Effects of Prior Infection with SARS-CoV-2 on B Cell Receptor Repertoire Response during Vaccination

Abstract

Understanding the B cell response to SARS-CoV-2 vaccines is a high priority. High-throughput sequencing of the B cell receptor (BCR) repertoire allows for dynamic characterization of B cell response. Here, we sequenced the BCR repertoire of individuals vaccinated by the Pfizer SARS-CoV-2 mRNA vaccine. We compared BCR repertoires of individuals with previous COVID-19 infection (seropositive) to individuals without previous infection (seronegative). We discovered that vaccine-induced expanded IgG clonotypes had shorter heavy-chain complementarity determining region 3 (HCDR3), and for seropositive individuals, these expanded clonotypes had higher somatic hypermutation (SHM) than seronegative individuals. We uncovered shared clonotypes present in multiple individuals, including 28 clonotypes present across all individuals. These 28 shared clonotypes had higher SHM and shorter HCDR3 lengths compared to the rest of the BCR repertoire. Shared clonotypes were present across both serotypes, indicating convergent evolution due to SARS-CoV-2 vaccination independent of prior viral exposure.

Keywords: B cell receptor heavy-chain sequencing; SARS-CoV-2; vaccine response.

Figure 1

Experimental design and antibody titers in response to vaccination. (A) Schematic showing experimental design and details. (B) Antibody titers IgG/M/A for SARS-CoV-2 spike 1 protein (S1), spike 2 protein (S2), receptor binding domain (RBD), and nucleocapsid protein (NP) of seropositive (red, n = 5) and seronegative (blue, n = 4) individuals: pre-vaccination (week 0) and 21 days after (week 3) first dose of Comirnaty^® (Pfizer, New York, NY, USA).

Figure 2

Isotype usage, V gene usage, and HCDR3 length of BCR repertoire across serotypes during vaccination. (A) BCR isotype usage (IgM IgG, IGHD, IgA, and IGHE) for seropositive and seronegative individuals at each time point (week 0, week 3): percentages as indicated. No changes were seen in the proportion of any isotype due to vaccination, nor significant variation observed between serotypes. (B) IgG Heavy chain V gene usage (IGHV1-7) of IgG clonotypes. Proportion as indicated for seropositive (red) and seronegative (blue). No significant differences were observed between serotypes at week 0 and week 3, and no changes within serotype over time were observed. (C) Distribution of IgG heavy chain complementary determining region 3 (HCDR3) lengths of IgG clones for week 0 and week 3. Seropositive (red) and seronegative (blue) and mean HCDR3 length are shown. No significant changes in the distribution of HCDR3 lengths were seen between serotypes at either time point, or within serotype between weeks.

Figure 3

Somatic hypermutation and diversity measures of B cell receptor (BCR) repertoire across serotypes during vaccination. (A) Plot depicting the proportion (0–100%) of IgG clones with less than 2 mutations (left) and greater than 2 mutations (right). There were no statistically significant differences in the proportions of seropositive (red) and seronegative (blue) at week 0 or week 3. (B) Violin plots depicting percent of SHM for IgG clonotypes in seropositive (red) and seronegative (blue) at weeks 0 and 3. Mean values for each violin are indicated on the plot and by strong dashed lines, quartiles are indicated by thin dashed lines. Statistical test performed was Welch’s t-test, p value **** p < 0.0001, *** p = 0.0002. (C) Diversity measures plots including species richness, Shannon diversity, and Simpson diversity indexes. Seropositive is indicated by red, and seronegative by blue and time points: week 0 and week 3.

Figure 4

Characteristics of expanded “top 50” IgG clonotypes in seropositive and seronegative individuals after one dose of Comirnaty^® (Pfizer, New York, NY, USA). (A) IGHV gene usage plotted for top 50 IgG clonotypes compared to the remaining clones in the repertoires of seropositive (left) and seronegative (right) individuals at week 3. No differences were observed in the V gene usage patterns between the clone groups (top 50 v. other) in either serotype. (B) Top 50 IgG clones’ HCDR3 length was shorter than “other” (the remaining clonotypes) for both seropositive and seronegative (Mann–Whitney test ** p= 0.0079, * p = 0.0286). No difference in top 50 HCDR3 length was observed between serotypes. (C) Violin plots depicting percentage SHM for top 50 IgG clones and other based on serotype, strong dashed line indicates mean value, fine dashed line indicates quartile, means are to the right of each violin. (Welch’s t-test; ** p = 0.0080, * p = 0.0123). (D) Pie charts depicting the proportion of IgG clones that were present at week 0 (black) and novel at week 3 (gray) for the entire repertoire (top) or just top 50 (bottom). Serotype indicated under pie charts. Right panel, plots depicting individual proportions of clones present at week 0 for the whole repertoire (top) and top 50 (bottom). No statistical differences were observed between serotypes.

Figure 5

Convergent clones present at week 3. (A) Upset plot depicting convergent clones. Intersection size (y axis) indicates number of clones, each bar is demarcated with number of unique clones. Connected dots below each bar indicate the number of individuals in which those clone(s) are present. Set size includes the total convergent clones for each sample. S1–9 indicate samples 1–9 red (seropositive) and blue (seronegative) (B) SHM percent comparison between the 28 convergent clones seen in (A), top 50 expanded clones and all other clones. Welch’s t-test, **** p < 0.0001. (C) HCDR3 length distribution of the 28 convergent clones (dark green), top 50 collapsed by serotype (jungle green), and other clones (lime green), means are indicated on the plot by color. Kolmogorov–Smirnov test, convergent vs. other, p = 0.0004.