Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

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

View ORCID ProfileRamya Rangan, View ORCID ProfileIvan N. Zheludev, View ORCID ProfileRhiju Das
doi: https://doi.org/10.1101/2020.03.27.012906
Ramya Rangan
1Biophysics Program, Stanford University, Stanford CA 94305
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ramya Rangan
Ivan N. Zheludev
2Department of Biochemistry, Stanford University School of Medicine, Stanford CA 94305
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ivan N. Zheludev
Rhiju Das
1Biophysics Program, Stanford University, Stanford CA 94305
2Department of Biochemistry, Stanford University School of Medicine, Stanford CA 94305
3Department of Physics, Stanford University, Stanford CA 94305
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Rhiju Das
  • For correspondence: rhiju@stanford.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

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. Using sequence alignments spanning a range of betacoronaviruses, we rank genomic regions by RNA sequence conservation, identifying 79 regions of length at least 15 nucleotides 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 reported to date from the current 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 5’ UTR, frame-shifting element, and 3’ UTR. Last, we predict regions of the SARS-CoV-2 viral genome 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 targeted in primer-based diagnostic and oligonucleotide-based therapeutic strategies.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted April 06, 2020.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses
Ramya Rangan, Ivan N. Zheludev, Rhiju Das
bioRxiv 2020.03.27.012906; doi: https://doi.org/10.1101/2020.03.27.012906
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses
Ramya Rangan, Ivan N. Zheludev, Rhiju Das
bioRxiv 2020.03.27.012906; doi: https://doi.org/10.1101/2020.03.27.012906

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genetics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3701)
  • Biochemistry (7822)
  • Bioengineering (5698)
  • Bioinformatics (21347)
  • Biophysics (10605)
  • Cancer Biology (8209)
  • Cell Biology (11977)
  • Clinical Trials (138)
  • Developmental Biology (6790)
  • Ecology (10426)
  • Epidemiology (2065)
  • Evolutionary Biology (13911)
  • Genetics (9733)
  • Genomics (13110)
  • Immunology (8173)
  • Microbiology (20069)
  • Molecular Biology (7879)
  • Neuroscience (43179)
  • Paleontology (321)
  • Pathology (1285)
  • Pharmacology and Toxicology (2268)
  • Physiology (3364)
  • Plant Biology (7256)
  • Scientific Communication and Education (1317)
  • Synthetic Biology (2012)
  • Systems Biology (5550)
  • Zoology (1135)