Age-related immune response heterogeneity to SARS-CoV-2 vaccine BNT162b2 methods
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Extended data figures and tables
Extended Data Table 2 Neutralization after the first dose of BNT162b2 vaccine against wild-type and B1.1.7 PVs
Neutralization following immunization
We explored the association between age and ability to neutralize virus by plotting the proportion of individuals whose sera produced detectable virus neutralization after the first dose at a given age. This analysis showed a nonlinear relationship with a marked drop around the age of 80 years (Fig. ). Given this nonlinear change in a correlate of protection, we performed selected subsequent analyses with age both as a continuous variable and as a categorical variable. When individuals aged 80 years or more were tested between 3 and 12 weeks after their first dose, around half showed no evidence of neutralization (Extended Data Fig. ). Geometric mean neutralization titre (GMT) was lower in participants aged 80 years or more than in younger individuals (48.2 (95% confidence interval (CI) 34.6-67.1) versus 104.1 (95% CI 69.7-155.2), P = 0.004;...
Neutralization following immunization
Given our observation that participants aged 80 years or more had lower neutralization responses following the first dose than younger individuals, we hypothesized that this could lead to sub-protective neutralizing responses against the B.1.1.7, B.1.351 and P.1 VOCs, which were first identified in the UK, South Africa and Brazil, respectively (Extended Data Fig. ). We therefore examined serum neutralization by age group against PVs bearing the wild-type spike protein or spike proteins from the three VOCs (Fig. ). There was a clear reduction in neutralizing titres against VOCs (Fig. ), and titres were lower for individuals over 80 years old than for younger individuals. The proportions of individuals with detectable neutralization showed a similar pattern (Fig., Extended Data Tables, ). Following the second dose, although there were differences in GMT for the VOCs between...
B cell responses to mRNA vaccination
We measured binding antibody responses to the full-length wild-type (Wuhan-1) spike protein. Levels of IgG and all IgG subclasses against spike protein increased between vaccine doses (Fig. ), and were similar after the second dose to those observed following natural infection. Like the neutralization titres, levels of IgG against spike declined with age (Fig., Extended Data Fig. ). IgG and its subclasses correlated with serum neutralization (Fig., Extended Data Fig. ). The concentrations of total and subclass anti-spike IgGs were significantly lower in participants aged 80 or older than in the younger group (Fig. ). IgA responses also increased between the two doses and correlated with neutralization after dose 1 (Extended Data Fig. ). In addition, phenotyping of peripheral blood mononuclear cells (PBMCs) by flow cytometry showed that neutralization in the over-80 age group was as...
B cell responses to mRNA vaccination
a, Isotype usage according to unique VDJ sequence in participants <80 ( n = 22) or ≥80 years old ( n = 28) and association with neutralization of spike pseudotyped virus. Neutralization cut-off for 50% neutralization was set at 20. Mann-Whitney U -test. b, Heat map showing differences in V gene usage between the <80 and ≥80 groups. Mann-Whitney U -test with Benjamini-Hochberg false discovery rate (FDR) correction; * P < 0.1. c, Mean somatic hypermutation for participants <80 or ≥80 years old, grouped according to isotype class. Mann-Whitney U -test. d, Diversity indices for neutralizing and non-neutralizing groups. The inverse is depicted for Simpson's index. t -test. e, BCR comparison of patients in the two age groups for the first 50 days after vaccination (<80, n = 27; ≥...
Autoantibodies and inflammatory molecules
Finally, we investigated the possibility of interactions between senescence and mRNA vaccine responses. Autoantibodies and inflammatory cytokines or chemokines are associated with immune senescence. We first measured a panel of autoantibodies in the sera of 101 participants following the first dose of the BNT162b2 vaccine. Eight participants had autoantibodies against myeloperoxidase (anti-MPO), two against fibrillarin and one against cardiolipin (Extended Data Fig. ). As expected, all but one of the participants with anti-MPO autoantibodies were over the age of 80 years (Extended Data Fig. ). There was a trend towards reduced anti-spike IgG levels and serum neutralization against the wild-type and B.1.17 spike proteins in participants with autoantibodies, although this did not reach statistical significance (probably owing to the small sample size; Extended Data Fig. ). Next, w...
