Proliferative Receptor Binding Domain (RBD)-specific CD4+ T cells correlate with neutralizing antibody levels after natural SARS-CoV-2 infection and are induced following vaccination

Long-term immunity to SARS-CoV-2 infection, comprising neutralizing antibodies and T cell-mediated immunity, in a very large majority of the population, is required to reduce the current pandemic. We have investigated in detail the association between memory CD4 and CD8 T cells in recovered COVID-19 subjects, and their levels of neutralizing antibodies.The results show that RBD-specific memory CD4 T cells were particularly variable, and up to half of recovered individuals lacked these CD4 T cells and had much lower neutralizing antibody titres. Conversely, study of additional subjects identified as having low neutralizing antibody titres had very low levels of RBD-specific CD4 T cells. Furthermore, at both the protein and transcriptomic levels, these low antibody subjects had spike-specific CD4 T cells with a higher proportion of an inhibitory phenotype, including Foxp3 and CTLA-4, and less effector phenotype with T-bet and cytotoxic granzymes and perforin. Vaccination led to an improvement in RBD-specific memory CD4 T cells and neutralizing antibody titres in these at-risk subjects. Our results suggest that epitopes within the RBD-region should be the particular target of booster vaccines. Overall design: scRNA seq of PBMC collected from 4 convalescent donor samples at 3 months post SARS-CoV-2 infection

为遏制当前新型冠状病毒（SARS-CoV-2）感染引发的大流行，绝大多数人群需建立由中和抗体与T细胞介导免疫共同构成的长期免疫保护。本研究针对新冠康复受试者体内的记忆性CD4及CD8 T细胞与中和抗体水平之间的关联展开了详尽分析。研究结果显示，靶向受体结合域（Receptor Binding Domain, RBD）的记忆性CD4 T细胞异质性极强，近半数康复者体内缺乏此类CD4 T细胞，且其中和抗体滴度显著偏低。反之，针对另一批中和抗体滴度偏低的受试群体开展的分析显示，其体内靶向RBD的CD4 T细胞水平同样极低。此外，在蛋白质组与转录组层面，中和抗体水平偏低的受试群体中，刺突蛋白（Spike protein）特异性CD4 T细胞的抑制性表型比例更高，包括叉头框蛋白P3（Forkhead box P3, Foxp3）与细胞毒性T淋巴细胞相关抗原4（Cytotoxic T Lymphocyte-associated Antigen 4, CTLA-4）标记的表型，而表达T盒转录因子T-bet、细胞毒性颗粒酶与穿孔素的效应表型比例则更低。接种疫苗可改善此类高风险受试群体体内靶向RBD的记忆性CD4 T细胞水平与中和抗体滴度。本研究结果提示，RBD区域内的表位应作为加强针疫苗的优先靶向靶点。实验整体设计：对4名感染SARS-CoV-2后3个月的康复供体采集的外周血单个核细胞（Peripheral Blood Mononuclear Cell, PBMC）进行单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）。