Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies

Abstract

The evolution of SARS-CoV-2 could impair recognition of the virus by human antibody-mediated immunity. To facilitate prospective surveillance for such evolution, we map how convalescent plasma antibodies are impacted by all mutations to the spike's receptor-binding domain (RBD), the main target of plasma neutralizing activity. Binding by polyclonal plasma antibodies is affected by mutations in three main epitopes in the RBD, but longitudinal samples reveal that the impact of these mutations on antibody binding varies substantially both among individuals and within the same individual over time. Despite this inter- and intra-person heterogeneity, the mutations that most reduce antibody binding usually occur at just a few sites in the RBD's receptor-binding motif. The most important site is E484, where neutralization by some plasma is reduced >10-fold by several mutations, including one in the emerging 20H/501Y.V2 and 20J/501Y.V3 SARS-CoV-2 lineages. Going forward, these plasma escape maps can inform surveillance of SARS-CoV-2 evolution.

Keywords: RBD; SARS-CoV-2; antibody escape; deep mutational scanning; polyclonal immunity; receptor-binding domain; spike.

Graphical abstract

Figure 1

RBD-binding antibodies are responsible for most of the neutralizing activity of human polyclonal plasma (A) Change in binding of plasma to RBD and spike before and after depletion of RBD antibodies, measured by ELISA area under the curve (AUC). The dashed orange line is binding of pre-pandemic pooled sera collected in 2017 and 2018. Raw ELISA binding curves in Figure S1A. (B) Neutralization titer 50% (NT50) of human plasma before and after depletion of RBD-binding antibodies. Legend is at left: filled and open circles are pre- and post-depletion samples, respectively, connected by a line. Orange indicates plasma for which we subsequently mapped mutations that reduce binding. The numbers at right indicate the percent of all neutralizing activity attributable to RBD-binding antibodies. Plasma are sorted in descending order of percent of neutralization due to RBD-binding antibodies, first by subject and then within subject. The dashed blue line is the limit of detection (NT50 of 20). Points on this line have an NT50 of 20, so the percent of neutralization due to RBD-binding antibodies may be an underestimate for these plasmas. See Figure S1 and Table S1 for additional data including sample metadata, full ELISA and neutralization curves, and numerical values plotted here.

Figure 2

Complete maps of RBD mutations that reduce binding by polyclonal plasma antibodies from 11 individuals (A) The line plots at left indicate the total effect of all mutations at each site in the RBD on plasma antibody binding, with larger values indicating a greater reduction in antibody binding. The logo plots at right zoom in on individual mutations at key sites (indicated by purple highlighting on the x axis of the line plots). In these logo plots, the height of each letter is that mutation’s escape fraction, so larger letters indicate mutations that cause a greater reduction in antibody binding. Escape fractions are comparable across sites within a sample, but not necessarily between samples due to the use of sample-specific FACS gates—therefore, for each plasma, the y axis is scaled independently (see STAR methods). Sites in the logo plots are colored by RBD epitope. (B) For coloring of the logo plots, we designated three RBD epitopes based on the structural locations where mutations had large effects on plasma antibody binding. The images show the structure of the RBD bound to ACE2 (PDB: 6M0J) (Lan et al., 2020) in several representations. The receptor-binding-ridge epitope is dark blue, the epitope containing the 443–450 loop is cyan, the core-RBD epitope is orange, the rest of the RBD is gray, and ACE2 is purple. For the cartoon rendering in the top structure, alpha carbons for sites of strong binding escape for any of the 11 plasma (i.e., all sites shown in the logo plots) are represented as spheres. Interactive versions of these escape maps are available at https://jbloomlab.github.io/SARS-CoV-2-RBD_MAP_HAARVI_sera/.

