Deep mutational scanning identifies SARS-CoV-2 Nucleocapsid escape mutations of currently available rapid antigen tests

• Published in: Cell Vol. 185; no. 19; pp. 3603 - 3616.e13
• Main Authors: Frank, Filipp, Keen, Meredith M., Rao, Anuradha, Bassit, Leda, Liu, Xu, Bowers, Heather B., Patel, Anamika B., Cato, Michael L., Sullivan, Julie A., Greenleaf, Morgan, Piantadosi, Anne, Lam, Wilbur A., Hudson, William H., Ortlund, Eric A.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 15.09.2022; The Authors. Published by Elsevier Inc
• Subjects: Animals; antibodies; Antibodies, Neutralizing; Antibodies, Viral; COVID-19; COVID-19 infection; deep mutational scanning; epitope mapping; epitopes; Epitopes - genetics; Humans; mammalian surface-display; Mammals; Mutation; Nucleocapsid; patients; public health; rapid diagnostic tests; SARS-CoV-2 - genetics; SARS-CoV-2 Nucleocapsid protein; Severe acute respiratory syndrome coronavirus 2; variants; mammalian surface-display; deep mutational scanning; SARS-CoV-2 Nucleocapsid protein; rapid diagnostic tests; antibodies; variants; epitope mapping
• ISSN: 0092-8674; 1097-4172; 1097-4172
• DOI: 10.1016/j.cell.2022.08.010

The effects of mutations in continuously emerging variants of SARS-CoV-2 are a major concern for the performance of rapid antigen tests. To evaluate the impact of mutations on 17 antibodies used in 11 commercially available antigen tests with emergency use authorization, we measured antibody binding for all possible Nucleocapsid point mutations using a mammalian surface-display platform and deep mutational scanning. The results provide a complete map of the antibodies’ epitopes and their susceptibility to mutational escape. Our data predict no vulnerabilities for detection of mutations found in variants of concern. We confirm this using the commercial tests and sequence-confirmed COVID-19 patient samples. The antibody escape mutational profiles generated here serve as a valuable resource for predicting the performance of rapid antigen tests against past, current, as well as any possible future variants of SARS-CoV-2, establishing the direct clinical and public health utility of our system. [Display omitted] •A mammalian surface-display platform for SARS-CoV-2 Nucleocapsid protein•Measured the effects of all Nucleocapsid mutations on antibody recognition•Provided escape mutation profiles for 17 antibodies used in 11 diagnostic tests•Rapid antigen tests efficiently detect all current and previous SARS-CoV-2 variants SARS-CoV-2 variants can disrupt the efficacy of rapid antigen tests. By developing a high-throughput mammalian surface-display platform to measure the direct binding of diagnostic antibodies, all possible Nucleocapsid point mutations in past, present, and future variants were evaluated for their potential to affect the performance of these diagnostics tests.