T-cell responses induced by SARS-CoV-2 index-virus nanoparticle protein vaccine to the ancestral and omicron variants 6 months following primary vaccination

Abstract

Background: The SARS-CoV-2 index-virus nanoparticle protein vaccine (NVX-CoV2373) induces humoral and cell-mediated immune responses that protect against severe COVID-19, including from SARS-CoV-2 variants. Limited information exists on NVX-CoV2373-induced cell-mediated immune responses to ancestral SARS-CoV-2 and the Omicron variant following a homologous booster (third dose), and on T-cell responses following a booster dose compared to a single dose.

Methods: T-cell responses were investigated in participants from a randomised, placebo-controlled, phase 2A/2B trial of NVX-CoV2373 in South Africa, who had a blinded crossover at 6 months post-enrolment. Peripheral blood mononuclear cells were available for 34 participants, 7 days post-vaccination with one NVX-CoV2373 dose (n = 17) or a homologous booster (n = 17). T-cell responses to the full-length spike (FLS) glycoprotein of ancestral Wuhan-Hu-1 SARS-CoV-2 and mutated spike protein regions found in Omicron (BA.4/BA.5) were characterised by intracellular cytokine staining.

Results: Here we show that FLS-specific T-cell responses are similar between single-dose and booster-dose recipients (CD4⁺: p = 0.871; CD8⁺: p = 0.491) and are predominantly monofunctional (IFN-γ or TNF-α). A third NVX-CoV2373 dose increases the FLS-specific polyfunctional cytokine production profile of CD4⁺ T cells compared with after a single dose (p = 0.045), whereas CD8⁺ T cells remain unaffected (p = 0.462). Only CD4⁺ T cells exhibit reduced reactivity to Omicron compared with ancestral SARS-CoV-2 in single-dose (p = 0.010) and in booster-dose recipients (p = 0.028).

Conclusions: NVX-CoV2373-induced T-cell responses to ancestral SARS-CoV-2 are comparable following vaccination with a single dose compared with a third dose administered 6 months after the second dose. Our findings suggest that an NVX-CoV2373 booster dose does not enhance T-cell immunity. Furthermore, NVX-CoV2373 vaccination induces greater T-cell response magnitudes to ancestral SARS-CoV-2, from which the vaccine is derived, compared with the Omicron variant.

Fig. 1. T-cell responses to full-length spike glycoprotein of ancestral SARS-CoV-2 and responder profiles among single- and booster-dose NVX-CoV2373 recipients.

a The proportion of CD4⁺ and CD8⁺ T cells producing any of the cytokines (IFN-γ, IL-2, or TNF-α) in response to the FLS protein of ancestral SARS-CoV-2. This includes T cells producing these cytokines either individually or in various combinations. Each participant is represented by an individual point, and medians in each group are represented by horizontal lines. Positive responders were defined by T-cell response values ≥ 0.02% (i.e., the threshold). Non-responders were defined by T-cell response values < 0.02% and were graphically represented with a value of 0.015%. b Responder profiles of each single- and booster-dose NVX-CoV2373 recipient. Responders were categorised as low, medium, or high responders, having T-cell responses between 0.02–0.49%, 0.50–1.49%, and ≥ 1.50%, respectively. c Summaries of CD4⁺ and CD8⁺ T-cell responder profiles in each treatment group, expressed as percentages. Statistical analyses were performed using the Mann–Whitney U-test and Wilcoxon signed-rank test for T-cell response comparisons between unpaired (Group-1 vs. Group-2) and paired (CD4⁺ vs. CD8⁺) groups, respectively. Pearson’s chi-squared test was used for comparing responder profiles. Denotations: FLS, full-length spike glycoprotein; IFN-γ, interferon gamma; IL-2, interleukin 2; TNF-α, tumour necrosis factor alpha.

Fig. 2. Polyfunctionality of CD4⁺ and CD8⁺ T cells to full-length spike glycoprotein of ancestral SARS-CoV-2 among single- and booster-dose NVXCoV2373 recipients.

a Comparisons of the polyfunctionality profiles of CD4⁺ and CD8⁺ T cells to the FLS protein of ancestral SARS-CoV-2 in recipients of a homologous NVX-CoV2373 booster dose (Group-1; n = 17; dark blue) and single-dose recipients (Group-2; n = 17; light blue). Each participant is represented by an individual point, and medians in each group are represented by horizontal lines. b Each polyfunctional response pattern is colour-coded, and response data are summarised in pie charts with overarching legends corresponding to cytokine production. The Mann–Whitney U-test was used for comparing unpaired CD4⁺ and CD8⁺ T-cell responses of positive responders between Group-1 and Group-2. Differences in overall polyfunctional T-cell response profiles were determined by a permutation test with 10,000 iterations. Significant P-values are indicated in bold (p < 0.05). Denotations: IFN-γ, interferon gamma; IL-2, interleukin 2; TNF-α, tumour necrosis factor alpha.

Fig. 3. T-cell responses to partial spike proteins of ancestral SARS-CoV-2 and the Omicron variant (BA.4/BA.5) among single- and booster-dose NVX-CoV2373 recipients.

The proportion of spike-specific a CD4⁺ and c CD8⁺ T cells producing any of the cytokines (IFN-γ, IL-2, or TNF-α) in response to peptide pools representing partial ancestral and Omicron spike proteins. This includes T cells producing these cytokines either individually or in various combinations. Each participant is represented by an individual point, and medians in each group are represented by horizontal lines. The fold change in spike-specific b CD4⁺ and d CD8⁺ T-cell responses. Ratios equal to 1.0 indicate equal responses to ancestral SARS-CoV-2 and the Omicron variant. Ratios below 1.0 indicate greater responses to ancestral SARS-CoV-2 compared to the Omicron variant. Ratios above 1.0 indicate greater responses to the Omicron variant compared to ancestral SARS-CoV-2. The threshold area between 0.5 and 1.5 is indicated in grey and represents similar responses to ancestral SARS-CoV-2 and the Omicron variant. Statistical analyses were performed using the Mann–Whitney U-test and Wilcoxon signed-rank test for comparisons between unpaired (Group-1 vs. Group-2) and paired (ancestral SARS-CoV-2 vs. Omicron; CD4⁺ vs. CD8⁺) T-cell responses and fold changes, respectively. Significant P-values are indicated in bold (p < 0.05). Denotations: IFN-γ, interferon gamma; IL-2, interleukin 2; TNF-α, tumour necrosis factor alpha.