UB-612, a Multitope Universal Vaccine Eliciting a Balanced B and T Cell Immunity against SARS-CoV-2 Variants of Concern

  1. Chang Yi Wang
  2. Kao-Pin Hwang
  3. Hui-Kai Kuo
  4. Be-Sheng Kuo
  5. Hope Liu
  6. Kuo-Liang Hou
  7. Wan-Yu Tsai
  8. Han-Chen Chiu
  9. Yu-Hsin Ho
  10. Jennifer Cheng
  11. Min-Sheng Wang
  12. Ya-Ting Yang
  13. Po-Yen Chang
  14. Yea-Huei Shen
  15. Wen-Jiun Peng

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Abstract

Importance

The SARS-CoV-2 non-spike structural proteins of nucleocapsid (N), membrane (M) and envelope (E) are critical in the host cell interferon response and memory T-cell immunity and have been grossly overlooked in the development of COVID vaccines.

Objective

To determine the safety and immunogenicity of UB-612, a multitope vaccine containing S1-RBD-sFc protein and rationally-designed promiscuous peptides representing sequence-conserved Th and CTL epitopes on the Sarbecovirus nucleocapsid (N), membrane (M) and spike (S2) proteins.

Design, setting and participants

UB-612 booster vaccination was conducted in Taiwan. A UB-612 booster dose was administered 6-8 months post-2 nd dose in 1,478 vaccinees from 3,844 healthy participants (aged 18-85 years) who completed a prior placebo (saline)-controlled, randomized, observer-blind, multi-center Phase-2 primary 2-dose series (100-μg per dose; 28-day apart) of UB-612. The interim safety and immunogenicity were evaluated until 14 days post-booster.

Exposure

Vaccination with a booster 3 rd -dose (100-μg) of UB-612 vaccine.

Main outcomes and measures

Solicited local and systemic AEs were recorded for seven days in the e-diaries of study participants, while skin allergic reactions were recorded for fourteen days. The primary immunogenicity endpoints included viral-neutralizing antibodies against live SARS-CoV-2 wild-type (WT, Wuhan strain) and live Delta variant (VNT 50 ), and against pseudovirus WT and Omicron variant (pVNT 50 ). The secondary immunogenicity endpoints included anti-S1-RBD IgG antibody, S1-RBD:ACE2 binding inhibition, and T-cell responses by ELISpot and Intracellular Staining.

Results

No post-booster vaccine-related serious adverse events were recorded. The most common solicited adverse events were injection site pain and fatigue, mostly mild and transient. The UB-612 booster prompted a striking upsurge of neutralizing antibodies against live WT Wuhan strain (VNT 50 , 1,711) associated with unusually high cross-neutralization against Delta variant (VNT 50 , 1,282); and similarly with a strong effect against pseudovirus WT (pVNT 50, 6,245) and Omicron variant (pVNT 50 , 1,196). Upon boosting, the lower VNT 50 and pVNT 50 titers of the elderly in the primary series were uplifted to the same levels as those of the young adults. The UB-612 also induced robust, durable VoC antigen-specific Th1-oriented (IFN-γ + -) responses along with CD8 + T-cell (CD107a + -Granzyme B + ) cytotoxicity.

Conclusions and relevance

With a pronounced cross-reactive booster effect on B- and T-cell immunity, UB-612 may serve as a universal vaccine booster for comprehensive immunity enhancement against emergent VoCs.

Trial registration

[ClinicalTrials.gov: NCT04773067 ]

KEY POINTS

Question

Facing ever-emergent SARS-CoV-2 variants and long-haul COVID, can composition-updated new vaccines be constructed capable of inducing striking, durable booster-recalled B/T-immunity to prevent infection by VoCs?

Findings

In a Phase-2 extension study, a booster dose of UB-612 multitope protein-peptide vaccine prompted high viral-neutralizing titers against live wild-type virus (VNT 50 , 1,711), Delta variant (VNT 50 , 1,282); pseudovirus wild-type (pVNT 50 , 6,245) and Omicron variant (pVNT 50 , 1,196). Robust, durable Th1-IFNγ + responses and CD8 + T cell-(CD107a + -Granzyme B + ) cytotoxic activity were both observed.

