Distinct antibody and memory B cell responses in SARS-CoV-2 naïve and recovered individuals following mRNA vaccination

Abstract

Novel mRNA vaccines for SARS-CoV-2 have been authorized for emergency use. Despite their efficacy in clinical trials, data on mRNA vaccine-induced immune responses are mostly limited to serological analyses. Here, we interrogated antibody and antigen-specific memory B cells over time in 33 SARS-CoV-2 naïve and 11 SARS-CoV-2 recovered subjects. SARS-CoV-2 naïve individuals required both vaccine doses for optimal increases in antibodies, particularly for neutralizing titers against the B.1.351 variant. Memory B cells specific for full-length spike protein and the spike receptor binding domain (RBD) were also efficiently primed by mRNA vaccination and detectable in all SARS-CoV-2 naive subjects after the second vaccine dose, though the memory B cell response declined slightly with age. In SARS-CoV-2 recovered individuals, antibody and memory B cell responses were significantly boosted after the first vaccine dose; however, there was no increase in circulating antibodies, neutralizing titers, or antigen-specific memory B cells after the second dose. This robust boosting after the first vaccine dose strongly correlated with levels of pre-existing memory B cells in recovered individuals, identifying a key role for memory B cells in mounting recall responses to SARS-CoV-2 antigens. Together, our data demonstrated robust serological and cellular priming by mRNA vaccines and revealed distinct responses based on prior SARS-CoV-2 exposure, whereby COVID-19 recovered subjects may only require a single vaccine dose to achieve peak antibody and memory B cell responses. These findings also highlight the utility of defining cellular responses in addition to serologies and may inform SARS-CoV-2 vaccine distribution in a resource-limited setting.

Fig. 1

Antibody responses following mRNA vaccination in SARS-CoV-2 naïve and recovered individuals. A) UPenn Immune Health COVID vaccine study design. B) Concentration of anti-spike and anti-RBD IgG antibodies in vaccinated individuals over time. C) Focus reduction neutralization titer 50% (FRNT₅₀) of vaccine-induced sera against pseudotyped virus expressing SARS-CoV-2 D614G (wild-type) or B.1.351 (South African) variant spike protein. D) Paired analysis of neutralization titers against D614G and B.1.351 in vaccine-induced sera at baseline (timepoint 1), pre-boost (timepoint 2), and post-boost (timepoint 4). E) Bivariate analysis of total anti-spike and anti-RBD binding antibodies with pseudovirus neutralization titers against D614G and B.1.351. Associations between total antibody levels and neutralizing ability were calculated using Spearman rank correlation and are shown with linear trend lines. Dotted lines indicate the limit of detection (LOD) for the assay. Statistics were calculated using unpaired Wilcoxon test (comparisons between timepoints and comparisons between naïve and recovered) or paired Wilcoxon test (comparisons between D614G and B.1.351) with Holm correction for multiple comparisons. Blue and red values indicate statistical comparisons within naïve or recovered groups. Black values indicate statistical comparisons between naïve or recovered groups.

Fig. 2

Antigen-specific memory B cell responses following mRNA vaccination in SARS-CoV-2 naïve and recovered individuals. A) Gating strategy and representative plots for flow cytometric analysis of SARS-CoV-2-specific B cells. B) Frequency of spike⁺, spike⁺/RBD⁺, and HA⁺ memory B cells over time in vaccinated individuals. Data are represented as frequency of antigen-specific cells in the total memory B cell compartment. C) Frequency of IgG and IgM isotypes over time in the antigen-specific memory B cell compartments. D) Frequency of RBD⁺ memory B cells over time in vaccinated individuals, as a percentage of spike⁺ memory B cells. E) Somatic hypermutation (SHM) status of spike+ memory B cell clones over time in SARS-CoV-2 recovered individuals. Data are represented as percent of VH-gene nucleotides that are mutated. F) SHM of productive spike-binding clones sampled at timepoint 1 which were also found in at least one other timepoint. Clones with fewer than 10 copies in each patient were excluded. G) Clonal evolution of spike-binding memory B cell lineages that were present prior to vaccination in a recovered individual. For representative lineages, numbers refer to mutations compared to the preceding vertical node. Colors indicate timepoint, black dots indicate inferred nodes, and size is proportional to sequence copy number; GL = germline sequence. All panels: Dotted lines indicate the mean at baseline. RD = non-vaccinated, SARS-CoV-2 recovered donors. Statistics were calculated using unpaired Wilcoxon test (comparisons between timepoints and comparisons between naïve and recovered) with Holm correction for multiple comparisons. Blue and red values indicate statistical comparisons within naïve or recovered groups. Black values indicate statistical comparisons between naïve or recovered groups.

Fig. 3

Association of age and side-effects with B cell responses following mRNA vaccination. A, C) Concentration of anti-spike and anti-RBD IgG antibodies over time compared with sex (A) and age (C) in SARS-CoV-2 naïve individuals. Dotted lines indicate the limit of detection for the assay. B, D) Frequency of spike⁺ and spike⁺/RBD⁺ memory B cells over time compared with sex (B) and age (D) in SARS-CoV-2 naïve individuals. Dotted lines indicate the mean frequency of cells at baseline. Pre-boost indicates samples collected at timepoint 2 (~15 days post-primary vaccination). Post-boost indicates samples collected at timepoint 4 (~7 days post-secondary vaccination). Statistics for sex were calculated using Wilcoxon test. Associations with age were calculated using Spearman rank correlation and are shown with linear trend lines. E) Concentration of anti-spike and anti-RBD IgG antibodies and frequency of spike⁺ and spike⁺/RBD⁺ memory B cells at the post-boost timepoint compared with self-reported side effects after the second dose. Reactogenicity was categorized into either no/local symptoms or systemic symptoms. F) Multivariable linear regression between antibody or memory B cell responses and side effects, controlling for sex and age. Data are represented as estimated regression coefficients with a 95% confidence interval.

Fig. 4

Antigen-specific memory B cells were a distinct measure of vaccine efficacy and correlated to antibody recall responses. A) Heatmap and hierarchical clustering of vaccine-induced antibody and memory B cell responses. B) Principal component analysis and biplot of vaccine-induced antibody and memory B cell responses. C) Association of post-boost (timepoint 4) antibody levels with post-boost (timepoint 4) antigen-specific memory B cell frequencies in SARS-CoV-2 naïve individuals. D) Association of baseline (timepoint 1) antigen-specific memory B cell frequencies with post-primary vaccination (timepoint 2) antibody levels in SARS-CoV-2 recovered individuals. Illustrations in (C) and (D) represent the corresponding immune relationship. Associations between immunological parameters were calculated using Spearman rank correlation and are shown with non-parametric trend lines (Theil-Sen estimator).

Fig. 5

Study summary and key findings). A) Cohort design and objectives. Longitudinal samples were collected from SARS-CoV-2 naïve and recovered individuals and measured for both antibodies and memory B cells. B) Distinct patterns of antibody and memory B cell responses to mRNA vaccination in SARS-CoV-2 naïve and recovered individuals. C) Age-associated differences in antibody and memory B cell responses to mRNA vaccination. D) Baseline memory B cells in SARS-CoV-2 recovered individuals contribute to recall responses following mRNA vaccination.