Bioinformatics Prediction and Identification of Sars-Cov-2-Derived Hla-a-Binding T Cell Epitopes

Abstract

T cell immunity is the core component for effective control of SARS-CoV-2 infection. Identification of epitopes that specifically activate T cell immunity helps facilitate vaccine and diagnostic tools development against SARS-CoV-2. Here, we selected 47 peptides corresponding to 15 HLA-A isoforms based on bioinformatics algorithms and detected T cell responses with ELISPOT assays in vitro from 31 COVID-19 convalescent individuals, 2 individuals injected with inactivated vaccines and 2 controls. These peptides induced specific T cell responses in 21 individuals, strong positive T cell responses in vaccinated individuals and negative T cell responses in unexposed individuals. The results of five convalescent individuals showed that the peptides induced strong T cell responses mainly included S1055-1073, M166-184 and N261-279. These validation results in vitro were consistent with the prediction results of the bioinformatics algorithm. Clinical phenotypic analysis indicated that the majority of individuals with T cell positive responses had the following characteristics: increased levels of interleukin 6 (IL-6) and interleukin 10 (IL-10) secretion, reduced absolute values of lymphocytes and lymphocyte classification. In conclusion, the predicted SARS-CoV-2-derived peptides induced specific T cell immunity in the majority of COVID-19 convalescent individuals and could be used for the effective prevention and treatment against SARS-CoV-2.

Note:

Funding Information: This research was funded by National Natural Science Foundation of China (62106248), Medical Scientific Research Foundation of Zhejiang Province, China (2021KY302), Ningbo Natural Science Foundation, China (2021J325), Research Foundation of Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, China (2020YJY0204).

Declaration of Interests: None.

Ethical Approval Statement: The study was conducted in accordance with the Declaration of Helsinki, and approved by the Ethics Committee of Ningbo No.2 Hospital (SL-NBEY-KY-2021-184-03).

Keywords: T cell immunity, COVID-19, Epitopes, Treatment, vaccine