Cytotoxic T cells targeting spike glycoprotein are associated with hybrid immunity to SARS-CoV-2

mRNA vaccination of individuals with prior SARS-CoV-2 infection provides superior protection against breakthrough infections with variants of concern compared to vaccination in the absence of prior infection. However, the immune mechanisms by which this ‘hybrid immunity’ is generated and maintained are unknown. While genetic variation in spike glycoprotein effectively subverts neutralizing antibodies, spike-specific T cells are generally maintained against SARS-CoV-2 variants. Thus, we comprehensively profiled T cell responses against the S1 and S2 domains of spike glycoprotein in a cohort of SARS-CoV-2-naive or convalescent individuals who received two-dose mRNA vaccine series and were matched by age, sex, and vaccine type. Using flow cytometry, we observed that the overall functional breadth of CD4 T cells as well as polyfunctional Th1 responses were similar between the two groups. However, polyfunctional cytotoxic CD4 T cell responses against both S1 and S2 domains trended higher among convalescent subjects. Multi-modal single-cell RNA sequencing revealed diverse functional programs in spike-specific CD4 and CD8 T cells in both groups. However, convalescent individuals displayed enhanced cytotoxic and antiviral CD8 T cell responses to both S1 and S2 in the absence of cytokine production. Taken together, our data suggest that cytotoxic CD4 and CD8 T cells targeting spike glycoprotein may partially account for hybrid immunity and protection against breakthrough infections with SARS-CoV-2. We performed multi-modal (surface protein, gene expression, and TCR) single-cell RNA sequencing on PBMC collected from SARS-CoV-2-naive (n = 4) and convalescent (n = 4) individuals following two-dose mRNA vaccination.

对于既往感染过严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的个体，接种mRNA疫苗相较于未感染该病毒的个体接种疫苗，可提供更优异的针对各类关切变异株的突破性感染防护效果。然而，这种"混合免疫（hybrid immunity）"产生与维持的免疫机制仍未明确。尽管刺突糖蛋白（spike glycoprotein）的遗传变异可有效逃逸中和抗体的识别，但刺突特异性T细胞通常仍能对SARS-CoV-2变异株产生应答。因此，我们对一组按年龄、性别与疫苗类型进行匹配的SARS-CoV-2未感染者或康复者队列展开了全面表征：这些受试者均完成了两剂mRNA疫苗接种方案，我们对其针对刺突糖蛋白S1和S2结构域的T细胞应答进行了多维度分析。通过流式细胞术（flow cytometry），我们观察到两组受试者的CD4 T细胞整体功能广度以及多功能Th1应答水平均较为相近。但康复组受试者针对S1和S2结构域的多功能细胞毒性CD4 T细胞应答呈上升趋势。多模态单细胞RNA测序（single-cell RNA sequencing，scRNA-seq）结果显示，两组受试者的刺突特异性CD4及CD8 T细胞均呈现出多样的功能程序。然而，康复个体在未伴随细胞因子产生的情况下，针对S1和S2的细胞毒性及抗病毒CD8 T细胞应答得到了增强。综上，我们的研究数据表明，靶向刺突糖蛋白的细胞毒性CD4及CD8 T细胞或可部分解释混合免疫的形成，以及其对SARS-CoV-2突破性感染的防护作用。我们对完成两剂mRNA疫苗接种的SARS-CoV-2未感染者（n=4）与康复者（n=4）采集的外周血单个核细胞（PBMC）开展了多模态（表面蛋白、基因表达及T细胞受体（TCR））单细胞RNA测序。