Shared Sequence Characteristics Identified in Non-Canonical Rearrangements of HSV-1 Genomes

To investigate genetic rearrangements in the double-stranded DNA genome of herpes simplex virus type-1 (HSV-1), the viral population was serially passaged in various cell types. The serial passaging led to formation of defective genomes, resulted from cell-specific non- canonical rearrangements (NCRs). Interestingly, we discovered shared sequence characteristics underlying the formation of these NCRs across all cell types. Moreover, most NCRs identified in clinical samples shared these characteristics. Based on our findings, we propose a model elucidating the formation of NCRs during viral replication within the nucleus of eukaryotic cells.