Functional RNAs in Virology

Dear Colleagues,

Functional RNAs are central to the biology of viruses. Far beyond serving as passive carriers of genetic information, viral RNAs actively shape every stage of the infection cycle, from regulating translation and replication to evading host immunity and coordinating genome packaging. Structured elements like IRESs, frame-shifting pseudoknots, and exoribonuclease-resistant RNAs, as well as unstructured sequence motifs, form an intricate regulatory network that enables viruses to thrive in diverse cellular environments. Recent discoveries, including computationally predicted highly conserved RNA elements across viral families, highlight the depth and evolutionary significance of RNA-based regulation. Understanding how viruses exploit RNA structure and sequence is essential not only for understanding viral strategies but also for identifying novel targets for antiviral intervention. This Special Issue aims to collate the latest knowledge on the functional roles played by viral RNAs, demonstrating that RNA is not merely a medium but rather a molecular toolkit that viruses rely on for survival and success.

Viral RNAs are no longer viewed as passive carriers of genetic information; they are now recognized as active players in nearly every aspect of the viral lifecycle. From translation and replication to genome packaging, immune evasion, and host adaptation, functional RNAs have emerged as essential regulatory elements in viruses. These include a wide range of cis-acting RNA structures, long-range interactions, and non-coding RNAs, all of which orchestrate key steps in infection and pathogenesis.

In recent years, both experimental advances and large-scale sequencing efforts have dramatically expanded our ability to detect and characterize functional RNA elements in viral genomes. This growing body of research is reshaping our understanding of viral strategies and opening up new opportunities for antiviral intervention.

This Special Issue aims to provide a comprehensive overview of functional RNAs in virology, highlighting both well-characterized elements and emerging discoveries. Topics of interest include experimentally validated RNA structures and regulatory motifs, as well as computational predictions with functional or evolutionary significance. This Special Issue lies at the core of Viruses’ mission to advance knowledge on virus biology, pathogenesis, and antiviral strategies. By focusing on RNA-mediated regulation across viral families, this Special Issue bridges molecular virology, RNA biology, and computational genomics.

This Special Issue will serve as a timely and interdisciplinary resource for researchers interested in RNA-based mechanisms in viruses, and we aim to showcase the central role played by RNA as a regulatory molecule in infection biology.

For this Special Issue, original research articles and reviews are welcome to be submitted.

Research areas may include, but are not limited to, the following:

• Functional RNA structures involved in translation, replication, and genome packaging;
• Long-range RNA–RNA interactions and RNA conformational switches;
• Viral non-coding RNAs;
• Exoribonuclease-resistant RNAs (xrRNAs) and RNA-based immune evasion mechanisms;
• RNA structural conservation and covariation across virus species or lineages;
• Computational predictions of structured RNAs and their functional validation;
• RNA–protein interactions involving viral RNAs and host factors;
• RNA structure probing and high-throughput functional RNA screening in viruses.

We look forward to receiving your contributions.

Dr. Michael T. Wolfinger
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

• functional RNA elements
• viral RNA structure
• cis-acting RNA motifs
• non-coding RNAs
• RNA–protein interactions
• RNA-based regulation
• RNA virus biology
• structured RNA
• computational RNA analysis
• virus bioinformatics