs) and activates signaling pathways to suppress viral replication and limit their spread. CircRNAs are involved in regulation of the host innate immune signaling pathways and play essential roles in viral pathogenesis. It has been shown that circRNAs can regulate gene expression by acting as miRNA sponges or protein sponges, or encoding small proteins in specific cases. For example, previous studies have revealed that circRNAs participate in the host antiviral immune response through the competitive endogenous RNA (ceRNA) network by acting as miRNA sponges. This review highlights research progress in the regulation and functions of host- and virus-encoded circRNAs in host-virus interactions, as well as their potential as diagnostic biomarkers and therapeutic targets in clinical applications.

Circular RNAs in Viral Infection and Antiviral Treatment

Circular RNAs (circRNAs) are a class of noncoding RNAs that lack the 5'-cap structure and the 3' poly(A) tail. Their distinguishing feature is that the 3' and 5' ends are covalently linked to form a closed circular structure. CircRNAs have a longer half-life and stronger ribonuclease resistance compared with linear RNA. Viral infections lead to the production of circRNA molecules through the transcription and splicing mechanisms of host cells. circRNAs are produced from the transcription and splicing of the viral genome or from the splicing reactions of the host cell gene. They participate in regulating the replication of many viruses, including coronaviruses, human herpesviruses, human immunodeficiency virus, and cytomegalovirus. CircRNAs regulate the infection process by modulating circRNA expression in host cells and affect cellular biological processes. Some circRNAs have been proposed as diagnostic markers for viral infections. In this review, we discussed the properties of virus-derived circRNAs, the biological functions of diverse viruses-derived and host circRNAs during viral infections, and the critical role of circRNAs in the host's antiviral immune defense. Extensive research on the applications of circRNAs can help us better understand gene regulatory networks and disease mechanisms.

Epigenetic reprograming in myalgic encephalomyelitis/chronic fatigue syndrome: A narrative of latent viruses

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic disease presenting with severe fatigue, post-exertional malaise, and cognitive disturbances-among a spectrum of symptoms-that collectively render the patient housebound or bedbound. Epigenetic studies in ME/CFS collectively confirm alterations and/or malfunctions in cellular and organismal physiology associated with immune responses, cellular metabolism, cell death and proliferation, and neuronal and endothelial cell function. The sudden onset of ME/CFS follows a major stress factor that, in approximately 70% of cases, involves viral infection, and ME/CFS symptoms overlap with those of long COVID. Viruses primarily linked to ME/CFS pathology are the symbiotic herpesviruses, which follow a bivalent latent-lytic lifecycle. The complex interaction between viruses and hosts involves strategies from both sides: immune evasion and persistence by the viruses, and immune activation and viral clearance by the host. This dynamic interaction is imperative for herpesviruses that facilitate their persistence through epigenetic regulation of their own and the host genome. In the current article, we provide an overview of the epigenetic signatures demonstrated in ME/CFS and focus on the potential strategies that latent viruses-particularly Epstein-Barr virus-may employ in long-term epigenetic reprograming in ME/CFS. Epigenetic studies could aid in elucidating relevant biological pathways impacted in ME/CFS and reflect the physiological variations among the patients that stem from environmental triggers, including exogenous viruses and/or altered viral activity.

Identification, characterization and expression analysis of circRNA encoded by SARS-CoV-1 and SARS-CoV-2

Virus-encoded circular RNA (circRNA) participates in the immune response to viral infection, affects the human immune system, and can be used as a target for precision therapy and tumor biomarker. The coronaviruses SARS-CoV-1 and SARS-CoV-2 (SARS-CoV-1/2) that have emerged in recent years are highly contagious and have high mortality rates. In coronaviruses, little is known about the circRNA encoded by the SARS-CoV-1/2. Therefore, this study explores whether SARS-CoV-1/2 encodes circRNA and characteristics and functions of circRNA. Based on RNA-seq data of SARS-CoV-1 and SARS-CoV-2 infections, we used circRNA identification tools (circRNA_finder, find_circ and CIRI2) to identify circRNAs. The number of circRNAs encoded by SARS-CoV-1 and SARS-CoV-2 was identified as 151 and 470, respectively. It can be found that SARS-CoV-2 shows more prominent circRNA encoding ability than SARS-CoV-1. Expression analysis showed that only a few circRNAs encoded by SARS-CoV-1/2 showed high expression levels, and the positive strand produced more abundant circRNAs. Then, based on the identified SARS-CoV-1/2-encoded circRNAs, we performed circRNA identification and characterization using the previously developed CirRNAPL. Finally, target gene prediction and functional enrichment analysis were performed. It was found that viral circRNA is closely related to cancer and has a potential role in regulating host cell functions. This study studied the characteristics and functions of viral circRNA encoded by coronavirus SARS-CoV-1/2, providing a valuable resource for further research on the function and molecular mechanism of coronavirus circRNA.

