https://orcid.org/0000-0003-2785-317X
Abstract
We compared antibody and T-cell responses against the severe acute respiratory syndrome coronavirus 2 vaccine strain spike protein to responses against the Omicron variant in 15 messenger RNA vaccine recipients. While these individuals had significantly lower levels of antibodies that inhibited Omicron spike protein binding to ACE2, there was no difference in T-cell responses.
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in November 2021 by scientists in South Africa. The variant contains >50 mutations, including 33 in the spike protein, and studies show that this results in evasion of vaccine-elicited neutralizing antibodies [1]. However, less is known about how these mutations impact the T-cell response to the virus. We compared antibody and T-cell responses to the vaccine strain and Omicron variant spike proteins in 15 messenger RNA (mRNA) vaccine recipients (VRs). Our data may partially explain the clinical outcomes seen in VRs with breakthrough Omicron variant infection.
METHODS
We obtained blood from 15 VRs (7 men, 8 women) after informed consent was obtained. The study was approved by the Johns Hopkins University institutional review board. Eleven VRs received the Pfizer-BioNTech (BNT162b2) vaccine with a homologous booster, 1 VR received BNT162b2 followed by the Moderna (mRNA-1273) vaccine, and 1 VR received mRNA-1273 followed by a homologous booster vaccine. The other 2 VRs received 2 doses of BNT162b2 without a booster vaccine.
Twelve of the VRs were 21–30 years old, 1 was 41–50 years old, and 2 were 51–60 years old. Informed consent was obtained from all study participants. Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using Ficoll centrifugation. mRNA for the nucleocapsid protein is not included in vaccines, so natural infection was ruled out by screening for T-cell responses to a pool of 57 nucleocapsid peptides at a concentration of 10 μg/mL (BEI, Manassas, Virginia). To measure the ability of participant plasma to inhibit ACE2 binding to spike proteins from the vaccine strain and multiple variants of concern, we used the Meso Scale Discoveries pseudoneutralization/ACE2 inhibition assay (Rockville, Maryland). The percentage inhibition of ACE2 binding measured with this assay correlates well with the results of culture-based neutralization assays [2]. The assay was performed with plasma diluted at 1:100 as previously described [2]. We determined cellular immunity to the SARS-CoV-2 spike protein by performing an interferon gamma (IFN-γ) enzyme-linked immunosorbent spot assay with unfractionated PBMCs as previously described [3]. The assay was also performed with CD8+ T-cell–depleted PBMCs to determine the relative contribution of CD4+ T cells and CD8+ T cells to the total T-cell response. CD8+ T cells were removed by positive selection with CD8 MicroBeads (Miltenyi Biotec, Gaithersburg, Maryland). This process typically removes >90% of CD8+ T cells as determined by flow cytometry. To compare recognition of spike proteins from the vaccine strain and the Omicron variant, we stimulated PBMCs with overlapping spike peptide pools from both viruses at a concentration of 1 μg/mL (JPT, Berlin, Germany). Both spike peptide pools were made up of 315 peptides that were mostly 15 amino acids long with an overlap of 11 amino acids. Statistical comparisons were done using GraphPad Prism 9.2.0. Comparisons were made with 1-way analysis of variance with Geisser-Greenhouse correction; Dunnett multiple comparison test was done, with individual variances computed for each comparison. P values < .05 were considered significant.
RESULTS
Vaccine recipient plasma contained significantly lower levels of antibodies that inhibited the binding of ACE2 to spike proteins from the Alpha, Beta, Delta, and Omicron variants than to the vaccine strain spike protein. ACE2 binding to the Omicron spike protein was least inhibited by the VR plasma (Figure 1A).
Antibody and T-cell responses to vaccine strain and Omicron variant spike proteins. A, The level of antibodies that inhibit ACE2 binding to spike are shown for the vaccine strain and different variants of concern. The number of spot-forming units (SFU) per million cells generated in response to stimulation with vaccine strain or Omicron variant spike peptides or nucleocapsid peptides (S2N) is shown for unfractionated peripheral blood mononuclear cells (PBMCs) (B) and CD8-depleted PBMCs (C). Horizontal bars represent the median value. The frequency of SFU per million cells generated in response to stimulation with the vaccine strain spike peptides is compared to the frequency of SFU per million cells generated in response to Omicron variant spike peptides for PBMCs (D) and CD8-depleted PBMCs (E). The hexagon and square represent 2 vaccine recipients (VRs) who received 2 vaccine shots but not a booster. The triangle represents the VR who received 3 messenger RNA (mRNA) 1273 shots and the diamond represents the VR who received 2 BNT162b vaccines and an mRNA 1273 booster. ** P = .0021; *** P = .0002; ****<.0001. Not significant (ns): P = .1234.
In contrast, the VRs made robust T-cell responses to peptide pools from both vaccine strain and Omicron spike proteins (Figure 1B). Interestingly, depletion of CD8+ T cells did not result in a significant decrease in the total T-cell response to both sets of spike peptides, implying that CD4+ T cells were the major producers of IFN-γ in the assay (Figure 1C). There was a strong correlation between T-cell responses to spike peptides from the vaccine strain and from the omicron variant with both total (Figure 1D) and CD8-depleted T cells (Figure 1E), suggesting cross-recognition of epitopes in both proteins. None of the VRs had T-cell responses to nucleocapsid peptides, supporting the absence of prior infection.
DISCUSSION
In this study, we extended the results of previous studies on the ability of vaccine-generated antibodies to block ACE2 binding by comparing antibody and T-cell responses in mRNA VRs. We found lower inhibition of binding of ACE2 to the Omicron spike protein vs vaccine strain, consistent with prior studies [1]. Despite discordant antibody responses, T cells from the vaccine recipients made comparably robust responses to overlapping peptides from vaccine and Omicron proteins. While prior studies have concluded that T cells induced by infection [4] and vaccination demonstrate recognition of prior variants [3, 5] and Omicron [6–9], we extend these findings by comparing these responses to functional antibody responses in the same individuals. We confirm T-cell cross-recognition of the Omicron variant and extend the findings by directly comparing these responses to functional antibody responses in the same individuals. Similar results have been recently reported by 2 other groups [10, 11]. Despite the large number of mutations present in the Omicron variant, the correlation between T-cell responses to the vaccine strain and Omicron variant spike proteins supports cross-recognition of epitopes. This lack of significant T-cell escape by Omicron and prior variants is most likely due to the fact that mRNA vaccines induce broad T-cell responses that target many different epitopes in the spike protein [3, 5, 9, 12]. These broad mRNA vaccine–elicited T-cell responses will likely be effective against future variants of concern that evade antibody responses.
Notes
Acknowledgments. The authors thank the study participants as well as Christopher Thoburn and Jennifer Gizzi of the Bloomberg Flow Cytometry and Immunology Core.
Financial support. This work was supported by the Johns Hopkins COVID-19 Vaccine-Related Research Fund and by awards from the National Cancer Institute (award number U54CA260492) and the National Institute of Allergy and Infectious Diseases (grant numbers K08AI156021 and U01AI138897).
References
Author notes
B. A. W. and C. C. G. contributed equally to this work.
Potential conflicts of interest. A. L. C. reports support from the National Institutes of Health for the present manuscript and outside of the submitted work and consulting fees from Janssen paid to hepatitis B virus cure strategies. A. H. K. reports consulting fees from Roche. All other authors report no potential conflicts of interest.
All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.
