Global Genomic Analysis of SARS-CoV-2 RNA Dependent RNA Polymerase Evolution and Antiviral Drug Resistance

Abstract

A variety of antiviral treatments for COVID-19 have been investigated, involving many repurposed drugs. Currently, the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp, encoded by nsp12-nsp7-nsp8) has been targeted by numerous inhibitors, e.g., remdesivir, the only provisionally approved treatment to-date, although the clinical impact of these interventions remains inconclusive. However, the potential emergence of antiviral resistance poses a threat to the efficacy of any successful therapies on a wide scale. Here, we propose a framework to monitor the emergence of antiviral resistance, and as a proof of concept, we address the interaction between RdRp and remdesivir. We show that SARS-CoV-2 RdRp is under purifying selection, that potential escape mutations are rare in circulating lineages, and that those mutations, where present, do not destabilise RdRp. In more than 56,000 viral genomes from 105 countries from the first pandemic wave, we found negative selective pressure affecting nsp12 (Tajima’s D = −2.62), with potential antiviral escape mutations in only 0.3% of sequenced genomes. Potential escape mutations included known key residues, such as Nsp12:Val473 and Nsp12:Arg555. Of the potential escape mutations involved globally, in silico structural models found that they were unlikely to be associated with loss of stability in RdRp. No potential escape mutation was found in a local cohort of remdesivir treated patients. Collectively, these findings indicate that RdRp is a suitable drug target, and that remdesivir does not seem to exert high selective pressure. We anticipate our framework to be the starting point of a larger effort for a global monitoring of drug resistance throughout the COVID-19 pandemic.

Genetic surveillance of SARS-CoV-2 Mpro reveals high sequence and structural conservation prior to the introduction of protease inhibitor Paxlovid

“…The accessibility of real-world sequences from the expansive GISAID dataset has enabled a global, collaborative effort by scientists to track emerging lineages, identify signature escape mutations, and classify new variants in real time (18). To our knowledge, a comprehensive genomic surveillance of mutations in SARS-CoV-2 nonstructural proteins is limited to the RdRp (19, 20). Large-scale genetic surveillance of the M pro enzyme from circulating SARS-CoV-2 variants has yet to be reported.…”

Mathematical Modeling of Remdesivir to Treat COVID-19: Can Dosing Be Optimized?

“…Remdesivir resistance mutations have been characterized both clinically and experimentally. Unfortunately, one mutation conferring mild resistance does not carry any fitness cost in vitro [ 26 , 27 , 28 ]. If this mutant has no fitness costs in all relevant environments in the host and during transmission, we would expect it to arise quite frequently in remdesivir treated patients and ultimately to spread between patients, irrespective of mitigation strategies.…”

“…Specifically, RDV inhibits the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp, encoded by nsp12-nsp7-nsp8), and mutations in RdRp can decrease sensitivity to RDV. Alarmingly, in vitro, these mutations leave viral fitness largely unaffected [ 26 , 27 , 28 ]. Thus, as we will show, resistance can easily be selected for by some RDV drug regimens.…”

Emerging mutations in the SARS-CoV-2 variants and their role in antibody escape to small molecule-based therapeutic resistance

“…Simultaneously, the scientists reported several mutations in RdRp variants [ 35 ]. However, Mari et al observed significant mutations in the RdRp (V557L, V473F, N491S, and F480L/S/C) that are significantly responsible for Remdesivir resistance [ 36 ]. It was noted that the V557L mutation in Nsp12 changes binding affinity to the RNA template and ultimately to remdesivir [ 37 ].…”

“…Similarly, V473F is a potential escape mutation described by Mari et al It is one of the essential residues in the structural context of RdRp, which is associated with the fingers region. At the same time, researchers found an association between V473F mutation and an SNP, which is positioned at 24,378 genomic positions [ 38 ]. Simultaneously, scientists found that N491S in Nsp12 is associated with high-frequency nsSNPs (non-synonymous SNPs) related to escape mutations.…”