FIG 1.

Transcription of SARS-Cov-2. (A) To transcribe the ORFs from S to N (8 ORFs shown in various colors), 8 corresponding sgmRNAs were discontinuously synthesized. In each sgmRNA, 5′ genomic sequences (from the 5′ leader UTR to the leader TRS) and 3′ genomic sequences (from the body TRS to the polyA tail) are fused, which is demonstrated with red dashed-solid lines; that is, each sgmRNA consists of a leader UTR (white rectangle with black frame) with a TRS (red circles), the ORF to be translated (colored rectangles; e.g., pink in S), downstream ORFs with a 3′ UTR (black rectangle), and a poly A tail. The 5′ structure of the S sgmRNA is enlarged (black dashed square). (B) Site-by-site sequencing depth of the SARS-CoV-2 genome from the +20,000 position to the 3′ end at 12 hpi. ORFs from S to N are shown with different colors. The junctions (red dashed circles) between ORF1ab and S, between S and ORF3, between E and M, and between ORF6 and ORF7 are enlarged in 4 inset figures. No shading is applied for the ORF1ab or sites not within the ORF (ORF gaps and 5′/3′ UTR of gRNA), with start sequences of repeated synthesis sites indicated at the junctions.