T cell responses to mRNA vaccination
Although it is increasingly recognized that neutralizing antibodies dominate protection against initial infection,, T cells might limit disease progression when neutralizing antibody titres are low. We therefore determined the T cell response to SARS-CoV-2 spike protein in vaccinated individuals by stimulating PBMCs with overlapping peptide pools to the wild-type SARS-CoV-2 spike, using an interferon-γ (IFNγ) and interleukin-2 (IL-2) FluoroSpot assay to count spike-specific T cells. When we plotted IFNγ-spike specific T cell responses against age as a continuous variable, there was a negative correlation with a drop-off at around 80 years (Fig. ). A similar effect, albeit less pronounced, was seen for IL-2 (Fig. ). However, there did not appear to be a relationship between cytokine production by PBMCs and neutralization titre after the first dose (Extended Data...
T cell responses to mRNA vaccination
Following the first dose of vaccine, the frequency of IFNγ-secreting T cells against a CEF+ peptide pool that included cytomegalovirus (CMV)-, Epstein-Barr virus (EBV)- and influenza-specific peptides did not differ by age category and was similar to healthy SARS-CoV-2 unexposed controls (Extended Data Fig. ). This indicates that differences in observed responses were likely to be vaccine-specific rather than resulting from generalized suboptimal T cell responses or immune paresis. However, IFNγ spike-specific T cell responses were significantly larger in immunized individuals below 80 years of age than in an unexposed population of the same age (Fig. ). However, in participants aged 80 years or more, the IFNγ spike-specific T cell response following the first dose did not differ from that of unexposed controls (Fig. ). By contrast, spike-specific IL-2 T cell...
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Extended Data Table 2 Neutralization after the first dose of BNT162b2 vaccine against wild-type and B1.1.7 PVs
We explored the association between age and ability to neutralize virus by plotting the proportion of individuals whose sera produced detectable virus neutralization after the first dose at a given age. This analysis showed a nonlinear relationship with a marked drop around the age of 80 years (Fig. ). Given this nonlinear change in a correlate of protection, we performed selected subsequent analyses with age both as a continuous variable and as a categorical variable. When individuals aged 80 years or more were tested between 3 and 12 weeks after their first dose, around half showed no evidence of neutralization (Extended Data Fig. ). Geometric mean neutralization titre (GMT) was lower in participants aged 80 years or more than in younger individuals (48.2 (95% confidence interval (CI) 34.6-67.1) versus 104.1 (95% CI 69.7-155.2), P = 0.004; Extended Data Table, Fig. ). GMT showed evidence of an inverse association with age (Extended Data Fig. ). The GMT following the second dose was significantly higher in individuals for whom there had been a 12-week interval between doses compared with a 3-week interval between doses (Extended Data...
Given our observation that participants aged 80 years or more had lower neutralization responses following the first dose than younger individuals, we hypothesized that this could lead to sub-protective neutralizing responses against the B.1.1.7, B.1.351 and P.1 VOCs, which were first identified in the UK, South Africa and Brazil, respectively (Extended Data Fig. ). We therefore examined serum neutralization by age group against PVs bearing the wild-type spike protein or spike proteins from the three VOCs (Fig. ). There was a clear reduction in neutralizing titres against VOCs (Fig. ), and titres were lower for individuals over 80 years old than for younger individuals. The proportions of individuals with detectable neutralization showed a similar pattern (Fig., Extended Data Tables, ). Following the second dose, although there were differences in GMT for the VOCs between the age groups (Fig. ), nearly all participants across age groups had detectable neutralization responses across the VOCs tested (Fig. ).
We measured binding antibody responses to the full-length wild-type (Wuhan-1) spike protein. Levels of IgG and all IgG subclasses against spike protein increased between vaccine doses (Fig. ), and were similar after the second dose to those observed following natural infection. Like the neutralization titres, levels of IgG against spike declined with age (Fig., Extended Data Fig. ). IgG and its subclasses correlated with serum neutralization (Fig., Extended Data Fig. ). The concentrations of total and subclass anti-spike IgGs were significantly lower in participants aged 80 or older than in the younger group (Fig. ). IgA responses also increased between the two doses and correlated with neutralization after dose 1 (Extended Data Fig. ). In addition, phenotyping of peripheral blood mononuclear cells (PBMCs) by flow cytometry showed that neutralization in the over-80 age group was associated with a higher proportion of spike-specific IgG + IgM - CD19 + memory B cells (Fig. ). Notably, the proportion of these cells did not differentiate neutralizers from non-neutralizers in the under-80 group (Fig., Extended Data Fig. ). Fig. 2 SARS-CoV-2 spike-binding antibody responses...
