ArticleRNA (New York, N.Y.)2020
RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look.
Article in RNA (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 189 papers.
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Who cites it
189 citing papers in PubMed, 286 citations in OpenAlex.
- A divergent betacoronavirus with a functional furin cleavage site in South American bats.Nature communications · 2026Article
- Functional analysis of stem-loop structures within the SARS-CoV-2 5' untranslated region using a plasmid-based reporter system.Archives of virology · 2026Article
- SARS-CoV-2 5'-UTR stem-loops activate the antiviral protein oligoadenylate synthetase 1 (OAS1).The Journal of biological chemistry · 2026Article
- LinearCapR: linear-time computation of per-nucleotide structural-context probabilities of RNA without base-pair span limits.Bioinformatics (Oxford, England) · 2026Article
- Open questions on viral frameshifting: Exploiting the structural plasticity of the frameshifting element for therapeutic intervention.Biophysical journal · 2026Review
- Domain arrangement-driven immunogenicity of a computationally designed mRNA vaccine targeting PPE68, IrtA, and PE9 of Mycobacterium tuberculosis.Scientific reports · 2026Article
- SARS-CoV-2 5'-UTR stem-loops activate the antiviral protein oligoadenylate synthetase 1 (OAS1).bioRxiv : the preprint server for biology · 2026Article
- Distinct virus-derived circular RNA molecule influences host response during SARS-CoV-2 infection.bioRxiv : the preprint server for biology · 2026Article
- RNA binding protein Musashi1 interacts with the viral genomic RNA and restricts SARS-CoV-2 infection by repressing translation.Nucleic acids research · 2026Article
- Predicting small molecule-RNA interactions without RNA tertiary structures.Nature biotechnology · 2026Article
- Article
- Functional Genomic Evidence for Candidate Small Viral RNA-Mediated Epigenetic Interference in SARS-CoV-1 and SARS-CoV-2.Computational and structural biotechnology journal · 2026Article
- Characterization of the binding features between SARS-CoV-2 5'-proximal transcripts of genomic RNA and nucleocapsid proteins.RNA biology · 2025Review
- "Fertile" Mutations in SARS-CoV-2 RNA More Frequently Occurred in Hairpin Loops That Determine Virus Evolution.APMIS : acta pathologica, microbiologica, et immunologica Scandinavica · 2025Article
- Integrated NMR and MD structure and dynamics of the stem-loop-II motif (s2m) from the Omicron variant of SARS-CoV-2.RNA (New York, N.Y.) · 2025Article
- Importance of De Novo Gene Evolution to Emerging Viral Threats: The ORF10 Strain-Restricted Orphan Gene of SARS-CoV-2 Promotes Pathogenesis.Molecular biology and evolution · 2025Article
- In silico screening and experimental validation identify riboflavin as an RNA-targeted antiviral against SARS-CoV-2.Scientific reports · 2025Article
- Structural heterogeneity and dynamics in the apical stem loop of s2m from SARS-CoV-2 Delta by an integrative NMR spectroscopy and MD simulation approach.Nucleic acids research · 2025Article
- Structural insights into the assembly and regulation of 2'-O RNA methylation by SARS-CoV-2 nsp16/nsp10.Structure (London, England : 1993) · 2025Article
- Developing, Characterizing, and Modeling CRISPR-Based Point-of-Use Pathogen Diagnostics.ACS synthetic biology · 2025Article
129 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
As the COVID-19 outbreak spreads, there is a growing need for a compilation of conserved RNA genome regions in the SARS-CoV-2 virus along with their structural propensities to guide development of antivirals and diagnostics. Here we present a first look at RNA sequence conservation and structural propensities in the SARS-CoV-2 genome. Using sequence alignments spanning a range of betacoronaviruses, we rank genomic regions by RNA sequence conservation, identifying 79 regions of length at least 15 nt as exactly conserved over SARS-related complete genome sequences available near the beginning of the COVID-19 outbreak. We then confirm the conservation of the majority of these genome regions across 739 SARS-CoV-2 sequences subsequently reported from the COVID-19 outbreak, and we present a curated list of 30 "SARS-related-conserved" regions. We find that known RNA structured elements curated as Rfam families and in prior literature are enriched in these conserved genome regions, and we predict additional conserved, stable secondary structures across the viral genome. We provide 106 "SARS-CoV-2-conserved-structured" regions as potential targets for antivirals that bind to structured RNA. We further provide detailed secondary structure models for the extended 5' UTR, frameshifting stimulation element, and 3' UTR. Lastly, we predict regions of the SARS-CoV-2 viral genome that have low propensity for RNA secondary structure and are conserved within SARS-CoV-2 strains. These 59 "SARS-CoV-2-conserved-unstructured" genomic regions may be most easily accessible by hybridization in primer-based diagnostic strategies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.