Kinetics of immune responses elicited after three mRNA COVID-19 vaccine doses in predominantly antibody-deficient individuals

Abstract

Mass vaccination campaigns reduced COVID-19 incidence and severity. Here, we evaluated the immune responses developed in SARS-CoV-2-uninfected patients with predominantly antibody-deficiencies (PAD) after three mRNA-1273 vaccine doses. PAD patients were classified based on their immunodeficiency: unclassified primary antibody-deficiency (unPAD, n = 9), common variable immunodeficiency (CVID, n = 12), combined immunodeficiency (CID, n = 1), and thymoma with immunodeficiency (TID, n = 1). unPAD patients and healthy controls (HCs, n = 10) developed similar vaccine-induced humoral responses after two doses. However, CVID patients showed reduced binding and neutralizing titers compared to HCs. Of interest, these PAD groups showed lower levels of Spike-specific IFN-γ-producing cells. CVID individuals also presented diminished CD8⁺T cells. CID and TID patients developed cellular but not humoral responses. Although the third vaccine dose boosted humoral responses in most PAD patients, it had limited effect on expanding cellular immunity. Vaccine-induced immune responses in PAD individuals are heterogeneous, and should be immunomonitored to define a personalized therapeutic strategies.

Keywords: Immune response; Immunology; Virology.

Graphical abstract

Figure 1

Kinetics of SARS-CoV-2 Spike-specific humoral immune response after vaccination (A) Vaccine regimen timeline and samples collection. (B–D) Anti-Spike IgG levels (in AU/ml) over time. CVID (n = 12, black circles), unPAD (n = 9, black triangles), other PADs (CID: n = 1, open triangles and TID: n = 1, open circles), and HC (n = 10, black diamonds) groups. Data were analyzed using Wilcoxon signed rank test. Vaccine-induced anti-Spike IgG titers in CVID, unPAD and HC responder individuals at w8 (C), and at w24 (D) after the first vaccination. In (B), Horizontal dotted line indicates limit of detection. (E) Vaccine-induced anti-Spike IgG titers in CVID and unPAD responder patients after 28 weeks compared to those elicited at w8 in HCs. In (C–E), Box-whiskers plots showing Min, Max, median and interquartile range are shown. Dunn’s multiple comparison test was utilized for detect differences among groups. ∗p<0.05; ∗∗p<0.01; ∗∗∗p<0.001.

Figure 2

Vaccine-induced neutralizing activity against WH1, Delta, and Omicron in PAD patients (A) NAb ID50 titers elicited in CVID (n = 12, black circles), unPAD (n = 9, black triangles), other PADs (CID: n = 1, open triangles and TID: n = 1, open circles), and HC groups (n = 10, black diamonds) against SARS-CoV-2 WH1, Delta, and Omicron variants at w8. (B) Time course of vaccine-induced neutralizing antibodies in all groups against WH1 variant. (C–E) Levels of NAbs at w24 in PAD patients and HC group against WH1, Delta, and Omicron variants, respectively. NAb titers against Delta (D) and Omicron (E) elicited in CVID, unPAD, other PADs, and HCs. (F) NAb levels after three vaccine doses (w28) in PAD patients compared to those elicited after two doses (w8) in HCs. ID50: Half maximal inhibitory dilution. In (A,C, and F), Box-whiskers plots showing Min, Max, median and interquartile range are shown. Data was analyzed using Dunn’s Multiple Comparison Test (A, C and F), and Wilcoxon signed rank test (B, D and E). ∗p<0.05; ∗∗p<0.01; ∗∗∗p<0.001; ∗∗∗∗p < 0.0001. Horizontal dotted line indicates limit of detection.

Figure 3

Avidity of vaccine-induced Spike-specific IgG binding (A–C) Anti-Spike IgG avidity over time in vaccinated CVID (black circles, n = 6), unPAD (black triangles, n = 9), and HCs (black diamonds, n = 10). Comparison of anti-Spike IgG avidity in vaccinated CVID, unPAD, and HCs at w8 (B), and w24 (C). (D) Comparison of anti-Spike IgG avidity in vaccinated CVID, unPAD at w28 and HCs at w8. In (B–D), Box-whiskers plots showing Min, Max, median and interquartile range are shown. Data in (A) was analyzed using Wilcoxon signed rank test. Data in (B–D) were analyzed using Dunn’s Multiple Comparison Test. ∗p<0.05; ∗∗p<0.01.

Figure 4

Vaccine-induced SARS-CoV-2-specific IFN-ɣ T cell responses (A) Number of antigen-specific IFN-ɣ-producing T cells in CVID (n = 12, black circles), unPAD (n = 9, black triangles), other PADs (CID: n = 1, open triangles and TID: n = 1, open circles), and HC groups (n = 10, black diamonds) per 100.000 cells. (B–E) Antigen-specific IFN-ɣ-producing T cells fold change respect to basal (w0). Comparison of Spike-specific spot-forming cells among CVID, unPAD, and HC groups at w8 (C), w24 versus w28 (D), and w28 versus w8 (E). In (C–E), Box-whiskers plots showing Min, Max, median and interquartile range are shown. (A and B) Horizontal dotted line indicates limit of detection and in (B) lines indicate median. Data in (A and B) were analyzed using Wilcoxon signed rank test. Data in (C–E) were analyzed using Dunn’s Multiple Comparison Test. ∗p<0.05; ∗∗p<0.01; ∗∗∗p < 0.001.

Figure 5

Frequency of Spike-specific CD4⁺T cell using activation-induced markers (A–E) Frequency (left panel) or fold change (right panel) in respect to w0 of Spike-specific CD4+T cells expressing CD69+CD154+ (A), CD69+CD137+ (B) or CD25+OX40+ (C) in CVID (n = 12, black circles), unPAD (n = 9, black triangles), other PADs (CID: n = 1, open triangles and TID: n = 1, open circles), and HC groups (n = 10, black diamonds) after vaccination. Comparison of Spike-specific CD4⁺T cell subsets in CVID, unPAD and HC groups at w8 (D), and w28 versus w8 (E). In (D and E), Box-whiskers plots showing Min, Max, median and interquartile range are shown. (A–C) Horizontal dotted line indicates limit of detection and lines indicate median. Data in (A–C) were analyzed using Wilcoxon signed rank test. Data in (D and E) were analyzed using Dunn’s Multiple Comparison Test. ∗p<0.05; ∗∗p<0.01; ∗∗∗p < 0.001.

Figure 6

Vaccine-induced SARS-CoV-2-specific CD8+T cells (A–C) Frequency of Spike-specific CD25+CD8+T cell (left panel) and fold change (right panel) in CVID (n = 12, black circles), unPAD (n = 9, black triangles), other PADs (CID: n = 1, open triangles and TID: n = 1, open circles), and HC groups (n = 10, black diamonds) after vaccination. Comparison of CD25+CD8+T cell frequency among CVID, unPAD, and HC groups at w8 (B) and w28 versus w8 (C). In (B), Box-whiskers plots showing Min, Max, median and interquartile range are shown and in (A) lines indicate median. Data in (A) was analyzed using Wilcoxon signed rank test. Data in (B and C) were analyzed using Dunn’s Multiple Comparison Test. ∗p<0.05; ∗∗p<0.01; ∗∗∗p < 0.001. Horizontal dotted line indicates limit of detection.