Sites in SARS-CoV-2 RBD where mutations escape antibody binding

Overview

This page allows you to interactively analyze how mutations to the SARS-CoV-2 receptor binding domain (RBD) affect escape from monoclonal antibodies or polyclonal sera. It does this by integrating multiple experimental studies by the Bloom lab and Y Cao, XS Xie and coworkers at Peking University that use deep mutational scanning to map how all mutations to the RBD affect antibody or sera binding. The citations for the data shown here are listed at the bottom of this page.

The upper line plot shows the per-site escape for each individual antibody, and you can zoom and click on specific lines for details. The lower line plot shows the mean escape at each site across all displayed antibodies, or those that you have currently selected by clicking (choose which option by clicking buttons below plot).

Antibodies are classfied using the Barnes et al scheme, and displayed in a multidimensional scaling plot using the approach described here. There is also a selection box on the right that lists individual antibodies. All these plots are interactive so you can select by clicking, make multiple selections by shift-clicking, and clear selections by double clicking.

At the bottom of the plot are options about what to display, including:

• Show data only from specific labs.
• Show only antibodies elicited by specific viruses. Note that not all categories are mutually exclusive: for instance, SARS-CoV-2 refers to any SARS-CoV-2 variant but not SARS-CoV-1 exposure. Also, this refers to the spike, which could be administered either by vaccination or infection.
• Show only antibodies known to neutralize specific viruses.

The escape metrics are normalized for each antibody so a value of one corresponds to the larger of the maximal escape at any site or 20 times the median escape across all sites. The site-level escape metric is the total mutation-level escape at each site.

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Escape calculator

Click here for an escape calculator that aggregates these data to estimate the antigenic effect on polyclonal sera of mutating combinations of RBD sites. This escape calculator is usually the best way to interact with the data unless you are interested in specific antibodies.

Raw data and code

The experimental data plotted here are in this CSV file.

The computer code that generates this plot and website is at https://github.com/jbloomlab//SARS2_RBD_Ab_escape_maps.

Citations for experimental data

The experimental data shown here are taken from the following papers:

• Dong et al. Nat Micro (2021)
• Greaney et al. Cell Host Microbe (2021a)
• Greaney et al. Cell Host Microbe (2021b)
• Greaney et al. NA (2021)
• Greaney et al. Nat Comm (2021)
• Greaney et al. Sci Transl Med (2021)
• Starr et al. Cell Reports Medicine (2021)
• Starr et al. Nature (2021)
• Starr et al. Science (2021)
• Tortorici et al. Nature (2021)
• Cao et al. Nature (2022a)
• Cao et al. Nature (2022b)
• Greaney et al. PLoS Path (2022)