Description

This track shows how much any amino acid mutations in the receptor binding domain affect the binding of antibodies from either convalescent Covid-19 patients in the Hospitalized or Ambulatory Adults with Respiratory Viral Infections (HAARVI) cohort or monoclonal antibodies.

The data is based on deep mutational scanning data measuring the effect of the change in binding from all wild type allele to all possible mutant alleles. The authors use a yeast display system to experimentally measure the effect of all possible point (amino acid) RBD mutations on antibody binding affinity. The resulting number per mutation and patient sample is a mutation's "escape fraction", the fraction of all yeast cells expressing RBD with that mutation that fall into the FACS escape bin. These escape fractions range from 0 (no effect on serum antibody binding) to 1 (all cells with this mutation are in the antibody-escape bin).

We show just a summary of the data. Better and detailed structural visualizations are available from the authors via dms-view using the following links: patient sera, 10 monoclonal antibodies, 4 treatment antibodies.

Display Conventions and Configuration

Shown with shading and on mouse over is the maximum escape, of all mutations, for every sample and amino acid.

Methods

Patient sera: data was downloaded from the jbloomlab Github file and parsed into bedGraph format.

10 Antibodies: Table S1 from Starr et al, was downloaded and parsed into bedGraph format.

4 treatment antibodies: Data was downloaded from the jbloomlab Github file and parsed into bedGraph format using the total and maximum values.

Data Access

The data of these tracks as stored at UCSC can be explored interactively with the Table Browser, or combined with other datasets in the Data Integrator tool.

Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

References

Greaney AJ, Loes AN, Crawford K, Starr T, Malone K, Chu H, Bloom JD. Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies . Biorxiv. 2021 Jan 04;.

Greaney AJ, Starr TN, Gilchuk P, Zost SJ, Binshtein E, Loes AN, Hilton SK, Huddleston J, Eguia R, Crawford KHD et al. Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition. Cell Host Microbe. 2020 Nov 19;. PMID: 33259788; PMC: PMC7676316

Starr TN, Greaney AJ, Addetia A, Hannon WW, Choudhary MC, Dingens AS, Li JZ, Bloom JD. Prospective mapping of viral mutations that escape antibodies used to treat COVID-19. bioRxiv. 2020 Dec 1;. PMID: 33299993; PMC: PMC7724661