SARS-CoV-2 Uses Nonstructural Protein 16 To Evade Restriction by IFIT1 and IFIT3

Craig Schindewolf, Kumari Lokugamage, Michelle N. Vu, Bryan A. Johnson, Dionna Scharton, Jessica Plante, Birte Kalveram, Patricia A. Crocquet-Valdes, Stephanea Sotcheff, Elizabeth Jaworski, Rojelio E. Alvarado, Kari Debbink, Matthew D. Daugherty, Scott C. Weaver, Andrew Routh, David H. Walker, Kenneth S. Plante, Vineet D. Menachery

Research output: Contribution to journalArticlepeer-review

11 Scopus citations

Abstract

Understanding the molecular basis of innate immune evasion by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important consideration for designing the next wave of therapeutics. Here, we investigate the role of the nonstructural protein 16 (NSP16) of SARS-CoV-2 in infection and pathogenesis. NSP16, a ribonucleoside 29-O-methyltransferase (MTase), catalyzes the transfer of a methyl group to mRNA as part of the capping process. Based on observations with other CoVs, we hypothesized that NSP16 29-O-MTase function protects SARS-CoV-2 from cap-sensing host restriction. Therefore, we engineered SARS-CoV-2 with a mutation that disrupts a conserved residue in the active site of NSP16. We subsequently show that this mutant is attenuated both in vitro and in vivo, using a hamster model of SARS-CoV-2 infection. Mechanistically, we confirm that the NSP16 mutant is more sensitive than wild-type SARS-CoV-2 to type I interferon (IFN-I) in vitro. Furthermore, silencing IFIT1 or IFIT3, IFN-stimulated genes that sense a lack of 29-O-methylation, partially restores fitness to the NSP16 mutant. Finally, we demonstrate that sinefungin, an MTase inhibitor that binds the catalytic site of NSP16, sensitizes wild-type SARS-CoV-2 to IFN-I treatment and attenuates viral replication. Overall, our findings highlight the importance of SARS-CoV-2 NSP16 in evading host innate immunity and suggest a target for future antiviral therapies.

Original languageEnglish (US)
JournalJournal of virology
Volume97
Issue number2
DOIs
StatePublished - Feb 2023

Keywords

  • 2'-O-methyltransferase
  • IFIT1
  • IFIT3
  • NSP16
  • SARS-CoV-2
  • antiviral agents
  • coronavirus
  • interferon-stimulated gene

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Insect Science
  • Virology

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