Nsp16 shields SARS-CoV-2 from efficient MDA5 sensing and IFIT1-mediated restriction

EMBO Rep. 2022 Dec 6;23(12):e55648. doi: 10.15252/embr.202255648. Epub 2022 Oct 26.


Methylation of the mRNA 5' cap by cellular methyltransferases enables efficient translation and avoids recognition by innate immune factors. Coronaviruses encode viral 2'-O-methyltransferases to shield their RNA from host factors. Here, we generate recombinant SARS-CoV-2 harboring a catalytically inactive 2'-O-methyltransferase Nsp16, Nsp16mut, and analyze viral replication in human lung epithelial cells. Although replication is only slightly attenuated, we find SARS-CoV-2 Nsp16mut to be highly immunogenic, resulting in a strongly enhanced release of type I interferon upon infection. The elevated immunogenicity of Nsp16mut is absent in cells lacking the RNA sensor MDA5. In addition, we report that Nsp16mut is highly sensitive to type I IFN treatment and demonstrate that this strong antiviral effect of type I IFN is mediated by the restriction factor IFIT1. Together, we describe a dual role for the 2'-O-methyltransferase Nsp16 during SARS-CoV-2 replication in avoiding efficient recognition by MDA5 and in shielding its RNA from interferon-induced antiviral responses, thereby identifying Nsp16 as a promising target for generating attenuated and highly immunogenic SARS-CoV-2 strains and as a potential candidate for therapeutic intervention.

Keywords: 2′-O-methyltransferase; IFIT1; MDA5; Nsp16; SARS-CoV-2.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing / genetics
  • COVID-19*
  • Humans
  • Methyltransferases / genetics
  • RNA
  • RNA-Binding Proteins / genetics
  • SARS-CoV-2*


  • RNA
  • Methyltransferases
  • IFIT1 protein, human
  • RNA-Binding Proteins
  • Adaptor Proteins, Signal Transducing

Associated data

  • PDB/6W4H