In-depth understanding of human T-cell-mediated immunity in coronavirus disease 2019 (COVID-19) is needed if we are to optimize vaccine strategies and immunotherapies. Identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) T-cell epitopes and generation of peptide–human leukocyte antigen (peptide–HLA) tetramers facilitate direct ex vivo analyses of SARS-CoV-2-specific T cells and their T-cell receptor (TCR) repertoires. We utilized a combination of peptide prediction and in vitro peptide stimulation to validate novel SARS-CoV-2 epitopes restricted by HLA-A*24:02, one of the most prominent HLA class I alleles, especially in Indigenous and Asian populations. Of the peptides screened, three spike-derived peptides generated CD8⁺IFNγ⁺ responses above background, S_1208–1216 (QYIKWPWYI), S_448–456 (NYNYLYRLF) and S_193–201 (VFKNIDGYF), with S₁₂₀₈ generating immunodominant CD8⁺IFNγ⁺ responses. Using peptide–HLA-I tetramers, we performed direct ex vivo tetramer enrichment for HLA-A*24:02-restricted CD8⁺ T cells in COVID-19 patients and prepandemic controls. The precursor frequencies for HLA-A*24:02-restricted epitopes were within the range previously observed for other SARS-CoV-2 epitopes for both COVID-19 patients and prepandemic individuals. Naïve A24/SARS-CoV-2-specific CD8⁺ T cells increased nearly 7.5-fold above the average precursor frequency during COVID-19, gaining effector and memory phenotypes. Ex vivo single-cell analyses of TCRαβ repertoires found that the A24/S₄₄₈⁺CD8⁺ T-cell TCRαβ repertoire was driven by a common TCRβ chain motif, whereas the A24/S₁₂₀₈⁺CD8⁺ TCRαβ repertoire was diverse across COVID-19 patients. Our study provides an in depth characterization and important insights into SARS-CoV-2-specific CD8⁺ T-cell responses associated with a prominent HLA-A*24:02 allomorph. This contributes to our knowledge on adaptive immune responses during primary COVID-19 and could be exploited in vaccine or immunotherapeutic approaches.

中文翻译：

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在突出的 HLA-A*24:02 异形体背景下，SARS-CoV-2 特异性 CD8+ T 细胞反应和 TCR 特征

如果我们要优化疫苗策略和免疫疗法，就需要深入了解 2019 年冠状病毒病 (COVID-19) 中人类 T 细胞介导的免疫。严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) T 细胞表位的鉴定和肽-人类白细胞抗原 (肽-HLA) 四聚体的产生促进了对 SARS-CoV-2 特异性 T 细胞及其特异性的直接离体分析T 细胞受体 (TCR) 库。我们结合肽预测和体外肽刺激来验证受 HLA-A*24:02 限制的新型 SARS-CoV-2 表位，HLA-A*24:02 是最突出的 HLA I 类等位基因之一，尤其是在土著和亚洲人群中。在筛选的肽中，三种尖峰衍生肽产生 CD8 ⁺ IFNγ⁺高于背景的反应，S _1208-1216 (QYIKWPWYI)、S _448-456 (NYNYLYRLF) 和 S _193-201 (VFKNIDGYF)，S ₁₂₀₈产生免疫显性 CD8 ⁺ IFNγ ⁺反应。使用肽-HLA-I 四聚体，我们对 COVID-19 患者和大流行前对照中的HLA-A*24:02 限制性 CD8 ⁺ T 细胞进行了直接的离体四聚体富集。HLA-A*24:02 限制性表位的前体频率在先前观察到的 COVID-19 患者和大流行前个体的其他 SARS-CoV-2 表位的范围内。Naïve A24/SARS-CoV-2 特异性 CD8 ⁺在 COVID-19 期间，T 细胞比平均前体频率增加了近 7.5 倍，获得了效应和记忆表型。TCRαβ 库的离体单细胞分析发现 A24/S ₄₄₈ ⁺ CD8 ⁺ T 细胞 TCRαβ 库是由一个常见的 TCRβ 链基序驱动的，而 A24/S ₁₂₀₈ ⁺ CD8 ⁺ TCRαβ 库在 COVID-19 中是多种多样的耐心。我们的研究提供了对 SARS-CoV-2 特异性 CD8 ^{+ 的}深入表征和重要见解与突出的 HLA-A*24:02 异形体相关的 T 细胞反应。这有助于我们了解初级 COVID-19 期间的适应性免疫反应，并可用于疫苗或免疫治疗方法。