Characterization of remdesivir resistance mutations in COVID-19 patients with various immunosuppressive diseases

Immunocompromised patients (ICPs), such as those who receive certain immunosuppressive therapies, occasionally experience prolonged viral infections even after antiviral treatment. In some cases, antiviral-resistant viruses may eventually emerge. Remdesivir (RDV) is an adenosine nucleoside analog that inhibits the activity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA polymerase, which is composed of a catalytic subunit known as nsp12. Previous studies have reported that amino acid mutations around loci 790-810 in nsp12 are responsible for RDV resistance. However, the host immune status that promotes the emergence of resistant viruses and their virological features remain unclear. We therefore collected clinical samples from 15 coronavirus disease 2019 (COVID-19) patients with various immunosuppressive conditions who received RDV. Variant analysis identified a total of seven nsp12 mutations—V792I, M794I, E796D, E796K, C799F, C799Y, and T803I—in 80% (12/15) of the participants, with M794I and V792I the most prevalent. The identified mutations were more frequently observed in severely ICPs (including patients with hematological malignancies or kidney transplantation) compared to non-severely ICPs (including patients with solid cancers or autoimmune diseases). In vitro analysis using recombinant viruses carrying each identified mutation demonstrated that all mutant viruses were less efficient in growth compared to wildtype but with a 1.8-fold (T803I) to 3.6-fold (V792I) increase in the half maximal effective concentration (EC 50 ) of RDV. The present study highlights the importance of monitoring resistance mutations to anti–SARS-CoV-2 drugs in severely ICPs. • Prolonged SARS-CoV-2 infection and the emergence of antiviral-resistant viruses have become significant concerns among immunocompromised patients. • Seven nsp12 mutations, including V792I and M794I, were detected in COVID-19 patients with various immunosuppressive conditions. • These nsp12 mutations were more frequently observed in patients with severe immunosuppression. • The viruses carrying each nsp12 mutation exhibited resistance to remdesivir, with a 1.8- to 3.6-fold increase in EC 50 value, and showed reduced replication efficiency compared to wildtype virus.