All relevant data within the manuscript and its supporting information are available on Enlighten: Research Data ( doi.org/10.5525/gla.researchdata.1184).įunding: This work was supported by the UK Medical Research Council (MC_UU_12014/8, MC_UU12014/2 and MC_UU_12014/12). We used the publicly available CoV-Glue database ( ) to examine for replacements at specific sites observed in the GISAID hCoV-19 sequences. Consensus sequences and raw FASTQ files have been uploaded to GenBank under BioProject number PRJNA692078. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: SARS-CoV-2Engl2 was supplied under a MTA between The University of Glasgow and Public Health England. Received: ApAccepted: AugPublished: September 17, 2021Ĭopyright: © 2021 Szemiel et al. PLoS Pathog 17(9):Įditor: Shin-Ru Shih, Chang Gung University, TAIWAN (2021) In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Our data indicate low-level Remdesivir resistance in SARS-CoV-2 is different to other RNA viruses and monitoring changes in vitro provides insight into general virus adaptation of newly emerging viruses.Ĭitation: Szemiel AM, Merits A, Orton RJ, MacLean OA, Pinto RM, Wickenhagen A, et al. A number occurred at the same sites but to different residues as those in emerging variants of concern indicating they arise in the absence of immune pressure. Unexpectedly, passage of SARS-CoV-2 led to an accumulation of mutations in Spike. Importantly, this change occurred at very low frequency globally. A change at this conserved site was not predicted, and the mutation did not cause a replication advantage or change in sensitivity to another antiviral drug. We identified a mutation in the virus polymerase responsible for decreased sensitivity to Remdesivir. Antivirals use comes at a risk, as viruses may acquire mutations overcome the inhibition. Remdesivir is the only antiviral with FDA approval for treatment. The emergence of SARS-CoV-2 has led to a worldwide pandemic with significant morbidity and mortality. The identification and characterisation of a drug resistant signature within the SARS-CoV-2 genome has implications for clinical management and virus surveillance. 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. Analysis of the globally circulating SARS-CoV-2 variants (>800,000 sequences) showed no evidence of widespread transmission of RDV-resistant mutants.
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. Introduction of the NSP12 E802D mutation into our SARS-CoV-2 reverse genetics backbone confirmed its role in decreasing RDV sensitivity in vitro. 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. Here, we selected drug-resistant viral populations by serially passaging SARS-CoV-2 in vitro in the presence of RDV. To date, there are no reports identifying SARS-CoV-2 RDV resistance in patients, animal models or in vitro. Remdesivir (RDV), a broadly acting nucleoside analogue, is the only FDA approved small molecule antiviral for the treatment of COVID-19 patients.