B cell receptor repertoire kinetics after SARS-CoV-2 infection and vaccination

Abstract

B cells are important in immunity to both severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and vaccination, but B cell receptor (BCR) repertoire development in these contexts has not been compared. We analyze serial samples from 171 SARS-CoV-2-infected individuals and 63 vaccine recipients and find the global BCR repertoire differs between them. Following infection, immunoglobulin (Ig)G1/3 and IgA1 BCRs increase, somatic hypermutation (SHM) decreases, and, in severe disease, IgM and IgA clones are expanded. In contrast, after vaccination, the proportion of IgD/M BCRs increase, SHM is unchanged, and expansion of IgG clones is prominent. VH1-24, which targets the N-terminal domain (NTD) and contributes to neutralization, is expanded post infection except in the most severe disease. Infection generates a broad distribution of SARS-CoV-2-specific clones predicted to target the spike protein, while a more focused response after vaccination mainly targets the spike's receptor-binding domain. Thus, the nature of SARS-CoV-2 exposure differentially affects BCR repertoire development, potentially informing vaccine strategies.

Keywords: B cell receptor repertoire; COVID-19; SARS-CoV-2 vaccination.

Graphical abstract

Figure 1

Altered isotype use after SARS-CoV-2 infection (A) Cartoon of BCR sequencing method. UMI denoted in blue, patient barcode in red, forward variable gene primer in green, and reverse constant primer in yellow. Region used to assess somatic hypermutation, clone identity, and isotype marked. (B) Study participant and sample numbers split by severity categories and time after screening (cat. A), symptom onset (cat. B–E), or vaccination (cat. VC and VI). The number of samples are shown, with the number of individuals from whom they were collected shown in brackets. (C) Boxplots showing B cell subset proportions according to disease severity at 0–25 days from symptom onset. Naive (CD19⁺IgD⁺CD27⁻), marginal zone B cells (MZ) (CD19⁺IgD⁺CD27⁺), double-negative B cells (DN) (CD19⁺IgD⁻CD27⁻), transitional (CD19⁺IgD⁺ CD27⁺CD24⁺CD38⁺), memory (CD19⁺IgD⁻CD27⁺CD24⁺CD38⁺), and plasmablasts (PB) (CD19⁻CD20⁻CD27⁺CD24⁺CD27⁺CD38⁺). Comparison with HC, unadjusted Wilcox test p value: ^∗p < 0.05, ^∗∗p < 0.005, ^∗∗∗p < 0.0005. (D) Heatmap showing log2 fold change in mean proportion between SARS-CoV-2 and vaccine cases and HC, within severity categories and across time bins. Wilcoxon test false discovery rate (FDR) adjusted p value: ^∗p < 0.05, ^∗∗p < 0.005, ^∗∗∗p < 0.0005. (E) Linear mixed-effects model showing the longitudinal expression of IGHD, IGHM, and IGHD proportions over time, grouped by severity. Gray band indicates the interquartile range of the corresponding isotype in HCs. Nominal p values for the time × severity group interaction term are reported.

Figure 2

Somatic hypermutation in the SARS-CoV-2 BCR repertoire (A) Heatmap showing the log2 fold change in mean frequency of replacement mutations covering regions CDR1 and CDR2 between SARS-CoV-2 infection and vaccine cases and HC, within severity categories and across time bins post screening (cat. A), symptom onset (cat. B–E), or vaccination (cat. VC and VI). Wilcoxon test FDR adjusted p value: ^∗p < 0.05, ^∗∗p < 0.005, ^∗∗∗p < 0.0005. (B) Boxplots showing the mean frequency of replacement mutations covering regions CDR1 and CDR2 in IGHG1 split by severity categories and time bins. Circles represent individual donors. (C) Density plot modeling IGHG1 SHM across HC, SARS-CoV-2 infection and vaccination at 11–20 and 101–200 days from symptom onset. (D) Boxplots showing the proportion of clones per patient with a mean level of SHM <0.05 nt across HC and infection and vaccination at 11–20 and 101–200 days from symptom onset. Wilcoxon test FDR adjusted p value: ^∗p < 0.05, ^∗∗p < 0.005, ^∗∗∗p < 0.0005. Circles represent individual donors. (E) Boxplots showing mean IGHG1 SHM per patient split according to days from symptom onset and IgG spike serostatus. Wilcoxon unpaired two-sided test. Circles represent individual donors. (F) Boxplots showing mean IGHG1 SHM per paired patient pre and post seroconversion. Visual representation of change in somatic hypermutation post seroconversion. Points represent B cell clones. Top row represents seronegative patients. Bottom row represents paired patients post seroconversion. IGHV gene is represented on the x axis, CDR3 length on the y axis, and point color represents level of SHM. (G) Boxplots showing mean SHM per patient split according to neutralizing activity. Circles represent individual donors. Wilcoxon unpaired two-sided test.

