Abstract
SARS-CoV-2 is the causative viral agent of COVID-19, the disease at the center of the current global pandemic. While knowledge of highly structured regions is integral for mechanistic insights into the viral infection cycle, very little is known about the location and folding stability of functional elements within the massive, ∼30kb SARS-CoV-2 RNA genome. In this study, we analyze the folding stability of this RNA genome relative to the structural landscape of other well-known viral RNAs. We present an in-silico pipeline to predict regions of high base pair content across long genomes and to pinpoint hotspots of well-defined RNA structures, a method that allows for direct comparisons of RNA structural complexity within the several domains in SARS-CoV-2 genome. We report that the SARS-CoV-2 genomic propensity for stable RNA folding is exceptional among RNA viruses, superseding even that of HCV, one of the most structured viral RNAs in nature. Furthermore, our analysis suggests varying levels of RNA structure across genomic functional regions, with accessory and structural ORFs containing the highest structural density in the viral genome. Finally, we take a step further to examine how individual RNA structures formed by these ORFs are affected by the differences in genomic and subgenomic contexts, which given the technical difficulty of experimentally separating cellular mixtures of sgRNA from gRNA, is a unique advantage of our in-silico pipeline. The resulting findings provide a useful roadmap for planning focused empirical studies of SARS-CoV-2 RNA biology, and a preliminary guide for exploring potential SARS-CoV-2 RNA drug targets.Importance The RNA genome of SARS-CoV-2 is among the largest and most complex viral genomes, and yet its RNA structural features remain relatively unexplored. Since RNA elements guide function in most RNA viruses, and they represent potential drug targets, it is essential to chart the architectural features of SARS-CoV-2 and pinpoint regions that merit focused study. Here we show that RNA folding stability of SARS-CoV-2 genome is exceptional among viral genomes and we develop a method to directly compare levels of predicted secondary structure across SARS-CoV-2 domains. Remarkably, we find that coding regions display the highest structural propensity in the genome, forming motifs that differ between the genomic and subgenomic contexts. Our approach provides an attractive strategy to rapidly screen for candidate structured regions based on base pairing potential and provides a readily interpretable roadmap to guide functional studies of RNA viruses and other pharmacologically relevant RNA transcripts.
Highlights
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19, the disease at the center of the current global pandemic
We performed the same analysis with the hepatitis C virus (HCV) genome, which is a hallmark example of globally structured viral RNA and one of the most highly structured RNA genomes ever characterized [12, 19, 23]
In the case of the West Nile virus genome, a Z-score distribution centered at 20.2 suggests the absence of globally ordered RNA folding, in agreement with trends observed for other Flavivirus RNA genomes [12] and for RNAs originated from the genomes of double-stranded DNA viruses like human herpesviruses [26]
Summary
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19, the disease at the center of the current global pandemic. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped positive-strand RNA virus and the etiological agent of COVID-19 [1], a highly infectious human disease at the center of a worldwide pandemic [2,3,4]. Consistent with reports on other coronaviruses, the SARS-CoV-2 genome contains highly conserved RNA structural elements that likely play pivotal roles in viral replication, including several structures in the untranslated regions (UTRs) and a ribosomal frameshifting element [7] Some of these motifs have been functionally studied and modeled in other betacoronaviruses [8,9,10,11], little is known about functional structural elements in the overwhelming majority of regions within the SARS-CoV-2 genome
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