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

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.

Rocaglates as Antivirals: Comparing the Effects on Viral Resistance, Anti-Coronaviral Activity, RNA-Clamping on eIF4A and Immune Cell Toxicity

“…In comparison with our findings, 13 passages of SARS-CoV-2 in the presence of the DAA remdesivir, which inhibits the viral RNA-dependent-RNA polymerase (RdRp), were reported to lead to partial resistance due to a non-synonymous mutation in the RdRp (E802D) [41]. Similar findings were also reported for other coronaviruses, such as the mouse hepatitis virus (MHV).…”

Antiviral activity of Molnupiravir precursor NHC against SARS-CoV-2 Variants of Concern (VOCs) and implications for the therapeutic window and resistance

“…However, as was seen with the Influenza anti-viral, Tamiflu, resistance to anti-virals can develop rapidly 19 . A thorough analysis of the potential of SARS-CoV-2 to develop resistance is necessary, though it is likely that any adaptation for resistance will correspond with a reduction in fitness as seen with remdesivir 20 . Use of molnupiravir would likely be most beneficial if used in combination with another treatment, preferably targeting a different part of the viral life cycle as has been used with success for HIV treatment.…”

Drug Combinations as a First Line of Defense against Coronaviruses and Other Emerging Viruses

“…These limitations contributed to the failure of many solo agents tested in clinical trials, including the highly publicized agents hydroxychloroquine ( 5 , 30 , 31 ) and ivermectin ( 43 ). While oral drugs to lower the risk of COVID-19-associated hospitalization and death are imminently available ( 18 , 22 ) (see below), we urge the development of drug combinations to prevent the emergence of SARS-CoV-2 drug-resistant mutants ( 44 , 45 ) and to potentially increase potency and breadth of coverage, and to reduce side effects.…”