Reannotation of the simian varicella virus lytic transcriptome and characterization of the latency-associated transcript

Varicella-zoster virus (VZV), an endemic human alphaherpesvirus, causes varicella and establishes lifelong latency in the neurons of the dorsal root and trigeminal ganglia. Later in life, reactivation from latency results in herpes zoster, a condition that is often complicated by untreatable debilitating chronic pain in the affected dermatome. Since VZV is highly species-specific, no small animal models exist that fully recapitulate the viral life cycle. Simian varicella virus (SVV) is the closest known relative of VZV and experimental infection of non-human primates with SVV recapitulates all features of human VZV disease, thus providing an opportunity to study the pathogenesis of VZV disease and latency in vivo. SVV and VZV genomes are co-linear, similar in size and share most open reading frames. The SVV transcriptome is currently annotated based on homology to VZV, likely underestimating complexity and differences between the two viruses. Here, we use direct long-read RNA sequencing to redefine the SVV transcriptome during in vitro and in vivo lytic infection, and reveal previously unrecognized isoforms, splicing events and fusion transcripts, of which some are conserved with VZV. Furthermore, we characterized the SVV homologue of the VZV latency-associated transcript (VLT), that, similar its VZV homologue is located antisense the immediate-early gene ORF61, multiply spliced and exists in many different isoforms during lytic infection, whereas a single dominant form is found during in vivo latency. In summary, this works contributes to understanding the molecular biology of SVV infection, thereby providing a solid basis for further studies into the pathogenesis of lytic and latent infection of both SVV and VZV.