Trial design and oversight. Safety and immunogenicity of UB-612 vaccine were evaluated in an open-label phase-1 study, conducted at China Medical University Hospital, Taiwan [ClinicalTrials.gov: NCT04545749] and an 84-day extension study to evaluate a 3rd booster dose [ClinicalTrials.gov: NCT04967742] (Fig. 1; Table 1). The primary-series 196-day Phase-1 study enrolled 60 healthy adults aged 20-55 years, who received two intramuscular (IM) injections (28 days apart) of 10-, 30- or 100-μg (N = 20/group). Seven to nine months following completion of the primary series, 50 participants were enrolled in the extension study to receive a booster-dose of 100 mg UB-612, with an interim analysis at 14 days and were also monitoring until 84 days post-booster.
The Principal Investigators at the study sites agreed to conduct the study according to the specifics of the study protocol and the principles of Good Clinical Practice (GCP); and all the authors assured accuracy and completeness of the data and analyses presented. The protocols were approved by the ethics committee at the site and all participants provided written informed consent. Full details of the trial design, inclusion and exclusion criteria, conduct, oversight, and statistical analyses are available in the study protocols.
Trial procedures and safety. The phase-1 trial was initiated with a sentinel group of 6 participants to receive the low 10-μg dose, followed with the remaining 14 participants if without vaccine-related ≥ grade 3 adverse reaction. The same procedure was extended for the escalating 30- and 100-μg dose groups. Additional follow-up visits were scheduled for all participants on Days 14, 28, 35, 42, 56, 112, and 196. Study participants were scheduled for visits 14 and 84 days after the booster. Electronic diaries were provided to the participants to be completed for the 7-day period after each injection to record solicited local reactions at the injection site (pain, induration/swelling, rash/redness, itch, and cellulitis) and solicited systemic reactions (17 varied constitutional symptoms). Severity was graded using a 5-level (0 to 4) scale from none to life-threatening. In addition, participants recorded their axillary temperature every evening starting on the day of the vaccination and for the 6 subsequent days. Complete details for solicited reactions are provided in the study protocols [Supplementary Appendix].
Vaccine product. UB-612 is a multitope vaccine to activate both humoral and cellular responses (Supplementary Fig. 1). For SARS-CoV-2 immunogens, UB-612 combines a CHO-expressed S1-RBD-sFc fusion protein (Wuhan strain) and a mixture of synthetic T helper (Th) and cytotoxic T lymphocyte (CTL) epitope peptides, which are selected from immunodominant M, S2 and N regions known to bind to human major histocompatibility complexes (MHC) I and II. This mixture of Th/CTL peptides is designed to elicit T cell activation, memory recall, and effector functions similar to that of natural infection with SARS-CoV-2. The S1-RBD-sFc fusion protein incorporates both linear and conformational epitopes and induces neutralizing antibodies. The two immunogen components are formulated with CpG1, a proprietary oligonucleotide (ODN). The vaccine product contained small amount of CpG1 at ≦2 mg, which is not likely high enough to serve as an immunostimulatory agents. Instead the CpG acts as an excipient to bind the peptide components through dipolar charge interactions into an immunostimulatory complex. The protein-pepide complex is then adsorbed to aluminum phosphate (Adju-Phos®) adjuvant, which promotes the activation of antigen-presenting cell pathways to induce an optimal immunogenicity profile intended to prevent infection with SARS‑CoV‑2. The UB-612 vaccine product is stored at 2 to 8 oC.
Immunogenicity. The primary immunogenicity endpoints were the geometric mean titers (GMT) of neutralizing antibodies against SARS-CoV-2 wild-type (Wuhan strain), and post-booster effects against Delta variant were explored as well. Viral-neutralizing antibody titers that neutralize 50% (VNT50) of live SARS-CoV-2 wild-type (WT) and Delta variant were measured by a cytopathic effect (CPE)-based assay using Vero-E6 (ATCC® CRL-1586) cells challenged with SARS-CoV-2-Taiwan-CDC#4 (Wuhan strain) and SARS-CoV-2-Taiwan-CDC#1144 (B.1.617.2; Delta variant). The replicating virus neutralization test conducted at Academia Sinica was fully validated using internal reference controls and results expressed as VNT50. The WHO reference standard was also employed and results reported in international units (IU/mL).
The secondary immunogenicity endpoints include binding IgG antibody responses to S1-RBD, inhibitory titers against S1-RBD:ACE2 interaction, and T-cell responses assayed by ELISpot and Intracellular Cytokine Staining (ICS). The RBD IgG ELISA was fully validated using internal reference controls and results expressed in end-point titers. The WHO reference standard was also employed and results reported in Binding Antibody Units (BAU/mL). The RBD IgG ELISA was fully validated using internal reference controls and results expressed in end-point titers. A panel of 20 human convalescent serum samples from COVID-19 Taiwan hospitalized patients aged 20 to 55 years were also tested for comparison with those in the vaccinees. Human peripheral blood mononuclear cells (PBMCs) were used for monitoring T cell responses. All bioassay methods are detailed below.
