The continuous evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to the emergence of numerous Omicron subvariants with enhanced immune escape. Peptide vaccines provide a flexible and rapidly updatable platform for responding to SARS-CoV-2 antigenic drift. However, many existing peptide vaccine candidates mainly target a single epitope class, making it difficult to simultaneously induce potent neutralizing antibodies and robust cellular immunity.

Recently, a research team led by GONG Likun from the Shanghai Institute of Materia Medica, Chinese Academy of Sciences, in collaboration with LI Honglin's group at East China Normal University, ZHAO Guangyu's group at the Academy of Military Medical Sciences, and GENG Xingchao's group at the National Institutes for Food and Drug Control, published a research article in Zoological Research. Based on the team's established peptide vaccine design platform (Cell Discovery, 2022), the current work integrated AI-aided epitope prediction, human T-cell receptor (TCR) repertoire analysis, TCR-peptide-major histocompatibility complex (TCR-pMHC) interaction modeling, and validation in humanized animal models. The developed workflow enables the design and evaluation of B‑cell and T‑cell epitopes in a complementary manner, aiming to elicit both cellular and humoral immune responses.

The researchers systematically analyzed the receptor-binding domain (RBD) sequences of 18 Omicron subvariants. Based on sequence conservation, structural characteristics, and predicted T-cell and B-cell epitopes, they identified two complementary candidate peptides, LY54-XBB and P67-XBB, derived from the XBB.1.5 RBD. Human TCR repertoire analysis using COVID-19 patient-derived datasets, together with TCR-pMHC interaction modeling, indicated that both peptides possessed broad T-cell recognition potential, with P67-XBB exhibiting particularly strong predicted T-cell immunogenicity.

The candidate peptides were formulated with the F2 nanoemulsion adjuvant and evaluated in mice and non-human primates. Vaccination induced broad RBD-specific binding antibodies, angiotensin-converting enzyme 2 (ACE2)-blocking antibodies, and pseudovirus-neutralizing antibodies against multiple Omicron subvariants. It also elicited a T helper type 1 (Th1)-biased cellular immune response characterized by interferon-γ (IFN-γ), interleukin-2 (IL-2), and tumor necrosis factor-α (TNF-α) production. Notably, combined immunization with LY54-XBB and P67-XBB generated stronger humoral and cellular immune responses than either peptide administered alone.

Protective efficacy was further demonstrated in HLA-A2/DR1-human angiotensin-converting enzyme 2 (hACE2) transgenic mice challenged with the SARS-CoV-2 BA.5 variant. The combined peptide vaccine significantly reduced lung viral loads and alleviated pulmonary pathological damage. In addition, ex vivo stimulation of peripheral blood mononuclear cells (PBMCs) from COVID-19 convalescent plasma (CCP) donors confirmed that both peptides elicited antigen-specific CD4⁺ and CD8⁺ T-cell responses, further validating the inclusion of effective T-cell epitopes.

This study established a comprehensive workflow integrating AI-aided epitope prediction, structural analysis, human TCR validation, and experimental evaluation for peptide vaccine development. By enabling the complementary design of neutralizing antibody epitopes and T-cell epitopes, the strategy provides a rapidly updatable framework for developing peptide vaccines against rapidly evolving SARS-CoV-2 variants. Beyond COVID-19, this workflow may also facilitate vaccine development against other antigenically diverse pathogens.

Figure 1 Workflow of the AI-aided multi-epitope peptide vaccine design strategy

(Image by GONG Likun's lab)

DOI: 10.24272/j.issn.2095-8137.2025.469

Link: https://www.zoores.ac.cn/en/article/doi/10.24272/j.issn.2095-8137.2025.469

Keywords: Peptide vaccine; AI-aided design; Omicron subvariants

Contact:

DIAO Wentong

Shanghai Institute of Materia Medica

E-mail: diaowentong@simm.ac.cn