Even though Cryo-electron microscopy and 3D electron tomography are powerful in delineating the global architectures of SARS-CoV-2, the entire RNA genome inside virions remains unrevealed 18, 19, 20. At this frontier, many efforts have been devoted to study the structure of SARS-CoV-2. RNA structures are widely recognized as critical modulators in regulating transcription, translation, and replications of coronavirus and other RNA viruses 10, 11, 12, 13, 14, 15, 16, 17. Because RNA structure can significantly influence the efficacy of siRNAs and ASOs 8, 9, deciphering the 3D structure of SARS-CoV-2 becomes an urgent need prior to RNA-based drug development. Considering the RNA nature of SARS-CoV-2, RNA-based therapeutics such as small interference RNAs (siRNAs) or antisense oligos (ASOs) are emerging as potent agents to cleave the viral RNA genome in infected host cells. Although global efforts and resources have been redirected to fight against SARS-CoV-2, there are no effective antiviral medicines available yet. Since its outbreak in late December 2019, SARS-CoV-2 has infected tens of millions of people and caused over one million deaths worldwide ( ). SARS-CoV-2 carries one of the largest RNA genomes (~30 kilobases, kb) among all RNA virus families and encodes about 29 proteins 1, 3, 5, 6, 7. As a single-stranded and positive-sense RNA virus, SARS-CoV-2, together with SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), all belong to the Coronaviridae family 4. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causal pathogen of coronavirus disease 2019 (COVID-19) 1, 2, 3. Overall, our work provides a framework for studying the genome structure, function, and dynamics of emerging deadly RNA viruses. Lastly, the structure-guided design of potent small interfering RNAs can obliterate the SARS-CoV-2 in Vero cells.
Unexpectedly, the D614G and the other two accompanying mutations may remodel duplexes into more stable forms. We uncover many long-range duplexes and higher-order junctions, both of which are under purifying selections and contribute to the sequential package of the SARS-CoV-2 genome.
Using vRIC-seq data, we reconstruct the tertiary structure of the SARS-CoV-2 genome and reveal a surprisingly “unentangled globule” conformation. To fill the knowledge gap and facilitate structure-based drug development, we develop a virion RNA in situ conformation sequencing technology, named vRIC-seq, for probing viral RNA genome structure unbiasedly. How the SARS-CoV-2 RNA genome is folded in the virion remains unknown. SARS-CoV-2 carries the largest single-stranded RNA genome and is the causal pathogen of the ongoing COVID-19 pandemic.