Evaluation of antiviral drugs against newly emerged SARS-CoV-2 Omicron subvariants

Abstract

Ongoing emergence of SARS-CoV-2 Omicron subvariants and their rapid worldwide spread pose a threat to public health. From November 2022 to February 2023, newly emerged Omicron subvariants, including BQ.1.1, BF.7, BA.5.2, XBB.1, XBB.1.5, and BN.1.9, became prevalent global strains (>5% global prevalence). These Omicron subvariants are resistant to several therapeutic antibodies. Thus, the antiviral activity of current drugs such as remdesivir, molnupiravir, and nirmatrelvir, which target highly conserved regions of SARS-CoV-2, against newly emerged Omicron subvariants need to be evaluated. We assessed the antiviral efficacy of the drugs using the half-maximal inhibitory concentration (IC₅₀) against human isolates of 23 Omicron subvariants and four former SARS-CoV-2 variants of concern (VOCs) and compared it with the antiviral efficacy of these drugs against the SARS-CoV-2 reference strain (hCoV/Korea/KCDC03/2020). Maximal IC₅₀-fold changes of remdesivir, molnupiravir, and nirmatrelvir were 1.9 (BA.2.75.2), 1.2 (B.1.627.2), and 1.4 (BA.2.3), respectively, compared to median IC₅₀ values of the reference strain. Moreover, median IC₅₀-fold changes of remdesivir, molnupiravir, and nirmatrelvir against the Omicron variants were 0.96, 0.4, and 0.62, respectively, similar to the 1.02, 0.88, and 0.67, respectively, median IC₅₀-fold changes for previous VOCs. Although K90R and P132H in Nsp 5, and P323L, A529V, G671S, V405F, and ins823D in Nsp 12 mutations were identified, these amino acid substitutions did not affect drug antiviral activity. These results indicate that current antivirals retain antiviral efficacy against newly emerged Omicron subvariants. It is important to continue active surveillance and testing of new variants for drug resistance to enable early identification of drug-resistant strains.

Keywords: Antiviral activity; Molnupiravir; Nirmatrelvir; Omicron subvariant; Remdesivir; SARS-CoV-2.

Fig. 1

Median IC50 value of the drugs in VeroE6 cells Median IC50 (left axis) of (A) remdesivir, (B) nirmatrelvir, and (C) molnupiravir. Vero E6 cells were infected with indicated SARS-CoV-2 variants at 0.1 multiplicity of infection for 1 h. Subsequently, seven concentrations of the drugs were treated with two-fold serial dilution (remdesivir and nirmatrelvir [antiviral component of Paxlovid]: 20 to 0.31 μM, molnupiravir: 40 to 0.62 μM) for 48 h. The cell infectivity ratio between the drug treatment and virus only-treated groups was assessed through high-content imaging analysis to determine the number of infected cells (N protein-expressing cells) using immunofluorescence images with viral N-specific antibody and total cells (number of nuclei) using DAPI staining. The IC₅₀ values were determined from dose-response curves and median IC₅₀ value was calculated. The experiments were performed in triplicate (the reference strain for remdesivir [n = 21], nirmatrelvir [n = 13], and molnupiravir [n = 12]).