Defining the Temporal Transcriptomic Landscape of a Viral Pathogen through Nanopore and CAGE sequencing

A member of the Varicellovirus genus of herpesviruses, equid alphaherpesvirus 1 (EHV-1) was subjected to timescale profiling in this research. We employed cap analysis gene expression sequencing (CAGE-Seq) on Illumina platform to determine the transcript start sites alongside long-read direct cDNA sequencing (dcDNA-Seq) on Oxford Nanopore Technology platform to detect full-length viral transcripts. Samples were collected at nine distinct stages of the viral lifecycle, with triplicates taken at each stage. We also applied protein synthesis inhibition to determine the immediate-early gene expression of the virus. Analysis of the time-course expression of the viral transcripts using dcDNA-Seq allowed their kinetic categorization. Moreover, the EHV-1 transcriptome was reannotated using CAGE-Seq, long-read dcDNA-Seq, and our previous data obtained from native RNA sequencing.