Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control its life cycle remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively the cellular and viral RBPs that are involved in SARS-CoV-2 infection. We reveal that SARS-CoV-2 infection profoundly remodels the cellular RNA-bound proteome, which includes wide-ranging effects on RNA metabolic pathways, non-canonical RBPs, and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Among them are several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.

严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 会导致 2019 年冠状病毒病 (COVID-19)。SARS-CoV-2 依赖细胞 RNA 结合蛋白 (RBP) 进行复制和传播，尽管哪些 RBP 控制其生命周期仍很大程度上未知。在这里，我们采用多组学方法来系统、全面地识别参与 SARS-CoV-2 感染的细胞和病毒 RBP。我们发现，SARS-CoV-2 感染深刻地重塑了细胞 RNA 结合蛋白质组，其中包括对 RNA 代谢途径、非典型 RBP 和抗病毒因子的广泛影响。此外，我们应用一种新方法来鉴定与病毒 RNA 直接相互作用的蛋白质，发现了数十种细胞 RBP 和六种病毒蛋白质。其中包括 tRNA 连接酶复合物的几个成分，我们证明它们可以调节 SARS-CoV-2 感染。此外，我们发现针对与 SARS-CoV-2 RNA 相互作用的宿主 RBP 的可用药物可抑制感染。总的来说，我们的结果揭示了宿主病毒相互作用的新领域，并具有针对 COVID-19 的新抗病毒疗法的潜力。