Systems biology decodes herpes simplex virus 1

Since the genome of herpes simplex virus 1 (HSV-1) was first sequenced more than 30 years ago, the 84 genes it was thought to encode have been intensively studied. Here, we unravel the full complement of viral transcription and translation during lytic infection with base-pair resolution by computational integration of multi-omics data. This includes a total of 201 viral transcripts and 296 open reading frames (ORFs), comprising all known large ORFs, 55 large novel ORFs including a novel spliced ORF in the ICP0 locus that initiates from a non-AUG start codon and a novel strongly translated ORF in the ICP34.5 locus as well as multiple short ORFs. By defining viral gene modules, we link translation of ORFs to the expression of transcript isoforms. This explained translation of the vast majority of viral ORFs as well as N-terminal extensions and truncations thereof. We show that N-terminal extensions initiating from non-AUG start codons govern subcellular protein localization and packaging of key viral regulators and structural proteins. This work has great implications for future functional studies, vaccine design and novel oncolytic therapies.