a, Isotype usage according to unique VDJ sequence in participants <80 ( n = 22) or ≥80 years old ( n = 28) and association with neutralization of spike pseudotyped virus. Neutralization cut-off for 50% neutralization was set at 20. Mann-Whitney U -test. b, Heat map showing differences in V gene usage between the <80 and ≥80 groups. Mann-Whitney U -test with Benjamini-Hochberg false discovery rate (FDR) correction; * P < 0.1. c, Mean somatic hypermutation for participants <80 or ≥80 years old, grouped according to isotype class. Mann-Whitney U -test. d, Diversity indices for neutralizing and non-neutralizing groups. The inverse is depicted for Simpson's index. t -test. e, BCR comparison of patients in the two age groups for the first 50 days after vaccination (<80, n = 27; ≥80, n = 5) with public clones known to be associated with SARS-CoV-2 using the CoV-AbDab database. Clones from participants and the database were co-clustered based on matching IGHV and IGHJ segments, matching CDR-H3 region length and 85% CDR-H3 sequence amino acid homology. One-sided t...
Finally, we investigated the possibility of interactions between senescence and mRNA vaccine responses. Autoantibodies and inflammatory cytokines or chemokines are associated with immune senescence. We first measured a panel of autoantibodies in the sera of 101 participants following the first dose of the BNT162b2 vaccine. Eight participants had autoantibodies against myeloperoxidase (anti-MPO), two against fibrillarin and one against cardiolipin (Extended Data Fig. ). As expected, all but one of the participants with anti-MPO autoantibodies were over the age of 80 years (Extended Data Fig. ). There was a trend towards reduced anti-spike IgG levels and serum neutralization against the wild-type and B.1.17 spike proteins in participants with autoantibodies, although this did not reach statistical significance (probably owing to the small sample size; Extended Data Fig. ). Next, we explored the association between serum cytokines or chemokines and neutralization of SARS-CoV-2 PV, as well as their association with age. PIDF, a known senescence-associated secretory phenotype (SASP) molecule, was the only molecule that was enriched in sera from participants aged over 80 ye...
Although it is increasingly recognized that neutralizing antibodies dominate protection against initial infection,, T cells might limit disease progression when neutralizing antibody titres are low. We therefore determined the T cell response to SARS-CoV-2 spike protein in vaccinated individuals by stimulating PBMCs with overlapping peptide pools to the wild-type SARS-CoV-2 spike, using an interferon-γ (IFNγ) and interleukin-2 (IL-2) FluoroSpot assay to count spike-specific T cells. When we plotted IFNγ-spike specific T cell responses against age as a continuous variable, there was a negative correlation with a drop-off at around 80 years (Fig. ). A similar effect, albeit less pronounced, was seen for IL-2 (Fig. ). However, there did not appear to be a relationship between cytokine production by PBMCs and neutralization titre after the first dose (Extended Data Fig. ). Fig. 4 T cell responses to BNT162b2 vaccine after the first and second doses. a, b, FluoroSpot analysis by age for IFNγ ( a ) and IL-2 ( b ) T cell responses specific to SARS-CoV-2 spike protein peptide pool following PBMC stimulation. SFU, spot-forming units. Scatter plots show linea...
Following the first dose of vaccine, the frequency of IFNγ-secreting T cells against a CEF+ peptide pool that included cytomegalovirus (CMV)-, Epstein-Barr virus (EBV)- and influenza-specific peptides did not differ by age category and was similar to healthy SARS-CoV-2 unexposed controls (Extended Data Fig. ). This indicates that differences in observed responses were likely to be vaccine-specific rather than resulting from generalized suboptimal T cell responses or immune paresis. However, IFNγ spike-specific T cell responses were significantly larger in immunized individuals below 80 years of age than in an unexposed population of the same age (Fig. ). However, in participants aged 80 years or more, the IFNγ spike-specific T cell response following the first dose did not differ from that of unexposed controls (Fig. ). By contrast, spike-specific IL-2 T cell frequencies were significantly higher in both vaccinated groups than in unexposed controls (Fig. ). Notably, although spike-specific IFNγ and IL-2 responses in PBMCs after the first dose of vaccine were similar to those found after natural infection (Extended Data Fig. ), the second dose did no...
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