Functional Structures in RNA Viruses

Dear Colleagues,

RNA viruses rely heavily on intricate RNA structures to regulate key steps of their life cycles, including replication, translation, packaging, interaction with proteins, and host defense evasion. These functional RNA structures are often more conserved than the viral sequences themselves, underscoring their essential role in viral fitness despite high mutation rates. Well-characterized examples include internal ribosome entry sites (IRESs) in picornaviruses, pseudoknots that mediate ribosomal frameshifting in coronaviruses, and XRN1-resistant RNA structures that promote immune evasion in the 3’ UTR of flaviviruses.

Advances in chemical probing techniques, particularly SHAPE, have significantly deepened our understanding of these elements and their dynamic roles. SHAPE was first used to understand the structural architecture of HIV-1 and has since been applied to numerous other viruses, including hepatitis C and dengue. In parallel, computational tools, especially machine learning-based predictors, are enabling de novo identification and large-scale analysis of conserved structural motifs, such as potential IRES elements across viral genomes. This growing understanding of viral RNA structures will enable novel therapeutic strategies and is likely to inform the rational design of next-generation RNA-based vaccines.

This Special Issue aims to highlight recent progress in identifying and characterizing functional RNA structures in RNA viruses, including their interactions with host proteins, with a focus on both experimental and computational approaches. We welcome original research, reviews, methods, databases, and perspectives, and encourage interdisciplinary contributions bridging virology, structural biology, and bioinformatics.

You may choose our Joint Special Issue in Viruses.

Dr. Riccardo Delli Ponti
Dr. Gian Gaetano Tartaglia
Dr. Andrea Vandelli
Dr. Laura Broglia
Guest Editors

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