Vaccination by inactivated vaccine is an effective strategy to prevent the COVID-19 pandemic. However, the detailed molecular immune response at single-cell level is poorly understood. In this study, we systematically delineated the landscape of the pre- and post-vaccination single-cell transcriptome, TCR (T cell antigen receptor) and BCR (B cell antigen receptor) expression profile of vaccinated candidates. The bulk TCR sequencing analysis of COVID-19 patients was also performed. Enrichment of a clonal CD8⁺ T cell cluster expressing specific TCR was identified in both vaccination candidates and COVID-19 patients. These clonal CD8⁺ T cells showed high expression of cytotoxicity, phagosome and antigen presentation related genes. The cell–cell interaction analysis revealed that monocytes and dendritic cells could interact with these cells and initiate phagocytosis via ICAM1-ITGAM and ITGB2 signaling. Together, our study systematically deciphered the detailed immunological response during SARS-CoV-2 vaccination and infection. It may facilitate understanding the immune response and the T-cell therapy against COVID-19.

接种灭活疫苗是预防 COVID-19 大流行的有效策略。然而，人们对单细胞水平的详细分子免疫反应知之甚少。在这项研究中，我们系统地描绘了接种疫苗的候选者的接种前和接种后单细胞转录组、TCR（T 细胞抗原受体）和 BCR（B 细胞抗原受体）表达谱的情况。还对 COVID-19 患者进行了批量 TCR 测序分析。在疫苗接种候选者和 COVID-19 患者中均发现了表达特定 TCR 的克隆 CD8 ^{+ T 细胞簇的富集。}这些克隆CD8 ⁺T细胞表现出细胞毒性、吞噬体和抗原呈递相关基因的高表达。细胞-细胞相互作用分析表明，单核细胞和树突状细胞可以与这些细胞相互作用，并通过 ICAM1-ITGAM 和 ITGB2 信号传导启动吞噬作用。我们的研究共同系统地解读了 SARS-CoV-2 疫苗接种和感染过程中详细的免疫反应。它可能有助于了解针对 COVID-19 的免疫反应和 T 细胞疗法。