In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2

PLoS Pathog. 2021 Sep 17;17(9):e1009929. doi: 10.1371/journal.ppat.1009929. eCollection 2021 Sep.

Abstract

Remdesivir (RDV), a broadly acting nucleoside analogue, is the only FDA approved small molecule antiviral for the treatment of COVID-19 patients. To date, there are no reports identifying SARS-CoV-2 RDV resistance in patients, animal models or in vitro. Here, we selected drug-resistant viral populations by serially passaging SARS-CoV-2 in vitro in the presence of RDV. Using high throughput sequencing, we identified a single mutation in RNA-dependent RNA polymerase (NSP12) at a residue conserved among all coronaviruses in two independently evolved populations displaying decreased RDV sensitivity. Introduction of the NSP12 E802D mutation into our SARS-CoV-2 reverse genetics backbone confirmed its role in decreasing RDV sensitivity in vitro. Substitution of E802 did not affect viral replication or activity of an alternate nucleoside analogue (EIDD2801) but did affect virus fitness in a competition assay. Analysis of the globally circulating SARS-CoV-2 variants (>800,000 sequences) showed no evidence of widespread transmission of RDV-resistant mutants. Surprisingly, we observed an excess of substitutions in spike at corresponding sites identified in the emerging SARS-CoV-2 variants of concern (i.e., H69, E484, N501, H655) indicating that they can arise in vitro in the absence of immune selection. The identification and characterisation of a drug resistant signature within the SARS-CoV-2 genome has implications for clinical management and virus surveillance.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Monophosphate / analogs & derivatives*
  • Adenosine Monophosphate / pharmacology
  • Alanine / analogs & derivatives*
  • Alanine / pharmacology
  • Animals
  • Antiviral Agents / pharmacology*
  • Biological Evolution
  • COVID-19* / drug therapy
  • Chlorocebus aethiops
  • Coronavirus RNA-Dependent RNA Polymerase / genetics*
  • Drug Resistance, Microbial / genetics*
  • Humans
  • Mutation
  • SARS-CoV-2 / drug effects*
  • SARS-CoV-2 / genetics
  • Spike Glycoprotein, Coronavirus / metabolism
  • Vero Cells

Substances

  • Antiviral Agents
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2
  • remdesivir
  • Adenosine Monophosphate
  • Coronavirus RNA-Dependent RNA Polymerase
  • NSP12 protein, SARS-CoV-2
  • Alanine

Supplementary concepts

  • COVID-19 drug treatment