Information Encoded by the Flavivirus Genomes beyond the Nucleotide Sequence.

Area of Science:

• Virology
• Molecular Biology
• Genomics

Background:

• The genus *Flavivirus* includes significant human pathogens that are small, single-stranded RNA viruses.
• Flaviviruses rely on genomic RNA structural elements and RNA-RNA interactions for replication and regulation.
• These elements function as cis-acting non-coding RNAs (ncRNAs) essential for the viral life cycle.

Purpose of the Study:

• To summarize current knowledge on the functions of flavivirus genome conformations.
• To review the role of RNA-RNA interactions in flavivirus genome regulation.
• To examine the role of RNA structure in the production of subgenomic RNAs (sfRNAs) and their presence in related viruses.

Main Methods:

• This work is a review and summary of existing research.
• It synthesizes findings on flavivirus genome structure and RNA-RNA interactions.
• It analyzes the role of RNA structure in sfRNA production.

Main Results:

• Flavivirus genomic RNA forms complex structures and dynamic RNA-RNA interaction networks.
• These interactions regulate viral processes, including the production of sfRNAs.
• sfRNAs are vital for flavivirus fitness by preventing complete genome degradation.

Conclusions:

• Genome conformation and RNA-RNA interactions are critical regulatory mechanisms in *Flavivirus*.
• RNA structure plays a key role in sfRNA biogenesis across the *Flavivirus* genus.
• Understanding these RNA elements offers insights into viral pathogenesis and potential therapeutic targets.