Chimeric Delta-Omicron RBD-dimer vaccine found to be effective against SARS-CoV-2 variants

By Pooja Toshniwal PahariaApr 29 2022Reviewed by Aimee Molineux

In a recent study published in Cell, researchers described their self-designed chimeric receptor-binding domain (RBD)-dimer vaccine approach to adapt severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) and variants of interest (VOI).

The emergence of novel SARS-CoV-2 variants and subsequent breakthrough infections have increased the difficulty of controlling the coronavirus disease 2019 (COVID-19) pandemic. All existing authorized vaccines are formulated based on the prototype (Wuhan-Hu-1) spike (S) RBD of SARS-CoV-2. This warrants the need for the development of novel vaccines with a wider breadth of immune protection.

About the study

The authors of the present study previously designed a protein subunit vaccine (F2001) based on the spike (S) protein RBD of the SARS-CoV-2 prototype and Beta variants. F2001 demonstrated significant immunogenicity and thus, the authors used a similar approach to design a chimeric vaccine to adapt the Omicron and Delta variants in the present study.

First, a prototype-Beta chimeric RBD-dimer vaccine was developed to adapt the Beta VOC followed by surface plasmon resonance (SPR) assays for verifying the main antigenic epitopes and the receptor-binding motifs (RBM). The SPR assays used proteins of the human angiotensin-converting enzyme (hACE2) and SARS-CoV-2 RBD-specific monoclonal antibodies (mAbs) that targeted the antigenic epitopes. The binding affinity of the immunogens to the receptor proteins was assessed and found to be preserved to almost all mAbs by the prototype and the prototype-Beta chimeric RBD-dimers.

To determine the immunogenicity of the chimeric vaccine, BALB/c mice were immunized with the prototype, Beta, or prototype-Beta chimeric RBD-dimers, with Addavax adjuvant with a 21-day-interval. Mice sera were obtained two weeks post-the second vaccine dose.  A vesicular stomatitis virus (VSV)-based panel was used to assess the neutralization of the SARS-CoV-2 strains [prototype strain, VOCs (Alpha, Beta, Gamma, Delta, Omicron, and Delta plus or Delta S with K417N mutation) and VOIs (Lambda and Kappa)].

Pseudovirus neutralization assays were performed to assess the 50 percent neutralization geometric mean titers (PVNT₅₀ GMT) of the SARS-CoV-2 variants.

To evaluate the effectiveness of the RBD-dimers, BALB/c mice were intranasally transduced with hACE2-expressing adenovirus (Ad5) and subsequently challenged with the SARS-CoV-2 prototype or directly challenged intranasally with the Beta variant. The mice were euthanized, and their lung tissues were obtained five days post-infection (dpi) for the quantification of the viral genomic ribonucleic acid (gRNA) and subgenomic RNA (sgRNA) to assess the viral replication.

In addition, the tissues were subjected to histopathological analysis, and their pathological scores were determined.

The prototype-Beta chimeric RBD-dimer immunogen was also assessed in 24 rhesus macaques immunized intramuscularly with three doses, at 21-day intervals. Post-immunization, their sera samples and peripheral blood mononuclear cells (PBMCs) were obtained to assess the viral neutralization and cytokine production, respectively. 

After the prototype and the prototype-Beta chimeric RBD, dimers vaccines were found effective, the Delta-Omicron chimeric RBD-dimer vaccine was designed to adapt the prototype, Beta, Delta, and Omicron strains. The antigenic epitopes of the vaccine were verified by SPR experiments. Its antigenic integrity, effectiveness, and immunogenic potentials were evaluated. In addition, the structure was assessed using cryo-electron microscopy (cryo-EM).

To assess the Delta-Omicron chimeric vaccine immunogenicity, BALB/c mice were immunized twice with the vaccine and an AddaVax adjuvant or the prototype RBD-dimer homotype, at a 21-day interval. To determine the vaccine effectiveness, the mice were challenged with Omicron and Delta. Additionally, they were transduced with hACE2-expressing Ad5 to increase sensitivity to Delta and their lung tissues were obtained for SARS-CoV-2 titration post euthanization.

Results

In the PVNT assays, the prototype vaccine-elicited GMTs for S of the prototype, Alpha, Beta, Gamma, Delta, Delta plus, Kappa, Lamba, and Omicron were 1779, 1479, 487, 699, 1100, 1119, 1205, 807, and 122, respectively.

The Beta RBD-dimer vaccine-elicited GMTs for Gamma and Beta were 1650 and 809, respectively, and between 104 and 385 for other variants. The prototype-Beta chimeric RBD-dimer vaccine-elicited GMTs for Omicron was 434 and ranged between 1140 and 2964 for other variants. This indicated that the prototype-Beta chimeric RBD-dimer vaccine outperformed the prototype vaccine with higher neutralization of Beta, Gamma, and Omicron and was also more effective than the Beta RBD vaccine with higher neutralization of prototype, Alpha, Delta, Delta plus, Kappa, Lambda, and Omicron.

The prototype and prototype-Beta chimeric vaccines substantially reduced viral gRNA compared to the Beta vaccine, strongly correlating with the neutralizing antibodies (nAbs) titers. In addition, both vaccines led to undetectable pulmonary viral sgRNA, indicating significant control of viral replication. Histopathological changes such as diffuse inflammation, vascular congestion, and vanished alveolar cavities were also substantially lower with the prototype and prototype-Beta chimeric vaccines compared to the sham immunization. Moreover, the prototype-Beta chimeric vaccine also elicited moderate production of cytokines such as interferon-gamma (IFN-γ) and interleukins (IL-2,4).

The Delta-Omicron chimeric RBD-dimer vaccine showed a similar binding affinity to hACE2 (8.4 nM) compared to those for RBDs of the prototype (6.5 nM), Omicron (6.6 nM) and Delta (5.1 nM). The vaccine bound all the mAbs, but with the reduced affinities to C110 and CV07-270 mAbs.

The vaccine induced high NAbs titers against Delta, Omicron (BA.1), and Omicron (BA.2) S which were 18.6, 19.2, and 19.1 times higher than those induced by the homotypic prototype RBD-dimer, respectively. Likewise, the neutralizing GMTs of the Delta-Omicron vaccine were also higher against the prototype, Alpha, and Beta variants compared to the homotypic prototype vaccine.

In Delta-challenged mice, the mean pulmonary viral gRNA was reduced by 474 folds to 2.4 × 10⁷ copies/g with undetectable viral sgRNA levels by the Delta-Omicron chimeric vaccine. In Omicron-challenged mice, viral replication was not detected. The NAb titers for significantly high for both Omicron and Delta. The vaccine relieved pulmonary injury with significantly lower pathological scores.

In the cryo-EM analysis, the prototype and prototype-Beta chimeric RBD dimers were arranged as axially symmetrical bilateral-lung-like structures. The prototype RBD-dimer was complexed with dual CB6 Fabs at both arms whereas the prototype-Beta chimeric RBD-dimer and the Delta-Omicron chimeric RBD-dimer engaged a single CB6 Fab at one arm. The analysis showed that the Delta-Omicron chimeric RBD-dimer was folded correctly, and presented the main antigenic epitopes and RBM.

Overall, the study findings showed that in comparison to its homotypic counterparts, the chimeric Delta-Omicron RBD vaccine outperformed with superior viral neutralization, immunogenicity, and effectiveness against SARS-CoV-2 variants. The study provided a proof-of-concept approach for rapidly updating immunogens and underpinned World Health Organization (WHO) recommendations to develop variant-adapted and multivalent SARS-CoV-2 vaccines.