Figure 3

V gene usage and diversity in COVID-19 (A) Heatmap showing log2 fold change in mean diversity indices between SARS-CoV-2 infection and vaccine cases and HC, within severity categories and across time bins post screening (cat. A), symptom onset (cat. B–E), or vaccination (cat. VC and VI). Wilcoxon test FDR adjusted p value: ^∗p < 0.05, ^∗∗p < 0.005, ^∗∗∗p < 0.0005. (B) Heatmap showing log2 fold change in mean Simpson's diversity between SARS-CoV-2 infection and vaccine cases and HC, within severity categories and across isotypes and time bins. Wilcoxon test FDR adjusted p value: ^∗p < 0.05, ^∗∗p < 0.005, ^∗∗∗p < 0.0005. (C) Heatmap showing the difference between V gene proportion between SARS-CoV-2 infection and vaccine cases and HC, within severity categories and time bins. Difference calculated using the following method: (mean V gene proportion of disease − mean V gene proportion of HC)/(mean V gene proportion of disease +mean V gene proportion of HC). Wilcoxon test FDR adjusted p value: ^∗p < 0.05, ^∗∗p < 0.005, ^∗∗∗p < 0.0005. (D) Boxplots showing IGHV1-24 proportion and mean clone size and SHM by severity categories and time bins. Uncorrected Wilcoxon test with HC as reference group, p value: ^∗p < 0.05, ^∗∗p < 0.005, ^∗∗∗p < 0.0005. Circles represent individual donors. (E) Boxplots showing proportion of IGHV1-24-positive clones/per patient split according to days from symptom onset/swab and IgG spike serostatus. Wilcoxon test p value: ^∗p < 0.05, ^∗∗p < 0.005, ^∗∗∗p < 0.0005. (F) Boxplots showing proportion of IGHV1-24-positive clones/per patient split according to neutralization ability. Wilcoxon test p value: ^∗p < 0.05, ^∗∗p < 0.005, ^∗∗∗p < 0.0005.

Figure 4

Clonal convergence after SARS-CoV-2 infection and vaccination (A) Convergent clone frequency across SARS-CoV-2 infection and vaccine cases and healthy controls with the CoV-AbDab database. This represents the percentage of unique clones in each patient that are also found in the CoV-AbDab database. Samples split by severity categories and time bins post screening (cat. A), symptom onset (cat. B–E), or vaccination. One-sided Wilcoxon test FDR adjusted p value: ^∗p < 0.05, ^∗∗p < 0.005, ^∗∗∗p < 0.0005. Circles represent individual donors. (B) Boxplots showing convergence per patient split according to days from symptom onset and IgG spike serostatus. Circles represent individual donors. (C) Boxplots showing convergence per patient split according to neutralization ability. Circles represent individual donors. Two-sided Wilcoxon test. (D) Bar plot representing the number of clonotypes shared by members within a group. Patients with SARS-CoV-2 infection are within 25 days from symptom onset/swab, and participants post vaccine are within 25–50 days. Two-sided Wilcoxon test. (E) Graph of convergent IGH clusters. The number of convergent clusters within a disease group are represented by the horizontal bars and across disease groups by lines. An unconnected dot indicates no sharing. The vertical histogram bars represent subtotals. (F) Pie chart comparing V gene usage of convergent clusters in HC and COVID-19 within 25 days from symptom onset/swab identified from (E).