De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report

Abstract

SARS-CoV-2 remdesivir resistance mutations have been generated in vitro but have not been reported in patients receiving treatment with the antiviral agent. We present a case of an immunocompromised patient with acquired B-cell deficiency who developed an indolent, protracted course of SARS-CoV-2 infection. Remdesivir therapy alleviated symptoms and produced a transient virologic response, but her course was complicated by recrudescence of high-grade viral shedding. Whole genome sequencing identified a mutation, E802D, in the nsp12 RNA-dependent RNA polymerase, which was not present in pre-treatment specimens. In vitro experiments demonstrated that the mutation conferred a ~6-fold increase in remdesivir IC₅₀ but resulted in a fitness cost in the absence of remdesivir. Sustained clinical and virologic response was achieved after treatment with casirivimab-imdevimab. Although the fitness cost observed in vitro may limit the risk posed by E802D, this case illustrates the importance of monitoring for remdesivir resistance and the potential benefit of combinatorial therapies in immunocompromised patients with SARS-CoV-2 infection.

Fig. 1. Clinical course of the immunocompromised patient with persistent SARS-CoV-2 infection.

Timeline of (a) patient symptoms and hospitalizations, (b) SARS-CoV-2 N1 RT-PCR Ct values and (c) clinical laboratory parameters from time of laboratory diagnosis of SARS-CoV-2 infection (day 0) to end of the follow-up period (day 292) and (d) computed tomography (CT) scans of chest at indicated days after time of initial diagnosis. The timing of remdesivir and casirivimab-imdevimab are shown as gray and light blue shading, respectively. RT-PCR results that were positive but performed on assays that did not generate a Ct value are denoted by the open circle in panel (b). The timing of filgrastim treatments are denoted by green diamonds in panel (c). lsCRP values were converted to hsCRP values using a correction factor of 9.2. Ground-glass opacities marked by white arrows in panel (d). Abbreviations: Real-time polymerase chain reaction (RT-PCR); Cycle threshold (Ct); Absolute neutrophil count (ANC); Absolute lymphocyte count (ALC); Hemoglobin (Hgb); high-sensitivity C-reactive protein (hsCRP).

Fig. 2. De novo emergence of remdesivir resistance mutation during and following treatment with the antiviral agent.

a Anti-SARS-CoV-2 Spike Protein IgG ELISA endpoint titers (1st panel), RT-PCR Ct values (2nd panel), subgenomic RNA (sgRNA, 3rd panel), and plaque forming units (PFU) on viral culture (4th panel) during the course of illness which include the period when remdesivir (gray shading) and casirivimab/imdevimab (light blue shading) were administered. b Allele frequencies of E802D in nsp12 as ascertained by whole genome sequencing. c Crystal structure (PDB:7BV2) depicting nsp12 E802 (dark blue), its putative hydrogen bonds (yellow dashed lines) within the palm domain (yellow), and the residues (green) that interact with the replicating RNA molecule (orange). Remdesivir monophosphate (RMP) is depicted in light blue. d Viral growth curves from icSARS-CoV-2 mNG WT, E802D (patient), and E802A (control) nsp12 mutants on a ORF7a depleted backbone. Results are depicted as mean and standard deviation (error bars) of data from biological replicates (n = 3). Significance between WT and E802D mutants was assessed by unpaired, two-sample t tests, **p < 0.01 (p = 0.002 at 24 h, p = 0.006 at 48 h). e SARS-CoV-2 inhibition by RDV assessed at 48 h post-infection (0.01 multiplicity of infection) as determined by quantitative image analysis of percentage of cells expressing mNG. Color-coded curves represent a non-linear least squares fit of biological replicates (n = 3) and shading represents 95% confidence intervals of the fit. Figure is representative of four biological experiments.