Figure 3

Regions of the RBD where mutations strongly reduced binding by the antibodies in plasma collected from 11 individuals The total effect of mutations at each site (sum of escape fractions) are projected onto the structure of the RBD (PDB: 6M0J), with white indicating no effect of mutations at that site and red indicating a large reduction in antibody binding. Two views of the RBD are shown: the surface of the RBD that is buried in the “down” conformation and the surface that is always exposed and accessible (Walls et al., 2020; Wrapp et al., 2020). (A) For some individuals (typified by subject B), antibody binding is predominantly reduced by mutations in the receptor-binding ridge, particularly at sites F456 and E484. (B) For some individuals (typified by subject G), antibody binding is strongly reduced by mutations in the 443–450 loop of the RBM in addition to the receptor-binding ridge. (C) For a few individuals (typified by subject J), antibody binding is affected by mutations in the core RBD epitope around site P384. (D) Samples from the other eight individuals fall in one of the three classes detailed in panels (A–C). For panels (A–D), the white-to-red coloring scale is set to span the same range as the y axis limits for that plasma in Figure 2. (E) Mutations in two major surface regions (the S309 epitope and the sites near E465) do not strongly affect plasma antibody binding for any of the subjects. Shown is a surface representation of the RBD, with the three polyclonal plasma epitopes colored as in Figure 2. The S309 epitope and region near E465 (“E465 patch”) are shown in pink and maroon. ACE2 is shown in a dark gray cartoon representation. Interactive versions of these structural visualizations are available at https://jbloomlab.github.io/SARS-CoV-2-RBD_MAP_HAARVI_sera/.

Figure 4

The RBD mutations that affect plasma antibody binding change over time for some individuals Escape maps, colored as in Figure 2, demonstrating temporal patterns: (A) no change over time, (B) broadening over time, (C) increasing prominence of one antigenic region, the 443–450 loop, or (D) narrowing over time. This figure shows the escape maps over time for 6 of the 11 individuals to illustrate representative trends; see Figure S3 for escape maps for all individuals at all time points. Figure S4 shows the effects of mutations at each site projected onto the RBD structure. Different sets of sites are shown in the logo plots in panels (A and C), and in panels (B and D). Sites highlighted in the logo plots are indicated in purple on the x axes of the associated line plots. The y axis limits were set as in Figure 2A (see STAR methods). Interactive versions of these visualizations are available at https://jbloomlab.github.io/SARS-CoV-2-RBD_MAP_HAARVI_sera/.

Figure 5

Mutations mapped to reduce plasma antibody binding often reduce viral neutralization (A–C) Violin plots at left show the distribution of how mutations at all sites in the RBD affect plasma binding in the mapping experiments. The plots at right then show the effects of tested mutations on neutralization (the fold-change in neutralization inhibitory concentration 50% [IC₅₀]). For instance, the top row in (A) shows that mutations at E484 and F456 are mapped to reduce plasma antibody binding for subject C at both days 32 and 104, and that multiple different mutations at E484 but not F456 greatly reduced plasma neutralization (e.g., a >100-fold increase in IC₅₀ for E484K for the day-32 plasma). Sites that are accessible in the down conformation of the RBD in the context of full spike are indicated by red circles (e.g., E484), and sites that are inaccessible in the RBD’s down conformation are indicated by blue triangles (e.g., F456). In the plots showing the fold-change in IC₅₀s, the dashed gray line indicates a value of one (no change in neutralization), and the dotted orange line indicates the change in inhibitory concentration if all RBD-binding antibodies are removed (see Figure 1B). (D) Full neutralization curves for a subset of plasma and viral mutants demonstrating how E484Q, E484K, G446V, and G485R substantially reduce viral neutralization for some plasma. Error bars are the standard error for n = 2 replicates. For all neutralization curves used to determine changes in neutralization plotted in (A–C), see Figure S5. The y axis limits in the violin plots are set as the maximum of the y axis limit for all time points of a subject in the escape maps in Figures 2A and S3. Numerical IC₅₀ values and fold-change IC₅₀ relative to wildtype are listed at https://github.com/jbloomlab/SARS-CoV-2-RBD_MAP_HAARVI_sera/blob/main/experimental_validations/results/mutant_neuts_results/mutants_foldchange_ic50.csv.

Figure 6

Frequencies of mutations that affect plasma antibody binding among circulating SARS-CoV-2 isolates (A) Effects of mutations at each RBD site on plasma antibody binding versus frequency of mutations at each site among all SARS-CoV-2 sequences in GISAID as of December 23, 2020. Key sites (see STAR methods) are labeled and colored according to epitope region as in Figure 2. (B) Cumulative prevalence for the four most frequent mutations and also any mutations at sites labeled in (A) with at least ten counts in GISAID. (C) Surface representations of the RBD (PDB: 6M0J). Sites where mutations have a strong effect on binding, have circulating variation with >50 total counts in GISAID, or both, are colored in olive, pink, or maroon, respectively. See STAR methods for precise description of highlighted sites. ACE2 is shown as a dark gray cartoon.