key: cord-0749002-ta3zlz4z
authors: Greaney, Allison J.; Starr, Tyler N.; Barnes, Christopher O.; Weisblum, Yiska; Schmidt, Fabian; Caskey, Marina; Gaebler, Christian; Cho, Alice; Agudelo, Marianna; Finkin, Shlomo; Wang, Zijun; Poston, Daniel; Muecksch, Frauke; Hatziioannou, Theodora; Bieniasz, Paul D.; Robbiani, Davide F.; Nussenzweig, Michel C.; Bjorkman, Pamela J.; Bloom, Jesse D.
title: Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies
date: 2021-07-07
journal: Nat Commun
DOI: 10.1038/s41467-021-24435-8
sha: d2cbf869837627f6cb021df6e651b645495b9d30
doc_id: 749002
cord_uid: ta3zlz4z

Monoclonal antibodies targeting a variety of epitopes have been isolated from individuals previously infected with SARS-CoV-2, but the relative contributions of these different antibody classes to the polyclonal response remains unclear. Here we use a yeast-display system to map all mutations to the viral spike receptor-binding domain (RBD) that escape binding by representatives of three potently neutralizing classes of anti-RBD antibodies with high-resolution structures. We compare the antibody-escape maps to similar maps for convalescent polyclonal plasmas, including plasmas from individuals from whom some of the antibodies were isolated. While the binding of polyclonal plasma antibodies are affected by mutations across multiple RBD epitopes, the plasma-escape maps most resemble those of a single class of antibodies that target an epitope on the RBD that includes site E484. Therefore, although the human immune system can produce antibodies that target diverse RBD epitopes, in practice the polyclonal response to infection is skewed towards a single class of antibodies targeting an epitope that is already undergoing rapid evolution.

Together, these are the minimal set of data required to replicate the analysis.

No sample size calculations were performed. n=2 independent, biological replicate libraries were used for all escape-mapping experiments. The mutation-and site-level escape metrics were well-correlated between the two independent libraries, so biological duplicate libraries were determined to be sufficient. The numbers of antibodies and plasma samples used in the study were determined by the number of available monoclonal antibodies and polyclonal plasma samples from individuals previously infected with SARS-CoV-2.

No data were excluded from analyses. n=2 independent, biological replicate SARS-CoV-2 RBD deep mutational scanning libraries were used for all escape-mapping experiments. All attempts at replication were successful and are reported in the manuscript.

For no analyses did we determine statistical significance of results. No randomization, covariate analyses, or statistical tests were performed. We did not determine statistical significance for the escape metrics as there is no established method for doing so. In the Methods, we report here the details of quantitative analysis of the effects of mutations on antibody binding to the RBD. Samples were not assigned to different cohorts or study arms, so randomization would not apply to the work done in this study. All samples were treated the same.

No group allocation or blinding was performed in this study.

C135 monoclonal antibodies were isolated from SARS-CoV-2 convalescent individuals as described by

Jackson ImmunoResearch 109-605-064) to label for bound plasma antibodies, and FITC-conjugated anti-Myc (Immunology Consultants Lab, CYMC-45F) to label for RBD surface expression. For this antibody, the manufacturer website

The neutralization properties of C135, C144, and C121 were functionally characterized in Weisblum et

Eligible participants were adults aged 18-76 years who were either diagnosed with a SARS-CoV-2 infection by RT-PCR and were free of symptoms of COVID-19 for at least 14 days (cases), or who were close contacts (for example, household members, co-workers or members of same religious community) of someone who had been diagnosed with a SARS-CoV-2 infection by RT-PCR and were free of symptoms suggestive of COVID-19 for at least 14 days (contacts)

Samples were obtained upon written consent from community participants under protocols approved by the Institutional Review Board of the Rockefeller University (DRO-1006)