Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms

Mol Cell. 2021 Feb 4;81(3):584-598.e5. doi: 10.1016/j.molcel.2020.12.041. Epub 2021 Jan 1.


Severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2) is the positive-sense RNA virus that causes coronavirus disease 2019 (COVID-19). The genome of SARS-CoV-2 is unique among viral RNAs in its vast potential to form RNA structures, yet as much as 97% of its 30 kilobases have not been structurally explored. Here, we apply a novel long amplicon strategy to determine the secondary structure of the SARS-CoV-2 RNA genome at single-nucleotide resolution in infected cells. Our in-depth structural analysis reveals networks of well-folded RNA structures throughout Orf1ab and reveals aspects of SARS-CoV-2 genome architecture that distinguish it from other RNA viruses. Evolutionary analysis shows that several features of the SARS-CoV-2 genomic structure are conserved across β-coronaviruses, and we pinpoint regions of well-folded RNA structure that merit downstream functional analysis. The native, secondary structure of SARS-CoV-2 presented here is a roadmap that will facilitate focused studies on the viral life cycle, facilitate primer design, and guide the identification of RNA drug targets against COVID-19.

Keywords: RNA genome; RNA motif; RNA secondary structure; RNA structure; RNA virus; SHAPE-MaP; chemical probing; coronavirus; locked nucleic acids; riboregulation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19* / genetics
  • COVID-19* / metabolism
  • Cell Line, Tumor
  • Genome, Viral*
  • Humans
  • Nucleic Acid Conformation*
  • RNA, Viral* / genetics
  • RNA, Viral* / metabolism
  • Response Elements*
  • SARS-CoV-2* / genetics
  • SARS-CoV-2* / metabolism


  • RNA, Viral