Meaning

UB-612 RBD-sFc vaccine armed with T cell immunity-promoting conserved N, M and S2 Th/CTL epitope peptides may serve as a universal vaccine to fend off new VoCs.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2022.04.11.22272364: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsIRB: The protocols were approved by the ethics committee at the site and all participants provided written informed consent.
    Consent: The protocols were approved by the ethics committee at the site and all participants provided written informed consent.
    Sex as a biological variable(eFigure 2A in the Supplement) [ClinicalTrials.gov: NCT04773067] in Taiwan with 3,844 healthy male or female adults aged >18 to 85 years (eFigure 2B in the Supplement) who received two intramuscular doses (28 days apart) of 100 μg UB-612 or saline placebo.
    RandomizationDesign of Extension Booster Trial, Objectives, and Oversight: Booster 3rd-dose following the Phase-2 trial primary 2-dose series: We conducted a booster vaccination study (n = 1,478) which was an extension arm of the phase-2, placebo-controlled, randomized, observer-blind, multi-center primary 2-dose study
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Scope of Immunogenicity Investigation: The primary immunogenicity endpoints were the geometric mean titers (GMT) of neutralizing antibodies against SARS-CoV-2 wild-type (WT, Wuhan strain), and the post-booster effects against Omicron and Delta variant were explored as well.
    SARS-CoV-2 wild-type ( WT , Wuhan strain) ,
    suggested: None
    For WT and Delta strains, viral-neutralizing antibody titers that neutralize 50% (VNT50) of live SARS-CoV-2 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).
    SARS-CoV-2-Taiwan-CDC#1144
    suggested: None
    The secondary immunogenicity endpoints include anti-S1-RBD IgG antibody, inhibitory titers against S1-RBD:ACE2 interaction, and T-cell responses assayed by ELISpot and Intracellular Staining.
    anti-S1-RBD IgG
    suggested: None
    Viral-neutralizing antibody titers against SARS-CoV-2 wild-type and variants by CPE based live virus neutralization assay: 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 Delta variant (SARS-CoV-2-Taiwan-CDC#1144, B.1.617.2), which was conducted in a BSL-3 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.
    SARS-CoV-2
    suggested: None
    wild-type
    suggested: None
    SARS-CoV-2-Taiwan-CDC#4 , Wuhan
    suggested: None
    Vero-E6
    suggested: None
    binding IgG antibody by ELISA: The 96-well ELISA plates were coated with 2 µg/mL recombinant S1-RBDWT-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 room temperature.
    S1-RBDWT-His protein antigen ( 100
    suggested: None
    The anti-S1-RBD antibody level is expressed as Log10 of an end point dilution for a test sample (SoftMax Pro 6.5
    anti-S1-RBD
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    For WT and Delta strains, viral-neutralizing antibody titers that neutralize 50% (VNT50) of live SARS-CoV-2 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).
    Vero-E6
    suggested: None
    For WT and Omicron strains, 50% pseudovirus neutralization titers (pVNT50) were measured by neutralization assay using HEK-293T-ACE2 cells challenged with SARS-CoV-2 pseudovirus variants expressed the spike protein of WT and Omicron BA.1variants.
    HEK-293T-ACE2
    suggested: None
    HEK-293-hACE2 cells (1×104 cells/well) were seeded in 96-well white isoplates and incubated for overnight.
    HEK-293-hACE2
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    To produce SARS-CoV-2 pseudoviruses, a plasmid expressing C-terminal truncated wild-type Wuhan-Hu-1 strain SARS-CoV-2 spike protein (pcDNA3.1-nCoV-SΔ18) was co-transfected into HEK-293T/17 cells with packaging and reporter plasmids (pCMVΔ8.91, and pLAS2w.FLuc.
    Wuhan-Hu-1
    suggested: None
    Recombinant DNA
    SentencesResources
    To produce SARS-CoV-2 pseudoviruses, a plasmid expressing C-terminal truncated wild-type Wuhan-Hu-1 strain SARS-CoV-2 spike protein (pcDNA3.1-nCoV-SΔ18) was co-transfected into HEK-293T/17 cells with packaging and reporter plasmids (pCMVΔ8.91, and pLAS2w.FLuc.
    pcDNA3.1-nCoV-SΔ18
    suggested: None
    pCMVΔ8.91
    suggested: None
    pLAS2w.FLuc
    suggested: None
    Software and Algorithms
    SentencesResources
    Upon completion of staining, cells were analyzed in a FACSCanto II flow cytometry (BD Biosciences) using BD FACSDiva software.
    BD FACSDiva
    suggested: (BD FACSDiva Software, RRID:SCR_001456)
    Statistical analyses were performed using SAS® Version 9.4 (SAS Institute, Cary, NC, USA) or Wilcoxon sign rank test.
    SAS Institute
    suggested: (Statistical Analysis System, RRID:SCR_008567)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Limitation: This study has four limitations. First, UB-612 has not yet been widely deployed geographically. Second, in-depth biomarker analysis beyond those described in this report was not conducted due to insufficient volume of blood and samples retained. Third, we used Th/CTL peptide pool for an overall in vitro assessment of immune enhancement upon booster without delineation as to which peptide contributes most to mounting T-cell immunity in each of the vaccinees, though pooling may produce synergistic effect. Fourth, the post-booster functional analyses were carried out for a short period of time, which lacks information as to how durable the B- and T-cell immune response would last. However, it is worthy to note that UB-612 multitope subunit vaccine is the first designer vaccine to elicit a potent balanced B- and T-cell immunity against SARS-CoV-2 infection. Development of a new generation of such B-T combined vaccines has been explored. Large scale efficacy trials in geographically diverse areas enrolling young and elderly with various comorbidities, in both homologous and heterologous booster studies, are undergoing to accelerate the vaccine development for its timely introduction to prevent and control COVID.

    Results from TrialIdentifier: We found the following clinical trial numbers in your paper:

    IdentifierStatusTitle
    NCT04773067Active, not recruitingA Study to Evaluate UB-612 COVID-19 Vaccine in Adolescent, Y…

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2022.04.11.22272364v1 on medRxiv