Viral-neutralizing antibody titers against SARS-CoV-2 wild-type and variants. Neutralizing antibody titers were measured by CPE-based live virus neutralization assay using Vero-E6 cells challenged with wild type (SARS-CoV-2-Taiwan-CDC#4, Wuhan and SARS-CoV-2-USA WA 1/2020) and Delta variant (SARS-CoV-2-Taiwan-CDC#1144, B.1.617.2), which was conducted in P3 lab at Academia Sinica, Taiwan. Vero-E6 (ATCC® CRL-1586) cells were cultured in DMEM (Hyclone) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1x Penicillin-Streptomycin solution (Thermo) in a humidified atmosphere with 5% CO2 at 37°C. The 96-well microtiter plates are seeded with 1.5×104 cells/100 μL/well. Plates are incubated at 37o C in a CO2 incubator overnight. The next day tested sera were heated at 56 °C for 30 min to inactivate complement, and then diluted in DMEM (supplemented with 2% FBS and 1x Penicillin/Streptomycin). Serial 2-fold dilutions of sera were carried out for the dilutions. Fifty μL of diluted sera were mixed with an equal volume of virus (100 TCID50) and incubated at 37°C for 1 hr. After removing the overnight culture medium, 100 μL of the sera-virus mixtures were inoculated onto a confluent monolayer of Vero-E6 cells in 96-well plates in triplicate. After incubation for 4 days at 37 °C with 5% CO2, the cells were fixed with 10% formaldehyde and stained with 0.5% crystal violet staining solution at room temperature for 20 min. Individual wells were scored for CPE as having a binary outcome of ‘infection” or ‘no infection’. Determination of SARS-CoV-2 virus specific neutralization titer was to measure the neutralizing antibody titer against SARS-CoV-2 virus based on the principle of VNT50 titer (≥50% reduction of virus-induced cytopathic effects). Virus neutralization titer of a serum was defined as the reciprocal of the highest serum dilution at which 50% reduction in cytopathic effects are observed and results are calculated by the method of Reed and Muench. In seroconversion detected by live virus neutralization test, it was defined as a 4-fold change in antibody titer from baseline.
In a separate study with D614G, Alpha B.1.1.7, Gamma P.1, Beta B.1.351, and Delta B.1.617.2, the CPE assay was conducted at Viral and Rickettsial Disease Laboratory, State of California Department of Public Health USA. Neutralizing antibody titers were measured by CPE-based live virus neutralization assay using cells challenged with SARS-CoV-2 variants. The study was conducted in BSL3 lab at Viral and Rickettsial Disease Laboratory (VRDL), California State Department of Public Health (CDPH), USA. SARS-CoV-2 virus specific neutralization against SARS-CoV-2 variants titers were measured by in vitro microneutralization assay using Vero-81cells challenged with SARS-CoV-2 variants. Vero-81 were cultured with MEM supplemented with 1x penicillin-streptomycin (Gibco) and glutamine (Gibco) and 5% Fetal calf serum (Hyclone). Determination of SARS-CoV-2 virus specific neutralization titer was to measure the neutralizing antibody titer against the viruses based on the principle of VNT50 titer (≥50% reduction of virus-induced cytopathic effects). Virus neutralization titer of a serum was defined as the reciprocal of the highest serum dilution at which 50% reduction in cytopathic effects. In seroconversion detected by live virus neutralization test, it was defined as a 4-fold change in antibody titer from baseline.
Inhibition of S1-RBD binding to ACE2 by ELISA. The 96-well ELISA plates are coated with 2 µg/mL ACE2-ECD-Fc antigen (100 mL/well in coating buffer, 0.1M sodium carbonate, pH 9.6) and incubated overnight (16 to 18 hr) at 4 °C. Plates are washed 6 times with Wash Buffer (25-fold solution of phosphate buffered saline, pH 7.0-7.4 with 0.05% Tween 20, 250 μL/well/wash) using an Automatic Microplate Washer. Extra binding sites are blocked by 200 μL/well of blocking solution (5 N HCl, Sucrose, Triton X-100, Casein, and Trizma Base). Five-fold dilutions of immune serum or a positive control (diluted in a buffered salt solution containing carrier proteins and preservatives) are mixed with 1:100 dilution of S1-RBD-HRP conjugate (horseradish peroxidase-conjugated recombinant protein S1-RBD-His), incubated for 30±2 min at 25±2 °C, washed and TMB substrate (3,3’,5,5’-tetramethylbenzidine diluted in citrate buffer containing hydrogen peroxide) is added. Reaction is stopped by stop solution (diluted sulfuric acid, H2SO4, solution, 1.0 M) and the absorbance of each well is read at 450nm within 10 min using the Microplate reader (VersaMax). Calibration standards for quantitation ranged from 0.16 to 2.5 μg/mL. Samples with titer value ran below 0.16 μg/mL was defined as half of detection limit. Samples with titer exceed 2.5 μg/mL were further diluted for reanalysis.