An updated database of virus circular RNAs provides new insights into the biogenesis mechanism of the molecule

Virus circular RNAs (circRNA) have been reported to be extensively expressed and play important roles in viral infections. Previously we build the first database of virus circRNAs named VirusCircBase which has been widely used in the field. This study significantly improved the database on both the data quantity and database functionality: the number of virus circRNAs, virus species, host organisms was increased from 46440, 23, 9 to 60859, 43, 22, respectively, and 1902 full-length virus circRNAs were newly added; new functions were added such as visualization of the expression level of virus circRNAs and visualization of virus circRNAs in the Genome Browser. Analysis of the expression of virus circRNAs showed that they had low expression levels in most cells or tissues and showed strong expression heterogeneity. Analysis of the splicing of virus circRNAs showed that they used a much higher proportion of non-canonical back-splicing signals compared to those in animals and plants, and mainly used the A5SS (alternative 5' splice site) in alternative-splicing. Most virus circRNAs have no more than two isoforms. Finally, human genes associated with the virus circRNA production were investigated and more than 1000 human genes exhibited moderate correlations with the expression of virus circRNAs. Most of them showed negative correlations including 42 genes encoding RNA-binding proteins. They were significantly enriched in biological processes related to cell cycle and RNA processing. Overall, the study provides a valuable resource for further studies of virus circRNAs and also provides new insights into the biogenesis mechanisms of virus circRNAs.

Expanding diversity of bunyaviruses identified in mosquitoes

Mosquitoes interact with various organisms in the environment, and female mosquitoes in particular serve as vectors that directly transmit a number of microorganisms to humans and animals by blood-sucking. Comprehensive analysis of mosquito-borne viruses has led to the understanding of the existence of diverse viral species and to the identification of zoonotic arboviruses responsible for significant outbreaks and epidemics. In the present study on mosquito-borne bunyaviruses we employed a broad-spectrum RT-PCR approach and identified eighteen different additional species in the Phenuiviridae family and also a number of related but unclassified bunyaviruses in mosquitoes collected in Zambia. The entire RNA genome segments of the newly identified viruses were further analyzed by RNA sequencing with a ribonuclease R (RNase R) treatment to reduce host-derived RNAs and enrich viral RNAs, taking advantage of the dsRNA panhandle structure of the bunyavirus genome. All three or four genome segments were identified in eight bunyavirus species. Furthermore, L segments of three different novel viruses related to the Leishbunyaviridae were found in mosquitoes together with genes from the suspected host, the Crithidia parasite. In summary, our virus detection approach using a combination of broad-spectrum RT-PCR and RNA sequencing analysis with a simple virus enrichment method allowed the discovery of novel bunyaviruses. The diversity of bunyaviruses is still expanding and studies on this will allow a better understanding of the ecology of hematophagous mosquitoes.

BmNPV circular RNA-encoded peptide VSP39 promotes viral replication

CircRNAs are covalently closed single-stranded circular RNA molecules, which are not easily degraded by endonucleases and play vital roles in many biological processes. Currently, most studies on circRNAs focus on endogenous circRNAs in cells, and there are few studies on virus-encoded circRNAs. In this study, a viral circRNA (circRNA-000010) derived from the region (-/bp: 114514-115,319) of the complementary strand of Bombyx mori Nucleopolyhedrovirus (BmNPV) genome was identified with the circRNA-sequencing. The authenticity of viral circRNA-000010 was further confirmed by reverse transcription PCR, reverse transcription-rolling circle amplification (TCA), in situ hybridization, immunofluorescent staining, and Northern blotting. The results of overexpression and knockdown experiments showed that circRNA-000010 promoted viral replication. Furthermore, a viral small peptide VSP39 with 39 amino acid residues translated by circRNA-000010 but not its linear molecule was confirmed. Finally, VSP39 was found to promote viral replication. Our findings indicated that a viral circRNA encoded by BmNPV promoted viral replication. These findings will provide new clues for further understanding coding information of the BmNPV genome and open a new insight for investigating host-virus interactions.