Antibody and memory B-cell immunity in a heterogeneously SARS-CoV-2 infected and vaccinated population

Abstract

Global population immunity to SARS-CoV-2 is accumulating through heterogenous combinations of infection and vaccination. Vaccine distribution in low- and middle-income countries has been variable and reliant on diverse vaccine platforms. We studied B-cell immunity in Mexico, a middle-income country where five different vaccines have been deployed to populations with high SARS-CoV-2 incidence. Levels of antibodies that bound a stabilized prefusion spike trimer, neutralizing antibody titers and memory B-cell expansion correlated with each other across vaccine platforms. Nevertheless, the vaccines elicited variable levels of B-cell immunity, and the majority of recipients had undetectable neutralizing activity against the recently emergent omicron variant. SARS-CoV-2 infection, experienced prior to or after vaccination potentiated B-cell immune responses and enabled the generation of neutralizing activity against omicron and SARS-CoV for all vaccines in nearly all individuals. These findings suggest that broad population immunity to SARS-CoV-2 will eventually be achieved, but by heterogenous paths.

Figure 1.. Frequency of SARS-CoV-2 variants in Mexico between February 2020 and January 2022.

A total of 48,221 viral genome sequences obtained from samples collected in Mexico and downloaded from GISAID on January 28^th, 2022, were analyzed. The frequency of variants was estimated over periods of a few months or individual months based on numbers of complete genomes sequenced. Most common lineages include variants circulating above 10% nationally in at least one period. In addition, less common lineages classified as variants of concern (VOC) and variants of interest (VOI) by the World Health Organization (WHO) were also included. Additional non-VOC/VOI lineages which circulated below 10% nationally during all periods were aggregated into the “Other” category. (B) Geographical distribution of viral genomes obtained in Mexico between February 2020 and January 2022. The number of genome sequences per 100,000 persons in the 32 states of Mexico is represented by a color gradient.

Figure 2.. Plasma neutralization activity against SARS-CoV-2 variants in vaccine recipients.

NT₅₀ values of plasmas from recipients of one of five SARS-CoV-2 vaccines against B.1 or other SARS-CoV-2 variants. (A) Recipients with no documented prior infection with SARS-CoV-2. (B) Recipients were infected with SARS-CoV-2 prior to the study as documented by a PCR positive test (closed circles) or at an unknown time prior to sample collection as indicated by presence of anti-N antibodies (closed triangles). Individuals with prior positive PCR tests but seronegative for anti-N are indicated by open circles. The median values of 2–4 independent experiments for each plasma is plotted. Dashed line indicates the lowest plasma dilution tested (1:50). Lines indicate group median NT₅₀ values.

Figure 3.. Plasma neutralization activity against SARS-CoV in in vaccine recipients.

NT₅₀ values measured in recipients who were infected with SARS-CoV-2 either prior to the study as documented by a PCR positive test (closed circles) or at an unknown time prior to sample collection as indicated by presence of anti-N antibodies (closed triangles). Individuals with prior positive PCR tests but seronegative for anti-N are indicated by (open circles). The median of 2 independent experiments for each plasma is plotted. Dashed line indicates the lowest plasma dilution tested (1:50). Lines indicated group median NT₅₀ values.

Figure 4.. Quantification of SARS-CoV-2 spike specific memory B-cells in vaccine recipients.

Memory B cells (Bm) in recipient PBMC were enumerated using FACS and a trimeric recombinant SARS-CoV-2 (B.1) spike protein. (A) Percentage of spike-binding (S+) Bm cells in recipients of one of five vaccines that were uninfected (left, black circles) or infected (right, red circles). (Open red circles = anti-N negative individuals as in Fig. 2B). Horizontal lines indicate the median percentage S+ (of Bm cells). (B) Correlation between neutralizing antibody titers (NT₅₀) and percentage of S-binding Bm cells across all vaccine recipients (C) Correlation of neutralizing antibody titers (NT₅₀) with percentage of S-binding Bm cells in each separate uninfected (black symbols) or infected (red symbols) vaccine recipient group. The r values indicate Spearman correlation coefficients

Figure 5.. Quantification of antibodies that bind a prefusion SARS-CoV-2 spike protein.

A conformationally stabilized trimer of a fusion protein between Spike (B.1) and NanoLuc (S-6P-NanoLuc) was used to measure Spike-binding antibodies. Antibodies in serially diluted participant plasmas were captured using protein G magnetic beads, then incubated with S-6P-NanoLuc and bound NanoLuc activity quantified. (A) Captured NanoLuc activity expressed as Relative Light Units (RLU) per μl of plasma from uninfected vaccine recipients (left, black circles) or infected (right, red circles). (Open red circles indicate anti-N-negative samples as described in Fig. 2B). Mean of two independent experiments. Lines indicate group median RLU/μl. (B, C) Correlation between neutralizing antibody titers (NT₅₀) (B) or Spike specific memory B-cell expansion (C) and Spike-binding antibodies (RLU/μl) across all vaccine recipients. (D, E) Correlation between neutralizing antibody titers (NT₅₀) (D) or spike specific memory B-cell expansion (E) and Spike-binding antibodies (RLU/μl) for each uninfected (black) or infected (red) vaccine recipient group. The r values indicate Spearman correlation coefficients

Figure 6.. Longitudinal analysis of neutralizing antibodies post vaccination.

Comparison of neutralizing antibody titers between the first and second plasma sample for each participant. (A) Uninfected participants (B) SARS-CoV-2 infected participants. (Open circles individuals that were seronegative for anti-N as in Fig 2B.) (C) Change in NT50 values for participants that were infected between the acquisition of the 2 samples as indicated by acquisition of, or large increase in, anti-N antibodies. (D, E) Neutralizing antibody titers against SARS-CoV-2 variants (D) and SARS-CoV (E) in second samples from participants who were infected between collection of the two samples. One sample from the Ad5-nCoV group with a prior positive PCR test and anti-N antibodies in the second but not the first sample was included in this group. The median of 2 independent experiments for each plasma is plotted. Dashed line indicates the lowest plasma dilution tested (1:50). Horizontal lines indicate group median NT₅₀ values.