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Fig. 1 | Genome Medicine

Fig. 1

From: Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein

Fig. 1

Overview of nanopore inferred transcriptome. a The classical transcription map of coronaviruses adapted for SARS-CoV-2. The genome is itself an mRNA which when translated gives rise to polyproteins pp1a and, upon a ribosomal frameshift, pp1ab. These polyproteins are proteolytically processed down to a range of non-structural proteins termed nsp1–16, some of which will form the viral replication-transcription complex (RTC). The RTC then generates subgenomic mRNA which canonically contains a sequence present at the 5′ end of the viral genome known as the leader sequence. The 3′-end of the leader sequence has a motif, the transcription regulatory sequence (TRS), and there are similar sequences which precede each of the functional ORFs downstream of the replicase gene (pp1ab). This TRS in the leader associates with one of the TRS regions present adjacent to each of the other functional ORFS and this mediates discontinuous transcription between the two during minus-strand RNA synthesis. These minus-strand RNA molecules are used as templates to generate positive sense mRNA, and in this manner, the remaining ORFs on the viral genome are placed 5′ most on the resulting subgenomic mRNAs and are subsequently translated. Orange boxes represent structural proteins and yellow boxes represent accessory proteins. b The total read depth across the viral genome for all reads; the maximum read depth was 511,129. c The structure of only the dominant transcript that codes for each of the identified ORFS. Only transcripts that start inside the leader TRS sequence are considered here. The rectangles represent mapped nucleotides and the arrowed lines represent regions of the genome that are not transcribed during the generation of mRNAs. To the right is noted the 5′ most ORF encoded in the transcript; in parenthesis we note how many individual transcripts were observed. Transcrits coding for proteins we subsequently detected by MS/MS are coloured in green

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