Advanced Vaccine Design Strategies against SARS-CoV-2 and Emerging Variants

The paper addresses how to design vaccines that remain effective against SARS-CoV-2 and its emerging variants. It situates vaccination as a core public health tool alongside infection source control and transmission interruption, emphasizing vaccines’ historical cost-effectiveness. Leveraging lessons from SARS-CoV, MERS-CoV, and influenza, the COVID-19 vaccine pipeline rapidly produced multiple platforms (inactivated, live-attenuated, subunit, viral vector, DNA, and mRNA). While mRNA vaccines such as BNT162b2 (95% efficacy) and mRNA-1273 (94.1% efficacy) achieved strong protection initially, the emergence of variants of concern (Alpha, Beta, Gamma, Delta, Omicron) has increased transmissibility and immune evasion, diminishing vaccine effectiveness in some settings. The review’s purpose is to summarize advanced, rational vaccine design strategies—structure-guided antigen design, T-cell-focused vaccines, respiratory mucosal delivery, and nanotechnology-enabled platforms—to inform next-generation vaccines that provide broader and more durable protection.

The review synthesizes current knowledge of SARS-CoV-2 biology and variants, focusing on the spike (S) protein as the principal target of neutralizing antibodies and T-cell responses. It outlines spike structure, the roles of S1/RBD in ACE2 binding and S2 in membrane fusion, and how spike mutations (e.g., D614G, N501Y) increase infectivity and facilitate immune escape. Omicron’s extensive spike mutations enable escape from many neutralizing antibodies, highlighting a need for updated strategies. The authors summarize the development status of multiple vaccine platforms (inactivated, live-attenuated, subunit, viral vector, DNA, mRNA), noting that 175 vaccines had entered clinical trials and 199 were in preclinical stages by December 2022. The literature further supports four focal design approaches: prefusion stabilization and multimerization of spike/RBD (e.g., S-2P, S-6P/HexaPro, S-Trimer, RBD dimers), T-cell-centric vaccine designs identifying conserved epitopes across diverse HLA alleles, mucosal vaccination (intranasal/oral aerosol) to elicit sIgA and tissue-resident T cells in the respiratory tract, and nanoparticle/viro-like particle platforms to multivalently display antigens and broaden responses (including mosaic designs).

- Structure-guided vaccine design preserves neutralization-sensitive epitopes by stabilizing spike in the prefusion state and optimizing antigen presentation. Proline substitutions (S-2P at K986/V987; S-6P/HexaPro with six prolines) improve stability and yield, enabling potent mRNA, adenoviral, and protein subunit vaccines. S-Trimer uses a Trimer-Tag to maintain native-like homotrimers and showed protection in phase 2/3 trials when adjuvanted with CpG and alum. RBD multimerization (e.g., disulfide-linked dimers, IFN-armed dimers) enhances immunogenicity; ZF2001 (disulfide-linked RBD dimer) has emergency authorization in China. - T-cell-based vaccines address short-lived or variant-evaded humoral responses by eliciting cross-reactive CD4+ and CD8+ T cells, including tissue-resident memory in the respiratory tract. Computational epitope prediction and proteome-wide mapping identify conserved CTL epitopes. Data indicate high conservation of T-cell epitopes (on average ~91% for CD4+ and 94% for CD8+) and preserved memory responses against variants (about 90% CD4+ and 87% CD8+ retained, including against Omicron), suggesting T cells underpin durable, cross-variant protection. - Respiratory mucosal delivery (intranasal/oral aerosol) can induce serum IgG, mucosal sIgA, and resident T-cell responses at the site of viral entry, potentially achieving sterilizing immunity and reducing transmission. Platforms include adenoviral vectors, live-attenuated influenza-based vectors, and intranasal subunits. An orally administered aerosolized Ad5-nCoV vaccine was authorized for emergency use as a heterologous booster in China, demonstrating safety and strong immunogenicity after CoronaVac priming. - Nanotechnologies: Virus-like particles and engineered self-assembling protein nanoparticles provide multivalent, high-valency antigen display, enhancing B-cell activation and breadth. Mosaic nanoparticles co-display distinct spike/RBD antigens from prototypes and variants, eliciting cross-reactive responses and protecting against matched and mismatched challenges in preclinical studies. Platforms like I53-50 and SpyCatcher/SpyTag enable modular assembly. - Comparative advantages and limitations (from Table 2): Structure-guided design improves immunogenicity and yields but requires high-resolution structures; T-cell vaccines can elicit strong CD8+ responses but need precise epitope identification; mucosal delivery rapidly elicits mucosal immunity but may induce lower systemic antibody titers than intramuscular routes; nanotechnology allows multivalent display but raises nanotoxicity and manufacturing scalability considerations.

The reviewed strategies collectively address the core challenge of variant-driven immune escape by broadening and reinforcing protective immunity. Prefusion-stabilized and multimerized spike/RBD antigens concentrate neutralization-sensitive epitopes, sustaining strong humoral responses even as variants emerge. T-cell-oriented designs target conserved epitopes less susceptible to antigenic drift, supporting durable cross-variant protection and complementing neutralizing antibodies. Mucosal vaccination focuses immunity at the portal of entry, potentially interrupting transmission by generating sIgA and tissue-resident T cells in the upper airway—an outcome that intramuscular vaccines struggle to achieve. Nanoparticle platforms enhance antigen valency and epitope diversity (including mosaic displays), driving stronger and broader B-cell responses and offering a flexible framework for rapid antigen updates. Together, these approaches provide a rational roadmap for next-generation COVID-19 vaccines that can maintain efficacy against current and future variants, reduce disease severity, and curb spread.

Interdisciplinary advances in structural biology, bioinformatics, immunology, and materials science have enabled diverse, effective COVID-19 vaccines that reduce severe disease and mortality. However, persistent variant evolution, waning immunity, and logistical constraints necessitate continued innovation. The review highlights structure-guided antigen stabilization, T-cell-focused designs, mucosal delivery, and nanotechnology-enabled multivalent platforms as key strategies for safer, broadly protective, and long-lasting vaccines. Future research should prioritize conserved epitope identification, optimization of adjuvants, enhancement of thermostability and manufacturability, and understanding of individual variability in vaccine responses to guide rational, next-generation vaccine development.

The paper identifies major challenges affecting vaccine performance and deployment: (1) Frequent spike mutations cause immune escape and breakthrough infections, undermining current vaccines and requiring updates focused on conserved epitopes. (2) Uncertainty about the durability of vaccine-induced immunity necessitates strategies like heterologous prime-boost schedules and long-term follow-up. (3) Thermosensitivity of many vaccines complicates cold-chain logistics, highlighting a need for thermostable formulations. (4) Individual differences (e.g., age, sex) modulate immune responses and need better characterization for tailored design. Strategy-specific constraints include: structure-guided design depends on high-resolution structural data; T-cell vaccines require robust identification and validation of conserved epitopes across HLA diversity; mucosal vaccines may yield lower systemic antibody titers compared to intramuscular routes; nanoparticle platforms face questions of nanotoxicity, biodistribution, clearance, and scalable, reproducible manufacturing.