Fig. 3
From: SARS-CoV-2: from its discovery to genome structure, transcription, and replication
A proposed model of viral RNA transcription and template switch during SARS-CoV-2 infection. A Continuous 5′–3′ transcription of viral genomic +gRNA leads to synthesis of the full-length, negative-sense viral genomic RNA (−gRNA) (left). Because RTC-mediated RNA transcription starts from the highly structured viral gRNA 3′ end, this transcription often leads to discontinuous 5′–3′ transcription by proposed template switch (right). Through interactions between transcription regulatory sequences (TRS) located in the leader (TRSL) and the genome body (TRSB), the template switch results in the production of viral subgenomic RNAs (−sgRNAs). B Diagram of SARS-CoV-2 genome with predicted ORFs (colored boxes) and TRS (smaller red boxes) upstream of individual ORFs. Above are the canonical TRSL-dependent junctions detected in the individual sgRNAs from SARS-CoV-2-infected cells by RNA-seq, with the junction reads corresponding to the sgRNA encoding N protein being the most abundant. Below are the TRSB-independent interactions of TRSL (red) and non-TRS dependent (blue) junctions detected by RNA-seq with unknown function [35, 38]