Characterization of various remdesivir-resistant mutations of SARS-CoV-2 by mathematical modeling and molecular dynamics simulation

Abstract

Mutations continue to accumulate within the SARS-CoV-2 genome, and the ongoing epidemic has shown no signs of ending. It is critical to predict problematic mutations that may arise in clinical environments and assess their properties in advance to quickly implement countermeasures against future variant infections. In this study, we identified mutations resistant to remdesivir, which is widely administered to SARS-CoV-2-infected patients, and discuss the cause of resistance. First, we simultaneously constructed eight recombinant viruses carrying the mutations detected in in vitro serial passages of SARS-CoV-2 in the presence of remdesivir. Time course analyses of cellular virus infections showed significantly higher infectious titers and infection rates in mutant viruses than wild type virus under treatment with remdesivir. Next, we developed a mathematical model in consideration of the changing dynamic of cells infected with mutant viruses with distinct propagation properties and defined that mutations detected in in vitro passages canceled the antiviral activities of remdesivir without raising virus production capacity. Finally, molecular dynamics simulations of the NSP12 protein of SARS-CoV-2 revealed that the molecular vibration around the RNA-binding site was increased by the introduction of mutations on NSP12. Taken together, we identified multiple mutations that affected the flexibility of the RNA binding site and decreased the antiviral activity of remdesivir. Our new insights will contribute to developing further antiviral measures against SARS-CoV-2 infection.

Antiviral Activity of Micafungin and Its Derivatives against SARS-CoV-2 RNA Replication

“…SARS-CoV-2 was handled at biosafety level 3. We used the SARS-CoV-2 Wuhan strain (2019-hCoV/Japan/TY/WK-521/2020, GISAID ID: EPI_ISL_408667), Delta variant AY.122 (hCoV-19/Japan/TY11-927/2021, GISAID ID: EPI_ISL_2158617), Omicron variant BA.1.18 (hCoV-19/Japan/TY38-873/2021, GISAID ID: EPI_ISL_7418017), an E406W variant that is resistant to casirivimab/imdevimab (REGN-COV2) antibody cocktail (the complete sequence was shown in Table S1 ) [ 23 ], and RDV-escape mutant R10/E796G C799F (GenBank ID: LC742929) [ 23 , 24 ]. VeroE6/TMPRSS2 cells were inoculated with the viruses at a multiplicity of infection (MOI) of 0.003 for 1 h and unbound viruses were removed by washing, as previously described [ 25 , 26 ].…”