The identification of CD4⁺ T cell epitopes is instrumental for the design of subunit vaccines for broad protection against coronaviruses. Here, we demonstrate in COVID-19–recovered individuals a robust CD4⁺ T cell response to naturally processed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein and nucleoprotein (N), including effector, helper, and memory T cells. By characterizing 2943 S-reactive T cell clones from 34 individuals, we found that the receptor-binding domain (RBD) is highly immunogenic and that 33% of RBD-reactive clones and 94% of individuals recognized a conserved immunodominant S346–S365 region comprising nested human leukocyte antigen DR (HLA-DR)– and HLA-DP–restricted epitopes. Using pre– and post–COVID-19 samples and S proteins from endemic coronaviruses, we identified cross-reactive T cells targeting multiple S protein sites. The immunodominant and cross-reactive epitopes identified can inform vaccination strategies to counteract emerging SARS-CoV-2 variants.

CD4 ⁺ T 细胞表位的鉴定有助于设计用于广泛保护冠状病毒的亚单位疫苗。在这里，我们在 COVID-19 康复的个体中展示了强大的 CD4 ⁺T 细胞对自然加工的严重急性呼吸系统综合症冠状病毒 2 (SARS-CoV-2) 刺突 (S) 蛋白和核蛋白 (N) 的反应，包括效应 T 细胞、辅助 T 细胞和记忆 T 细胞。通过表征来自 34 个个体的 2943 个 S 反应性 T 细胞克隆，我们发现受体结合域 (RBD) 具有高度免疫原性，33% 的 RBD 反应性克隆和 94% 的个体识别出一个保守的免疫显性 S346-S365 区域，包括巢式人类白细胞抗原 DR (HLA-DR) 和 HLA-DP 限制性表位。我们使用来自地方性冠状病毒的 COVID-19 前后样本和 S 蛋白，鉴定了靶向多个 S 蛋白位点的交叉反应性 T 细胞。确定的免疫显性和交叉反应表位可以为疫苗接种策略提供信息，以抵消新出现的 SARS-CoV-2 变体。