Fig. 1

Transcription map of detected transcripts in non-permissive and permissive human cells. a A simplified schematic of the S glycoprotein expression cassette as inserted into the ChAdOx1 nCoV-19 vector backbone in place of the E1 region of ChAdOx1. The nucleotide positions of major features in the expression cassette are indicated. Black transcripts originate from the top strand of the dsDNA viral genome (illustrated by two black lines with circles at the 5′ ends) and blue transcripts originate from the complementary strand. Each arrow depicts the expected transcription start and polyadenylation site but omits splicing events within each transcript that give rise to mature mRNA. Most ChAdOx1 structural proteins are transcribed starting at the same promoter (known as the major late promoter) ending at one of 5 different polyadenylation sites (known as L1–L5). However, the 22K gene can also be expressed from its own promoter as shown. Typically, every member of this late transcript group has three obligate exons at the beginning known as the tripartite leader. In addition, an occasional 4th exon is included containing an ORF known as the i-leader protein. In each subsequent part (b to e), the drawing from IGV viewer illustrates the structure of the dominant transcripts expressed from the 35,539 bp ChAdOx1 nCoV-19 genome that codes for each indicated ORF as detected by dRNAseq in MRC5 cells (b), A549 cells (c) and 293 cells (d). For the E4 region, we have marked with an asterisk those E4 ORFs that are in fact derived from HuAd5. The rectangles indicate exons joined by lines indicating introns. In each case, the dominant transcript for the S glycoprotein of SARS-CoV-2 is indicated in red. Transcripts that map to the top strand of the virus genome are in black and those that map to the bottom strand (and are reversed in orientation) are in blue. e The structure of dominant transcripts derived from the 4323 bp of the HuAd5 E1 region integrated into the genome of HEK293 cells