Aromaticity at spike position 456 affects functional immunogenicity of SARS-CoV-2 Omicron variant receptor-binding domain.
7 affiliations
- 1Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, People's Republic of China.
- 2Division of Gastrointestinal Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China. [email protected].
- 3Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China. [email protected].
- 4National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan, China. [email protected].
- 5Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, People's Republic of China. [email protected].
- 6Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, People's Republic of China. [email protected].
- 7Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, People's Republic of China. [email protected].
Abstract
The recurrent emergence of the F456L substitution in SARS-CoV-2 Omicron sublineages has been associated with immune evasion, yet its impact on vaccine-induced immune responses remains poorly understood. Using a trimeric RBD-HR subunit vaccine platform, we investigated how residue 456 influences the functional immunogenicity of the receptor-binding domain (RBD). We found that the F456L substitution markedly reduced neutralizing antibody responses against multiple SARS-CoV-2 variants, despite maintaining comparable levels of total antigen-specific IgG, indicating a selective impairment of functional immunogenicity rather than overall antigenicity. Single-cell RNA sequencing and B-cell receptor (BCR) repertoire analyses further revealed that the F456L mutation weakened germinal center responses, reduced clonal expansion, and impaired repertoire remodeling of antigen-specific B cells. Structural modeling, biolayer interferometry, and calcium flux assays demonstrated that aromatic residues at position 456 promote effective germline BCR recognition and activation. Importantly, replacing the non-aromatic leucine residue with aromatic amino acids, including tyrosine or tryptophan, restored the neutralizing antibody-eliciting capacity of the antigen. Together, these findings identify aromaticity at residue 456 as a critical determinant of RBD functional immunogenicity and demonstrate how a single amino acid substitution can reshape B-cell responses and antibody quality. This work provides important insights for rational vaccine antigen design and advances our understanding of how site-specific mutations regulate antiviral immunity.
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BibTeX
@article{peng2026aromaticity,
title = {{Aromaticity at spike position 456 affects functional immunogenicity of SARS-CoV-2 Omicron variant receptor-binding domain.}},
author = {Dandan Peng and Zimin Chen and Minyang Fu and Weiqi Hong and Mengzhe Dai and Hao Zeng and Sheng Lin and Hong Lei and Jingyun Yang and Jie Shi and Xiya Huang and Chunjun Ye and Furong Qin and Yu Zhang and Ying Hao and Binhan Wang and Wenyan Ren and Li Chen and Jian Liu and Aqu Alu and Yishan Lu and Xinyi Du and Jiong Li and Huashan Shi and Yuquan Wei and Yi Chen and Shuaiyao Lu and Cai He and Guangwen Lu and Xiawei Wei},
journal = {Signal transduction and targeted therapy},
year = {2026},
month = oct,
doi = {10.1038/s41392-026-02939-3},
url = {https://europepmc.org/article/MED/42957648},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Aromaticity at spike position 456 affects functional immunogenicity of SARS-CoV-2 Omicron variant receptor-binding domain.
AU - Dandan Peng
AU - Zimin Chen
AU - Minyang Fu
AU - Weiqi Hong
AU - Mengzhe Dai
AU - Hao Zeng
AU - Sheng Lin
AU - Hong Lei
AU - Jingyun Yang
AU - Jie Shi
AU - Xiya Huang
AU - Chunjun Ye
AU - Furong Qin
AU - Yu Zhang
AU - Ying Hao
AU - Binhan Wang
AU - Wenyan Ren
AU - Li Chen
AU - Jian Liu
AU - Aqu Alu
AU - Yishan Lu
AU - Xinyi Du
AU - Jiong Li
AU - Huashan Shi
AU - Yuquan Wei
AU - Yi Chen
AU - Shuaiyao Lu
AU - Cai He
AU - Guangwen Lu
AU - Xiawei Wei
PY - 2026
DA - 2026/10/28
JO - Signal transduction and targeted therapy
DO - 10.1038/s41392-026-02939-3
UR - https://europepmc.org/article/MED/42957648
AB - The recurrent emergence of the F456L substitution in SARS-CoV-2 Omicron sublineages has been associated with immune evasion, yet its impact on vaccine-induced immune responses remains poorly understood. Using a trimeric RBD-HR subunit vaccine platform, we investigated how residue 456 influences the functional immunogenicity of the receptor-binding domain (RBD). We found that the F456L substitution markedly reduced neutralizing antibody responses against multiple SARS-CoV-2 variants, despite maintaining comparable levels of total antigen-specific IgG, indicating a selective impairment of functional immunogenicity rather than overall antigenicity. Single-cell RNA sequencing and B-cell receptor (BCR) repertoire analyses further revealed that the F456L mutation weakened germinal center responses, reduced clonal expansion, and impaired repertoire remodeling of antigen-specific B cells. Structural modeling, biolayer interferometry, and calcium flux assays demonstrated that aromatic residues at position 456 promote effective germline BCR recognition and activation. Importantly, replacing the non-aromatic leucine residue with aromatic amino acids, including tyrosine or tryptophan, restored the neutralizing antibody-eliciting capacity of the antigen. Together, these findings identify aromaticity at residue 456 as a critical determinant of RBD functional immunogenicity and demonstrate how a single amino acid substitution can reshape B-cell responses and antibody quality. This work provides important insights for rational vaccine antigen design and advances our understanding of how site-specific mutations regulate antiviral immunity.
SN - 2095-9907
SN - 2059-3635
ER -