The Coronaviridae is a family of positive-strand RNA viruses that includes SARS-CoV-2, the etiologic agent of the COVID-19 pandemic. Bearing the largest single-stranded RNA genomes in nature, coronaviruses are critically dependent on long-distance RNA-RNA interactions to regulate the viral transcription and replication pathways. Here we experimentally mapped the in vivo RNA-RNA interactome of the full-length SARS-CoV-2 genome and subgenomic mRNAs. We uncovered a network of RNA-RNA interactions spanning tens of thousands of nucleotides. These interactions reveal that the viral genome and subgenomes adopt alternative topologies inside cells and engage in different interactions with host RNAs. Notably, we discovered a long-range RNA-RNA interaction, the FSE-arch, that encircles the programmed ribosomal frameshifting element. The FSE-arch is conserved in the related MERS-CoV and is under purifying selection. Our findings illuminate RNA structure-based mechanisms governing replication, discontinuous transcription, and translation of coronaviruses and will aid future efforts to develop antiviral strategies.

冠状病毒科是一个正链 RNA 病毒家族，其中包括 SARS-CoV-2（COVID-19 大流行的病原体）。冠状病毒拥有自然界中最大的单链RNA基因组，严重依赖长距离RNA-RNA相互作用来调节病毒转录和复制途径。在这里，我们通过实验绘制了全长 SARS-CoV-2 基因组和亚基因组 mRNA 的体内RNA-RNA 相互作用组。我们发现了一个跨越数万个核苷酸的 RNA-RNA 相互作用网络。这些相互作用表明，病毒基因组和亚基因组在细胞内采用不同的拓扑结构，并与宿主 RNA 进行不同的相互作用。值得注意的是，我们发现了一种长程 RNA-RNA 相互作用，即 FSE-arch，它包围着编程的核糖体移码元件。 FSE-arch 在相关的 MERS-CoV 中是保守的，并且正在纯化选择中。我们的研究结果阐明了基于 RNA 结构的冠状病毒复制、不连续转录和翻译的机制，并将有助于未来开发抗病毒策略。