RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses

Ramya Rangan; Ivan N. Zheludev; Rhiju Das

Understanding the RNA structure of the SARS-CoV-2 genome can guide RNA-targeting interventions and diagnostics. Here we have presented an initial analysis of RNA sequence conservation across betacoronaviruses and current SARS-CoV-2 sequences, predictions for structured and unstructured domains of the viral RNA genome, and homology-derived secondary structure models for classic structured elements of the SARS-CoV-2 genome: the 5´ UTR, the frame-shifting element, and the 3´ UTR. By filtering for sequences that have more than one of these properties, we have curated three sets of RNA genomic regions of potential interest for further structural analysis, which we have termed the SARS-related-conserved, SARS-CoV-2-conservedstructured, and SARS-CoV-2-conserved-unstructured sets. Fig. 5 gives a more extensive presentation of how these sets overlap. Our hope is that these steps will provide useful starting points for efforts to develop antivirals and diagnostics that depend on targeting either structured or unstructured viral genomic regions.