Transcription Regulatory Sequences in Coronaviruses: Mechanistic Foundations for Antivirals and Vaccines

Coronaviruses employ a distinctive discontinuous transcription mechanism to generate a nested set of subgenomic mRNAs (sgRNAs) from a single large positive-strand RNA genome. Transcription regulatory sequences (TRSs)-comprising a leader TRS (TRS-L) near the 5' end and multiple body TRSs (TRS-Bs) upstream of downstream open reading frames-serve as the primary cis-acting signals that direct polymerase pausing and template switching during negative-strand synthesis. The COVID-19 pandemic spurred intensive investigation of SARS-CoV-2 gene expression, yielding high-resolution transcriptome maps, genome-wide RNA structure data, and detailed structural models of the replication-transcription complex (RTC). TRS function is therefore best understood as a multi-scale property determined not by the core motif alone, but by the integration of primary-sequence complementarity, local RNA secondary structure, long-range RNA-RNA interactions, and RTC dynamics. This review provides an integrated view of TRS structure-function relationships, with emphasis on how these features collectively shape sgRNA abundance, junction diversity, recombination potential, and prospects for diagnostic and antiviral applications, including vaccines and therapeutics.