The molecular properties of CD8⁺ T cells that respond to SARS-CoV-2 infection are not fully known. Here, we report on the single-cell transcriptomes of >80,000 virus-reactive CD8⁺ T cells, obtained using a modified Antigen-Reactive T cell Enrichment (ARTE) assay, from 39 COVID-19 patients and 10 healthy subjects. COVID-19 patients segregated into two groups based on whether the dominant CD8⁺ T cell response to SARS-CoV-2 was ‘exhausted’ or not. SARS-CoV-2-reactive cells in the exhausted subset were increased in frequency and displayed lesser cytotoxicity and inflammatory features in COVID-19 patients with mild compared to severe illness. In contrast, SARS-CoV-2-reactive cells in the dominant non-exhausted subset from patients with severe disease showed enrichment of transcripts linked to co-stimulation, pro-survival NF-κB signaling, and anti-apoptotic pathways, suggesting the generation of robust CD8⁺ T cell memory responses in patients with severe COVID-19 illness. CD8⁺ T cells reactive to influenza and respiratory syncytial virus from healthy subjects displayed polyfunctional features and enhanced glycolysis. Cells with such features were largely absent in SARS-CoV-2-reactive cells from both COVID-19 patients and healthy controls non-exposed to SARS-CoV-2. Overall, our single-cell analysis revealed substantial diversity in the nature of CD8⁺ T cells responding to SARS-CoV-2.

^{CD8 +} T 细胞对 SARS-CoV-2 感染作出反应的分子特性尚不完全清楚。^{在这里，我们报告了超过 80,000 个病毒反应性 CD8 +} T 细胞的单细胞转录组，这些细胞是使用改良的抗原反应性 T 细胞富集 (ARTE) 测定从 39 名 COVID-19 患者和 10 名健康受试者中获得的。根据对 SARS-CoV-2 的主要 CD8 ⁺ T 细胞反应是否“耗尽”，将 COVID-19 患者分为两组。与重症患者相比，轻症 COVID-19 患者中，衰竭亚群中 SARS-CoV-2 反应细胞的频率增加，并且表现出较低的细胞毒性和炎症特征。相比之下，来自严重疾病患者的主要非衰竭亚群中的 SARS-CoV-2 反应细胞显示出与共刺激、促生存 NF-κB 信号传导和抗凋亡途径相关的转录物富集，这表明患有严重的 COVID-19 疾病的患者中强大的 CD8 ⁺ T 细胞记忆反应。来自健康受试者的对流感和呼吸道合胞病毒有反应的CD8 ^{+ T 细胞表现出多功能特征和增强的糖酵解。}来自 COVID-19 患者和未暴露于 SARS-CoV-2 的健康对照的 SARS-CoV-2 反应细胞中基本上不存在具有此类特征的细胞。总体而言，我们的单细胞分析揭示了响应 SARS-CoV-2 的CD8 ^{+ T 细胞的性质存在显着多样性。}