Mapping the temporal transcriptomic signature of a viral pathogen through CAGE and nanopore sequencing

• DOI: 10.1371/journal.pone.0320439
• Publication Date: 2025-04-15T17:28:14Z
• Authors: Dóra Tombácz; Balázs Kakuk; Gábor Torma; Ádám Fülöp; Ákos Dörmő; Gábor Gulyás; Zsolt Csabai; Zsolt Boldogkői

Introduction Equid alphaherpesvirus 1 (EHV-1), a veterinary pathogen belonging to the Varicellovirus genus, is responsible for significant economic losses in global equine sector. This research involved timescale gene expression profiling and transcriptional reannotation of this herpesvirus. Methods We employed CAGE sequencing on Illumina platform determine transcript start sites, alongside long-read direct cDNA Oxford Nanopore Technology detect full-length viral transcripts. Samples were collected triplicate at nine distinct stages lifecycle. also applied protein synthesis inhibition immediate-early virus. Earlier data native RNA was utilized validate results. The processed using LoRTIA NAGATA software tools. Results time-course analysis dcDNA-Seq enabled characterization these transcripts based their kinetic behavior throughout replication cycle. Furthermore, study comprehensive EHV-1 transcriptome. helped identify transcription sites promoter regions, while provided more accurate approach capturing isoform diversity. Through an integrated approach, we identified validated numerous novel transcripts, thereby refining transcriptome annotation. These methods allowed detailed mapping transcriptome, uncovering previously unknown existing annotations. Conclusions shifting patterns isoforms overlaps suggest sophisticated regulatory network that enables precisely modulate its presence multiple per indicates virus can adapt different infection by producing variety likely enhances genomic efficiency allows it respond effectively host’s environment.