T cell-mediated immunity may play a critical role in controlling and establishing protective immunity against SARS-CoV-2 infection; yet the repertoire of viral epitopes responsible for T cell response activation remains mostly unknown. Identification of viral peptides presented on class I human leukocyte antigen (HLA-I) can reveal epitopes for recognition by cytotoxic T cells and potential incorporation into vaccines. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two human cell lines at different times post-infection using mass spectrometry. We found HLA-I peptides derived not only from canonical ORFs, but also from internal out-of-frame ORFs in Spike and Nucleoprotein not captured by current vaccines. Proteomics analyses of infected cells revealed that SARS-CoV-2 may interfere with antigen processing and immune signaling pathways. Based on the endogenously processed and presented viral peptides that we identified, we estimate that a pool of 24 peptides would provide one or more peptides for presentation by at least one HLA allele in 99% of the human population. These biological insights and the list of naturally presented SARS-CoV-2 peptides will facilitate data-driven selection of peptides for immune monitoring and vaccine development.

中文翻译：

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SARS-CoV-2 感染的细胞呈现来自规范和框外 ORF 的 HLA-I 肽

T 细胞介导的免疫可能在控制和建立针对 SARS-CoV-2 感染的保护性免疫中发挥关键作用；然而，负责 T 细胞反应激活的病毒表位库仍然大多未知。对 I 类人类白细胞抗原 (HLA-I) 上呈递的病毒肽的鉴定可以揭示细胞毒性 T 细胞识别的表位和潜在掺入疫苗的表位。在这里，我们使用质谱法在感染后不同时间在两种人类细胞系中报告了 SARS-CoV-2 的第一个 HLA-I 免疫肽组。我们发现 HLA-I 肽不仅来自规范的 ORF，而且来自当前疫苗未捕获的刺突和核蛋白中的内部框外 ORF。对感染细胞的蛋白质组学分析表明，SARS-CoV-2 可能会干扰抗原加工和免疫信号通路。根据我们鉴定的内源性加工和呈递的病毒肽，我们估计 24 种肽库将提供一种或多种肽，用于 99% 的人群中至少一个 HLA 等位基因的呈递。这些生物学见解和自然呈现的 SARS-CoV-2 肽列表将促进数据驱动的肽选择，用于免疫监测和疫苗开发。