Antibodies elicited by mRNA-1273 vaccination bind more broadly to the receptor binding domain than do those from SARS-CoV-2 infection

Abstract

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with mutations in key antibody epitopes has raised concerns that antigenic evolution could erode adaptive immunity elicited by prior infection or vaccination. The susceptibility of immunity to viral evolution is shaped in part by the breadth of epitopes targeted by antibodies elicited by vaccination or natural infection. To investigate how human antibody responses to vaccines are influenced by viral mutations, we used deep mutational scanning to compare the specificity of polyclonal antibodies elicited by either two doses of the mRNA-1273 COVID-19 vaccine or natural infection with SARS-CoV-2. The neutralizing activity of vaccine-elicited antibodies was more targeted to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein compared to antibodies elicited by natural infection. However, within the RBD, binding of vaccine-elicited antibodies was more broadly distributed across epitopes compared to infection-elicited antibodies. This greater binding breadth means that single RBD mutations have less impact on neutralization by vaccine sera compared to convalescent sera. Therefore, antibody immunity acquired by natural infection or different modes of vaccination may have a differing susceptibility to erosion by SARS-CoV-2 evolution.

Fig. 1. RBD-binding antibodies are responsible for most neutralizing activity of mRNA-1273 vaccine–elicited sera.

(A) Binding of serum antibodies to SARS-CoV-2 RBD, as measured by ELISA area under the curve (AUC), for vaccine-elicited sera and convalescent plasma before and after depletion of RBD-binding antibodies. The dashed pink line indicates binding of prepandemic sera. (B) Binding of serum antibodies to the full spike ectodomain. The y-axis scale units in (A) and (B) are not comparable between samples from vaccinated and convalescent individuals owing to different dilution factors (beginning at 1:500 for vaccine sera and 1:100 for convalescent plasma samples). (C) Neutralization titer (NT₅₀) of vaccine-elicited sera and convalescent plasma samples before and after depletion of RBD-binding antibodies. The limit of detection is shown as a dashed horizontal pink line. (D) Percentage of neutralizing activity of vaccine-elicited sera and convalescent plasma samples due to RBD-binding antibodies. P values are from a log-rank test accounting for censoring. n = 17 for each time point for convalescent plasma samples and n = 14 for each time point for vaccine sera. ns, not significant. All measurements of convalescent plasma binding and neutralization were previously reported in (15).

Fig. 2. Complete maps of RBD mutations that reduce binding by sera collected 119 days after vaccination with the 250-μg dose of the mRNA-1273 vaccine.

(A) The epitopes of four major classes (24) of RBD-binding antibodies are colored on the RBD surface (PDB 6M0J). ACE2 is shown as a gray ribbon diagram. (B) Number of sera that fell into each of the four major categories of binding-escape maps as categorized by subjective visual inspection. (C) Escape maps for six representative sera are shown. The line plots on the left indicate the sum of effects of all mutations at each RBD site on serum antibody binding, with larger values indicating more escape. The logo plots on the right show key sites (highlighted in purple on the line plot x axes). The height of each letter is that mutation’s escape fraction; larger letters indicate a greater reduction in binding. Escape fractions are not strictly comparable between samples owing to the use of sample-specific FACS selection gates; therefore, for each sample, the y axis is scaled independently. RBD sites are colored by epitope as in (A). The escape fractions were correlated between independent libraries, and we report the average of duplicate measurements throughout. Interactive versions of logo plots and structural visualizations are at https://jbloomlab.github.io/SARS-CoV-2-RBD_MAP_Moderna/.

Fig. 3. Comparison of escape maps for sera collected at days 36 and 119 after vaccination shows that the RBD-binding response becomes more focused over time.

(A and B) Escape maps for sera at day 36 (A) and day 119 (B) from five individuals who received the 250-μg vaccine dose are shown. The day 36 maps are all relatively flat, indicating that no RBD mutation has a large effect on serum antibody binding. By day 119, the maps are often more focused on sites 456 and 484. The y axis is scaled separately for each serum sample. Interactive versions are at https://jbloomlab.github.io/SARS-CoV-2-RBD_MAP_Moderna/.

Fig. 4. The binding of vaccine-elicited polyclonal antibodies is more broadly distributed across the RBD than the binding of infection-elicited antibodies.

(A) Escape from RBD-binding antibodies at each site in the RBD was mapped for vaccine sera or convalescent plasma samples collected at early or late time points. Thin gray lines show individual serum or plasma samples, and the thick black line shows the mean (number of samples is indicated in the plot titles). Key sites within the epitopes of each major RBD antibody class are highlighted with the colors defined in Fig. 2A and in (B). (B) Relationships among escape maps of vaccine sera, convalescent plasma samples, and monoclonal antibodies visualized with a multidimensional scaling projection. Vaccine sera include both doses and time points. Convalescent plasma samples include all time points. (C) Total binding escape at each site mapped onto the RBD surface after averaging across all serum or plasma in each group. The RBD surface coloring is scaled from white to red, with white indicating no escape, and red indicating the site with the greatest escape. The color scaling spans the full range of white to red for each serum or plasma group, so a quantitative scale is not comparable across groups. Escape maps for monoclonal antibodies are previously described in (, , –29), and convalescent plasma samples are described in (15, 16). An interactive version of (B) where you can mouse over points for details is at https://jbloomlab.github.io/SARS-CoV-2-RBD_MAP_Moderna/mds.html.

Fig. 5. Effects of RBD mutations on neutralization by day 100 to 150 sera from vaccinated and convalescent individuals.

(A) Total binding escape at each RBD site is shown for the samples from vaccinated (n = 6) or convalescent (n = 6) individuals tested in neutralization assays. The thin gray lines show individual samples, and the dark black line shows the mean. Key sites within each epitope are highlighted using the same color scheme as in Fig. 2A. (B) Neutralization of G614 spike-pseudotyped lentiviral particles with the indicated RBD mutations, shown as the fold decrease in NT₅₀ compared to G614 spike with no additional mutations. Mutations that have been observed in human SARS-CoV-2 isolates are colored white, and nonnaturally occurring mutations are in gray. The orange dashed line represents the effect of depleting all RBD-binding antibodies. (C) The fold decrease in neutralization titer caused by individual mutations in each of the three major neutralizing epitopes of the RBD: K417 in the class 1 epitope, E484K in the class 2 epitope, and G446V in the class 3 epitope. The combination of all three mutations is also shown. Horizontal lines represent the median. In (B) and (C), the dashed gray line indicates no change in neutralization relative to unmutated spike. (D) Representative neutralization curves from two vaccine and two convalescent samples against the triple mutant and its composite single mutations.