Journal article

Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection

Jessie J-Y Chang, Daniel Rawlinson, Miranda Pitt, George Taiaroa, Josie Gleeson, Chenxi Zhou, Francesca Mordant, Ricardo De Paoli-Iseppi, Leon Caly, Damian FJ Purcell, Tim Stinear, Sarah Londrigan, Michael Clark, Deborah Williamson, Kanta Subbarao, Lachlan JM Coin

Cold Spring Harbor Laboratory | Published : 2020

Abstract

Summary SARS-CoV-2 uses subgenomic (sg)RNA to produce viral proteins for replication and immune evasion. We applied long-read RNA and cDNA sequencing to in vitro human and primate infection models to study transcriptional dynamics. Transcription-regulating sequence (TRS)-dependent sgRNA was upregulated earlier in infection than TRS-independent sgRNA. An abundant class of TRS-independent sgRNA consisting of a portion of ORF1ab containing nsp1 joined to ORF10 and 3’UTR was upregulated at 48 hours post infection in human cell lines. We identified double-junction sgRNA containing both TRS-dependent and independent junctions. We found multiple sites at which the SARS-CoV-2 genome is consistently ..

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