Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses subgenomic RNA (sgRNA) to produce viral proteins for replication and immune evasion. We apply long-read RNA and cDNA sequencing to in vitro human and primate infection models to study transcriptional dynamics. Transcription-regulating sequence (TRS)-dependent sgRNA upregulates earlier in infection than TRS-independent sgRNA. An abundant class of TRS-independent sgRNA consisting of a portion of open reading frame 1ab (ORF1ab) containing nsp1 joins to ORF10, and the 3′ untranslated region (UTR) upregulates at 48 h post-infection in human cell lines. We identify double-junction sgRNA containing both TRS-dependent and -independent junctions. We find multiple sites at which the SARS-CoV-2 genome is consistently more modified than sgRNA and that sgRNA modifications are stable across transcript clusters, host cells, and time since infection. Our work highlights the dynamic nature of the SARS-CoV-2 transcriptome during its replication cycle. Graphical abstract SARS-CoV-2 is the pathogen that is responsible for the global COVID-19 pandemic. Chang et al. demonstrate that the transcriptome of SARS-CoV-2 is dynamic and complex, with expression and relative proportions of viral mRNA changing to reflect the stage of infection in vitro . In contrast, the epi-transcriptome is stable throughout infection.
【저자키워드】 COVID-19, RNA modification, SARS-CoV-2, coronavirus, Direct RNA sequencing, nanopore sequencing, discontinuous transcription, differential expression, direct cDNA sequencing, poly(A) tail,