ABSTRACT
Background: ChAdOx1 nCoV-19 is a recombinant adenovirus vaccine candidate against SARS-CoV-2. Although replication defective in normal cells, 28kbp of adenovirus genes are delivered to the cell nucleus alongside the SARS-CoV-2 S glycoprotein gene.Methods: We used direct RNA sequencing to analyse transcript expression from the ChAdOx1 nCoV-19 genome in human MRC-5 and A549 cell lines that are non-permissive for vector replication alongside the replication permissive cell line, HEK293. In addition, we used quantitative proteomics to study over time the proteome and phosphoproteome of A549 and MRC5 cells infected with the ChAdOx1 nCoV-19 vaccine candidate.Results: The expected SARS-CoV-2 S coding transcript dominated in all cell lines. We also detected rare S transcripts with aberrant splice patterns or polyadenylation site usage. Adenovirus vector transcripts were almost absent in MRC-5 cells but in A549 cells there was a broader repertoire of adenoviral gene expression at very low levels. Proteomically, in addition to S glycoprotein, we detected multiple adenovirus proteins in A549 cells compared to just one in MRC5 cells. Conclusions: Overall the ChAdOx1 nCoV-19 vaccine’s transcriptomic and proteomic repertoire is as expected. The combined transcriptomic and proteomics approaches provide an unparalleled insight into the behaviour of this important class of vaccine candidate and illustrate the potential of this technique to inform future viral vaccine vector design.