Pervasive RNA Secondary Structure in the Genomes of SARS-CoV-2 and Other Coronaviruses

Abstract

The ultimate outcome of the coronavirus disease 2019 (COVID-19) pandemic is unknown and is dependent on a complex interplay of its pathogenicity, transmissibility, and population immunity. In the current study, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was investigated for the presence of large-scale internal RNA base pairing in its genome. This property, termed genome-scale ordered RNA structure (GORS) has been previously associated with host persistence in other positive-strand RNA viruses, potentially through its shielding effect on viral RNA recognition in the cell. Genomes of SARS-CoV-2 were remarkably structured, with minimum folding energy differences (MFEDs) of 15%, substantially greater than previously examined viruses such as hepatitis C virus (HCV) (MFED of 7 to 9%). High MFED values were shared with all coronavirus genomes analyzed and created by several hundred consecutive energetically favored stem-loops throughout the genome. In contrast to replication-associated RNA structure, GORS was poorly conserved in the positions and identities of base pairing with other sarbecoviruses—even similarly positioned stem-loops in SARS-CoV-2 and SARS-CoV rarely shared homologous pairings, indicative of more rapid evolutionary change in RNA structure than in the underlying coding sequences. Sites predicted to be base paired in SARS-CoV-2 showed less sequence diversity than unpaired sites, suggesting that disruption of RNA structure by mutation imposes a fitness cost on the virus that is potentially restrictive to its longer evolution. Although functionally uncharacterized, GORS in SARS-CoV-2 and other coronaviruses represents important elements in their cellular interactions that may contribute to their persistence and transmissibility. IMPORTANCE The detection and characterization of large-scale RNA secondary structure in the genome of SARS-CoV-2 indicate an extraordinary and unsuspected degree of genome structural organization; this could be effectively visualized through a newly developed contour plotting method that displays positions, structural features, and conservation of RNA secondary structure between related viruses. Such RNA structure imposes a substantial evolutionary cost; paired sites showed greater restriction in diversity and represent a substantial additional constraint in reconstructing its molecular epidemiology. Its biological relevance arises from previously documented associations between possession of structured genomes and persistence, as documented for HCV and several other RNA viruses infecting humans and mammals. Shared properties potentially conferred by large-scale structure in SARS-CoV-2 include increasing evidence for prolonged infections and induced immune dysfunction that prevents development of protective immunity. The findings provide an additional element to cellular interactions that potentially influences the natural history of SARS-CoV-2, its pathogenicity, and its transmission.

Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution

“…Over half of the sites in human mRNA that were edited by A3A were flanked by short palindromic sequences and typically located in the unpaired termini of stem-loops ( Sharma et al, 2016 ). Supporting this, an analysis of RNA structural contexts of edited sites in SARS-CoV-2 and rubella identified preferential C→U mutations in terminal loop compared to stem sequences ( Klimczak et al, 2020 ), or in predicted paired compared to unpaired regions ( Simmonds, 2020a ).…”

SARS‐CoV‐2, the pandemic coronavirus: Molecular and structural insights

“…They act as a regulatory elements, hence are essential for the virus life cycle. It has also been proposed that the evolution in RNA viruses is more aggressive in RNA structures than that of coding sequences [10]. Thus, it becomes equally essential to study the SS in SARS‐COV‐2 RNA genome.…”

“…The GORS protects viral RNA genome from getting recognized by the host vigilance system. The contour plotting method has been used to analyze GORS in the viral genome [10]. This relatively new method is a promising technique for a deep study of the structural features and positions of the RNA SS.…”

Genome composition and genetic characterization of SARS-CoV-2

“…There is no doubt that the presented outcome of the pandemic regarding morbidity is scary ( Simmonds, 2020 ). As the number of COVID-19 patients increased worldwide, there was an urgent need to find a quick and sensitive diagnostic tool as it is crucial for controlling the outbreak of SARS-CoV-2 in the community.…”