Anti-S1-RBD binding IgG antibody by ELISA. The 96-well ELISA plates were coated with 2 µg/mL recombinant S1-RBD-His protein antigen (100 µL/well in coating buffer, 0.1 M sodium carbonate, pH 9.6) and incubated overnight (16 to 18 hr) at 4 °C. One hundred μL/well of serially diluted serum samples (diluted from 1:20, 1:1,000, 1:10,000 and 1:100,000, total 4 dilutions) in 2 replicates were added and plates are incubated at 37 °C for 1 hr. The plates are washed six times with 200 μL Wash Buffer (PBS-0.05% Tween 20, pH 7.4). Bound antibodies were detected with HRP-rProtein A/G at 37 oC for 30 min, followed by six washes. Finally, 100 μL/well of TMB (3,3’,5,5’-tetramethylbenzidine) prepared in Substrate Working Solution (citrate buffer containing hydrogen peroxide) was added and incubated at 37 oC for 15 min in the dark, and the reaction stopped by adding 100 μL/well of H2SO4, 1.0 M. Sample color developed was measured on ELISA plate reader (Molecular Device, SpectraMax M2e). UBI® EIA Titer Calculation Program was used to calculate the relative titer. The anti-S1-RBD antibody level is expressed as Log10 of an end point dilution for a test sample (SoftMax Pro 6.5, Quadratic fitting curve, Cut-off value 0.5).
T cell responses by ELISPOT. Human peripheral blood mononuclear cells (PBMCs) were used in the detection of T cell response. For the primary-series 196-day Phase 1 study, antigen-specific interferon-gamma (IFN-γ) measurement to assess cellular (T cell) immune response were measured by ELISpot method by using human IFN-γ ELISpotPLUS kit (ALP) (MABTECH). For the booster-series third-dose series extension study, ELISpot assays were performed using the human IFN-γ/IL-4 FluoroSpotPLUS kit (MABTECH). Aliquots of 250,000 PBMCs were plated into each well and stimulated, respectively, with pools of S1-RBD+Th/CTL, Th/CTL, or Th/CTL pool without UBITh1a (CoV2 peptides), and cultured in culture medium alone as negative controls for each plate for 24 hours at 37 °C with 5% CO2. The analysis was conducted according to the manufacturer’s instructions. Spot-forming unit (SFU) per million cells was calculated by subtracting the negative control wells.
Intracellular Cytokine Staining (ICS). Intracellular cytokine staining and flow cytometry was used to evaluate CD4+ and CD8+ T cell responses. PBMCs were stimulated, respectively, with S1-RBD-His recombinant protein plus with Th/CTL peptide pool, Th/CTL peptide pool only, CoV2 peptides, PMA + Inonmycin (as positive controls), or cultured in culture medium alone as negative controls for 6 hours at 37°C with 5% CO2. Following stimulation, cells were washed and stained with viability dye for 20 minutes at room temperature, followed by surface stain for 20 minutes at room temperature, cell fixation and permeabilization with BD cytofix/cytoperm kit (Catalog # 554714) for 20 minutes at room temperature, and then intracellular stain for 20 minutes at room temperature. Intracellular cytokine staining of IFN-γ, IL-2 and IL-4 was used to evaluate CD4+ T cell response. Intracellular cytokine staining of IFN-γ, IL-2, CD107a and Granzyme B was used to evaluate CD8+ T cell response. Upon completion of staining, cells were analyzed in a FACSCanto II flow cytometry (BD Biosciences) using BD FACSDiva software.
Statistics. As the studies were not powered for formal statistical comparisons of between-dose and between-phase vaccination, we report descriptive results of safety and immunogenicity. Immunogenicity results for GMT in titer are presented with the associated 95% confidence intervals. Seroconversion is defined as ≥ 4-fold increase in antibody titers from baseline. Statistical analyses were performed using SAS® Version 9.4 (SAS Institute, Cary, NC, USA) or Wilcoxon sign rank test. Spearman correlation was used to evaluate the monotonic relationship between non-normally distributed data sets. The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment.