A multitope SARS-CoV-2 vaccine provides long-lasting B cell and T cell immunity against Delta and Omicron variants

Abstract

BackgroundThe Delta and Omicron variants of SARS-CoV-2 are currently responsible for breakthrough infections due to waning immunity. We report phase I/II trial results of UB-612, a multitope subunit vaccine containing S1-RBD-sFc protein and rationally designed promiscuous peptides representing sarbecovirus conserved helper T cell and cytotoxic T lymphocyte epitopes on the nucleocapsid (N), membrane (M), and spike (S2) proteins.MethodWe conducted a phase I primary 2-dose (28 days apart) trial of 10, 30, or 100 μg UB-612 in 60 healthy young adults 20 to 55 years old, and 50 of them were boosted with 100 μg of UB-612 approximately 7 to 9 months after the second dose. A separate placebo-controlled and randomized phase II study was conducted with 2 doses of 100 μg of UB-612 (n = 3,875, 18-85 years old). We evaluated interim safety and immunogenicity of phase I until 14 days after the third (booster) dose and of phase II until 28 days after the second dose.ResultsNo vaccine-related serious adverse events were recorded. The most common solicited adverse events were injection site pain and fatigue, mostly mild and transient. In both trials, UB-612 elicited respective neutralizing antibody titers similar to a panel of human convalescent sera. The most striking findings were long-lasting virus-neutralizing antibodies and broad T cell immunity against SARS-CoV-2 variants of concern (VoCs), including Delta and Omicron, and a strong booster-recalled memory immunity with high cross-reactive neutralizing titers against the Delta and Omicron VoCs.ConclusionUB-612 has presented a favorable safety profile, potent booster effect against VoCs, and long-lasting B and broad T cell immunity that warrants further development for both primary immunization and heterologous boosting of other COVID-19 vaccines.Trial RegistrationClinicalTrials.gov: NCT04545749, NCT04773067, and NCT04967742.FundingUBI Asia, Vaxxinity Inc., and Taiwan Centers for Disease Control, Ministry of Health and Welfare.

Keywords: COVID-19; Peptides.

Figure 1. Flow of the UB-612 phase I trial primary 2-dose series with extended booster third-dose study and characteristics of study participants.

(A and B) Sixty healthy young adults, male and female, 20 to 55 years old were enrolled for the primary series of the open-label, 196-day phase I study of UB-612 (NCT04545749), conducted between September 21, 2020 and May 24, 2021. They were administered intramuscularly with 2 vaccine doses at 10, 30, or 100 μg. All but one participant completed the study. The extension study (NCT04967742) that involved 50 enrollees was conducted from days 255 to 316, a time period over 6 months after the second vaccine shot. The 50 participants in the 10 μg (n = 17), 30 μg (n = 15), and 100 μg (n = 18) dose groups received a booster UB-612 dose of 100 μg and were followed up for 14 days for interim evaluation. They were monitored until 84 days after booster.

Figure 2. Flow of the UB-612 phase II study and characteristics of study participants.

(A and B) The phase II trial (NCT04773067) was conducted between February 26, 2021 and April 16, 2021, and enrolled a total of 3,875 participants (18–85 years old) to receive 100 μg UB-612 (3,321 on 100 μg UB-612 and 554 on placebo at a 6:1 ratio).

Figure 3. In phase I trial of primary and booster series, selected solicited local and systemic reactions within 7 days of each vaccination recorded for the 3 different doses of UB-612 vaccine.

Both local and systemic reactions are shown as the percentage of participants who reported grade 1 (mild; yellow) or grade 2 (moderate, orange) for (A) local and (B) systemic adverse reactions. For dose 1 and dose 2, there were 20 participants in each dose group receiving 2 doses of UB-612 at 10, 30, or 100 μg. For the booster dose 3 at 100 μg, there were 17, 15, and 18 participants who originally were assigned to the 10, 30, and 100 μg dose groups, respectively.

Figure 4. Incidence of adverse effects in the phase II interim data analysis.

(A) Solicited local adverse reaction within 7 days after each vaccination. (B) Skin allergic reaction within 14 days after each vaccination. (C) Solicited systemic adverse reaction events 7 days after each vaccination.

Figure 5. In the phase II trial, virus-neutralizing titer (VNT₅₀) against live SARS-CoV-2 WT after the primary 2-dose vaccination and the booster third dose.

In the primary 2-dose vaccination series of the 196-day phase I UB-612 trial, 60 participants were enrolled for the 10 μg, 30 μg, and 100 μg dose groups (n = 20 per group), of which 50 participants were enrolled for the extension study and received a booster third dose at 100 μg (n = 17 for the 10 μg; n = 15 for the 30 μg, and n = 18 for the 100 μg dose group). The virus-neutralizing antibody geometric mean titers (GMT, 95% CI) that inhibit 50% of live SARS-CoV-2 WT were measured and expressed as VNT₅₀ for the (A) 10 μg, (B) 30 μg, and (C) 100 μg dose groups. (D) Illustrated with the 100 μg dose group, the VNT₅₀ data were recorded on day 0 (before dose 1), day 14 (14 days after dose 1), day 28 (1 month after dose 1, before dose 2), day 42 (14 days after dose 2), day 56 (1 month after dose 2), day 112 (3 months after dose 2), day 196 (6 months after dose 2), days 255 to 316 before dose 3, the pre-booster, average day 286), and days 269 to 330 (14 days after booster, average day 300) for study participants of the 3 dose groups. The international unit (IU/mL) corresponding to 50% neutralizing GMT and 95% CI (VNT₅₀) is shown in Supplemental Figure 3. The titers for individual participants are shown by the circles. The horizontal dotted lines indicate the lower limit of quantification. HCS, human convalescent serum samples in the control group (n = 20).

Figure 6. In the phase I trial, UB-612 booster third-dose produced potent neutralizing titers against SARS-CoV-2 WT, Delta, Omicron, and other VoCs, and the virus-neutralizing antibodies were long-lasting as revealed with the live WT virus.

The primary 2-dose series (days 0 and 28) of the 196-day phase I trial and the extended booster third dose of 100 μg administered on mean day 286 (days 255–316). (A) In the participants of the 100 μg group, the VNT₅₀ observed 14 days after booster reached 3,992 against live SARS-CoV-2 WT and 2,358 against live Delta. Similar high anti-WT and anti-Delta VNT₅₀ levels were observed for the lower 30 and 10 μg dose groups. (B) In the participants of the 100 μg group, the pVNT₅₀ observed 14 days after booster against pseudo-SARS-CoV-2 WT and against pseudo-SARS-CoV-2 variants, including Omicron. (C) Antibody persistence after 2 doses (phase I trial): The anti-WT neutralizing VNT₅₀ decayed slowly, with a t_1/2 of 187 days, based on the first-order exponential model fitting (SigmaPlot) over days 42–196 (r² = 0.9877; the decay rate constant K_el = –0.0037; t_1/2 = 0.693/K_el).

Figure 7. In the phase II trial primary 2-dose series, neutralizing antibody titers (VNT₅₀) against SARS-CoV-2 variants.

(A) Measurement of VNT₅₀ against live SARS-CoV-2 virus variants in day 57 immune sera randomly selected from 48 vaccinees (n = 39 for young adults 18–65 years old; n = 9 for elderly adults ≥65 years old) who received 2 UB-612 vaccine doses in the phase II trial. Live WT SARS-CoV-2-TCDC#4 and USA WA1/2020, and 2 VoCs (B.1.1.7 and B.1.617.2 lineages) listed by WHO, were employed for CPE assays. The VNT₅₀ values are marked on top of each column, with 95% CIs shown as horizontal bars. (B) The fold change (reduction) in VNT₅₀ against each of the variants compared with WT strains Wuhan and USA WA1/2020 by the 2-sample t test. **P < 0.01; ****P < 0.0001. The 2.7- and 1.4-fold reductions also indicate 37% and 72% preservation of neutralization titers relative to the 2 WT strains isolated from 2 separate geographic locations where CPE assays were performed. Sinica, Academia Sinica, Taiwan; CDPH, California Department of Public Health.

Figure 8. Inhibition titers against S1-RBD–ACE2 binding by ELISA in the primary 2-dose vaccination and after the booster third dose.

ELISA-based neutralization (inhibition) of S1-RBD–ACE2 binding titers in the primary 2-dose vaccination series of a 196-day phase I trial (60 participants) and in the extension study with a booster third dose. Participants of (A) 10 μg, (B) 30 μg, and (C) 100 μg dose groups (n = 20 per dose group) received 2 assigned vaccine doses, 28 days apart, and a booster third dose of 100 μg at a time over 6 months administered to 50 participants (n = 17 for the 10 μg, n = 15 for the 30 μg, and n = 18 for the 100 μg dose groups). Serum samples were collected at the indicted time points for measuring the inhibition titers against S1-RBD binding to ACE2 by ELISA. The horizontal dotted lines indicate the lower limit of quantification. (D) Good correlation was found between S1-RBD–ACE2 binding inhibition and VNT₅₀. Data are plotted for all prime/boost vaccinated participants (10, 30, and 100 μg dose groups). Data points for participants on day 0 were excluded from correlation analysis. Correlation analyzed by nonparametric Spearman’s correlation method.

Figure 9. UB-612–induced long-lasting, robust Th1-predominant cell response measured by IFN-γ and IL-4 ELISpot after restimulation of PBMCs with designer peptide antigens.

In the 196-day phase I trial with 2 UB-612 doses on days 0 and 28, vaccine-induced T cell responses were measured by IFN-γ ELISpot with PBMCs from young adults (20–55 years old) in (A) 10, (B) 30, or (C) 100 μg dose group (n = 20 each). In the phase II trial study, participants (younger adults, 18–65 years old) received 2 doses of UB-612 at 100 μg (n = 88) or saline placebo (n = 12), and T cell responses in PBMCs of vaccinees on day 57 restimulated with designer antigen protein/peptides were measured by (D) IFN-γ and (E) IL-4 ELISpot. Shown are spot-forming units (SFU) per 1 × 10⁶ PBMCs producing IFN-γ and IL-4 after stimulation with S1-RBD plus Th/CTL peptide pool, Th/CTL peptide pool, or SARS-CoV-2 T peptides (Th/CTL peptide pool without UBITh1a). Statistical analysis was performed with the use of the 2-sample t test. ****P < 0.0001.

Figure 10. In phase II primary 2-dose vaccination series, UB-612–induced Th1-predominant T cell responses (CD4⁺ and CD8⁺) measured by IFN-γ and IL-4 ICS after restimulation of PBMCs with designer peptide antigens.

In a phase II trial, study participants (younger adults 18–65 years old) receiving 2 doses (28 days apart) of UB-612 at 100 μg (n = 88) or saline placebo (n = 12). Their PBMCs harvested on days 1 and 57 (4 weeks after the second shot) were restimulated with designer antigen protein/peptides to evaluate T cell responses by intracellular cytokine staining (ICS). Frequencies of CD4⁺ and CD8⁺ T cells that produce indicated cytokines in response to the stimulation of (A) S1-RBD plus Th/CTL peptide pool, (B) Th/CTL peptide pool, and (C) SARS-CoV-2 T peptides (Th/CTL peptide pool without UBITh1a). Statistical analysis was performed using the Mann-Whitney t test. *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001. NS, not significant.