Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection

Abstract

Background: Control of the COVID-19 pandemic will rely on SARS-CoV-2 vaccine-elicited antibodies to protect against emerging and future variants; an understanding of the unique features of the humoral responses to infection and vaccination, including different vaccine platforms, is needed to achieve this goal.

Methods: The epitopes and pathways of escape for Spike-specific antibodies in individuals with diverse infection and vaccination history were profiled using Phage-DMS. Principal component analysis was performed to identify regions of antibody binding along the Spike protein that differentiate the samples from one another. Within these epitope regions, we determined potential sites of escape by comparing antibody binding of peptides containing wild-type residues versus peptides containing a mutant residue.

Results: Individuals with mild infection had antibodies that bound to epitopes in the S2 subunit within the fusion peptide and heptad-repeat regions, whereas vaccinated individuals had antibodies that additionally bound to epitopes in the N- and C-terminal domains of the S1 subunit, a pattern that was also observed in individuals with severe disease due to infection. Epitope binding appeared to change over time after vaccination, but other covariates such as mRNA vaccine dose, mRNA vaccine type, and age did not affect antibody binding to these epitopes. Vaccination induced a relatively uniform escape profile across individuals for some epitopes, whereas there was much more variation in escape pathways in mildly infected individuals. In the case of antibodies targeting the fusion peptide region, which was a common response to both infection and vaccination, the escape profile after infection was not altered by subsequent vaccination.

Conclusions: The finding that SARS-CoV-2 mRNA vaccination resulted in binding to additional epitopes beyond what was seen after infection suggests that protection could vary depending on the route of exposure to Spike antigen. The relatively conserved escape pathways to vaccine-induced antibodies relative to infection-induced antibodies suggests that if escape variants emerge they may be readily selected for across vaccinated individuals. Given that the majority of people will be first exposed to Spike via vaccination and not infection, this work has implications for predicting the selection of immune escape variants at a population level.

Funding: This work was supported by NIH grants AI138709 (PI JMO) and AI146028 (PI FAM). JMO received support as the Endowed Chair for Graduate Education (FHCRC). The research of FAM was supported in part by a Faculty Scholar grant from the Howard Hughes Medical Institute and the Simons Foundation. Scientific Computing Infrastructure at Fred Hutch was funded by ORIP grant S10OD028685.

Trial registration: ClinicalTrials.gov NCT04283461.

Keywords: SARS-CoV-2; antibody epitope; escape mutations; human; immunology; infectious disease; inflammation; microbiology.

Conflict of interest statement

MG, JG, CW, JL, NF, FM No competing interests declared, HC reported consulting with Ellume, Pfizer, The Bill and Melinda Gates Foundation, Glaxo Smith Kline, and Merck. She has received research funding from Gates Ventures, Sanofi Pasteur, and support and reagents from Ellume and Cepheid outside of the submitted work, JO Reviewing editor, eLife

© 2022, Garrett et al.

Figures

Figure 1.. A schematic of sample cohorts.

Characteristics of individual participants sampled as part of the Moderna Trial Cohort (left) or the Hospitalized or Ambulatory Adults with Respiratory Viral Infections (HAARVI) Cohort (right). Sample sizes of unique individuals in each group are designated below each figure.

Figure 2.. Enrichment of wild-type peptides by serum antibodies.

(A) Heatmap with a sample in each row and groups of samples colored on the left. Columns represent peptide locations, with each square on the heatmap indicating the summed enrichment value within a 10-peptide interval. Darker purple indicates higher enrichment values, and values above 150 were capped. Transparent boxes above the heatmap annotate the Spike protein domains, while the smaller gray boxes indicate epitope binding regions defined in this analysis (B) The loading vectors from the principal component analysis with the four epitope sites highlighted; enrichments in each of these regions are summed together for subsequent analysis. (C) Boxplots describing the distribution of summed wild-type enrichment values for each sample within each of the four epitope sites, each named according to its associated protein domain. Color indicates the sample group. The bars between boxplots give statistical significance (p-value) tests using a Mann–Whitney–Wilcoxon test. All sample group comparisons with the nonhospitalized infected group were performed, and only significant values are shown.

Figure 2—figure supplement 1.. Principal component analysis on wild-type enrichment features of all samples.

(A) Scatterplot depicting the unit scaled sample ‘scores’ represented by the columns to visualize sample relationship in principal component space. Colors represent the group that each sample belongs to. (B) Vector plots showing the component loadings, scaled by the square root of the respective eigenvalues in the eigendecomposition. Colors represent the genomic location of each component loading score. (C) Line plots showing the first three principal axes/directions in feature space, plotted as a function of the wild-type peptide feature location on Spike.

Figure 3.. Comparison of epitope binding for NIH Moderna Trial subgroups.

Boxplots of summed wild-type enrichment within epitope binding regions for samples grouped by (A) timepoint post vaccination, (B) vaccine dose, or (C) participant age. Samples were taken either at 36 (n = 64) or 119 (n = 64) days post vaccination. (B) and (C) are additionally separated by timepoint post vaccination. Results of a Wilcoxon rank-sum test between the groups appear only where p<0.05 after Bonferroni multiple testing correction (36 group comparisons). Figures containing all p-values for both replicate batches are available at https://github.com/matsengrp/phage-dms-vacc-analysis (swh:1:rev:d4c770ad49ed2f8ab31e499265dd02273cff6f86, Matsen, 2022).

Figure 3—figure supplement 1.. Comparison of epitope binding for Hospitalized or Ambulatory Adults with Respiratory Viral Infections (HAARVI) subgroups.

Boxplots of summed wild-type enrichment within epitope binding regions for samples grouped by (A) timepoint post symptom onset or (B) vaccine type (Pfizer/BioNTech BNT162b2 or Moderna mRNA-1273). Results of a Mann–Whitney test between the groups are shown. p-Values were adjusted for multiple testing using Bonferroni correction. *p<0.05, ns, not significant.

Figure 4.. NTD and CTD-N epitope escape profiles.

(A, B) Logo plots depicting the effect of mutations on epitope binding in either the NTD (A) or CTD-N (B) epitope for paired samples from the Moderna Trial Cohort. The height of the letters corresponds to the magnitude of the effect of that mutation on epitope binding, that is, its scaled differential selection value. Letters below zero indicate mutations that cause poorer antibody binding as compared to wild-type peptide, and letters above zero indicate mutations that bind better than the wild-type peptide. Letter colors denote the chemical property of the amino acids. Logo plots on the left and right are paired samples from the same individual, with the participant ID noted on the left.

Figure 4—figure supplement 1.. Thresholding of total epitope binding within major epitope regions.

Histogram showing the summed enrichment values within each epitope region for every sample in the Moderna Trial Cohort (left two panels) or Hospitalized or Ambulatory Adults with Respiratory Viral Infections (HAARVI) Cohort (right two panels). Blue line delineates the threshold chosen for each epitope region. Samples above the line were included in the escape profile analyses.

Figure 5.. Fusion peptide (FP) epitope escape profiles.

(A, B) Logo plots depicting the effect of mutations on epitope binding within the FP epitope region for paired samples from the (A) Hospitalized or Ambulatory Adults with Respiratory Viral Infections (HAARVI) Cohort or (B) Moderna Trial Cohort. Details are as described in Figure 4.

Figure 6.. SH-H epitope escape profiles.

(A, B) Logo plots depicting the effect of mutations on epitope binding within the SH-H epitope region for paired samples from the (A) Hospitalized or Ambulatory Adults with Respiratory Viral Infections (HAARVI) Cohort or (B) Moderna Trial Cohort. Details are as described in Figure 4.