Predominant T-cell epitopes of SARS-CoV-2 restricted by multiple prevalent HLA-B and C allotypes in Northeast Asia

Yu Zhao¹Min Peng¹Chengtao He²Min Li³Xuelian Han³Qiang Fu²Yandan Wu¹Yue Fangping¹Chunguang Yan¹Guangyu Zhao^3*Chuanlai Shen^1*

• ¹Southeast University, Nanjing, China
• ²Nanjing Red Cross Blood Center, Nanjing, Jiangsu Province, China
• ³Academy of Military Medical Sciences (AMMS), Beijing, Beijing Municipality, China

Since the outbreak of novel coronavirus pneumonia (COVID-19), numerous T-cell epitopes in SARS-CoV-2 proteome have been reported. However, most of the identified CD8 + T-cell epitopes have been restricted primarily by HLA-A allotypes. The epitopes restricted by HLA-B and C allotypes are limited. This study focuses on the screening of T-cell epitopes restricted by 13 prevalent HLA-B and 13 prevalent HLA-C allotypes, which cover over 70% and 90% of the Chinese and Northeast Asian populations, respectively. Totally, 67 HLA-B restricted and 53 HLA-C restricted epitopes were validated as immunogenic epitopes with a herd predominance rate by peptide-PBMCs ex vivo coculture experiments using the PBMCs from convalescent Chinese cohort. In addition, 26 transfected cell lines expressing indicated HLA-B or C allotype were established, and used in the competitive peptide binding assays to define the affinities and cross-restriction of each validated epitope binding to HLA-B or C allotypes. These data will facilitate the design of T cell-directed vaccines and SARS-CoV-2 specific T cell detection tools tailored to the Northeast Asian population. The herd test of functionally validated T-cell epitopes and the competitive peptide binding assay onto cell line array expressing prevalent HLA allotypes may serve as an additional criterion for selecting T-cell epitopes used in vaccine.