The architecture of the simian varicella virus transcriptome
Open Access
- 22 November 2021
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLoS Pathogens
- Vol. 17 (11), e1010084
- https://doi.org/10.1371/journal.ppat.1010084
Abstract
Primary infection with varicella-zoster virus (VZV) causes varicella and the establishment of lifelong latency in sensory ganglion neurons. In one-third of infected individuals VZV reactivates from latency to cause herpes zoster, often complicated by difficult-to-treat chronic pain. Experimental infection of non-human primates with simian varicella virus (SVV) recapitulates most features of human VZV disease, thereby providing the opportunity to study the pathogenesis of varicella and herpes zoster in vivo. However, compared to VZV, the transcriptome and the full coding potential of SVV remains incompletely understood. Here, we performed direct long-read RNA sequencing to annotate the SVV transcriptome in lytically SVV-infected African green monkey (AGM) and rhesus macaque (RM) kidney epithelial cells. We refined structures of canonical SVV transcripts and uncovered numerous RNA isoforms, splicing events, fusion transcripts and non-coding RNAs, mostly unique to SVV. We verified the expression of canonical and newly identified SVV transcripts in vivo, using lung samples from acutely SVV-infected cynomolgus macaques. Expression of selected transcript isoforms, including those located in the unique left-end of the SVV genome, was confirmed by reverse transcription PCR. Finally, we performed detailed characterization of the SVV homologue of the VZV latency-associated transcript (VLT), located antisense to ORF61. Analogous to VZV VLT, SVV VLT is multiply spliced and numerous isoforms are generated using alternative transcription start sites and extensive splicing. Conversely, low level expression of a single spliced SVV VLT isoform defines in vivo latency. Notably, the genomic location of VLT core exons is highly conserved between SVV and VZV. This work thus highlights the complexity of lytic SVV gene expression and provides new insights into the molecular biology underlying lytic and latent SVV infection. The identification of the SVV VLT homolog further underlines the value of the SVV non-human primate model to develop new strategies for prevention of herpes zoster. Varicella-zoster virus (VZV)–a ubiquitous human pathogen–infects most individuals during childhood, leading to chickenpox, after which the virus persists in the host for decades. Later in life, VZV reactivates to cause shingles, frequently associated with difficult-to-treat chronic pain. Our limited understanding of the viral life-cycle hampers the development of more effective treatment options. Simian varicella virus (SVV) is the non-human primate homologue of VZV and causes a natural disease in Old World monkeys with clinical, pathological, and immunological features resembling human VZV infection. However, it is unclear how similar both viruses are at the molecular level. Here, we have revisited the genome-wide transcriptional activity of SVV during lytic infection of kidney epithelial cells derived from two non-human primate species and validated expression of newly identified viral transcripts in lung tissue from SVV-infected animals. Together, this has led to the identification of numerous alternative RNA isoforms, mostly unique to SVV, and some of which may have functional implications for the virus. Notably, we defined the SVV latency-associated transcript, which is highly similar to its VZV counterpart. In conclusion, our study shows the value of understanding the molecular biology of a given animal model and identifies potentially conserved mechanism of latency.Keywords
Funding Information
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (022.005.032)
- National Institute of Allergy and Infectious Diseases (R01AI151290)
- National Institute of Allergy and Infectious Diseases (R01AI151290)
This publication has 56 references indexed in Scilit:
- Integrative Genomics Viewer (IGV): high-performance genomics data visualization and explorationBriefings in Bioinformatics, 2012
- Simian varicella virus infection of Chinese rhesus macaques produces ganglionic infection in the absence of rashJournal of NeuroVirology, 2012
- Simian varicella virus gene expression during acute and latent infection of rhesus macaquesJournal of NeuroVirology, 2011
- Herpesvirus systematicsVeterinary Microbiology, 2010
- Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell IdentitiesMolecular Cell, 2010
- BEDTools: a flexible suite of utilities for comparing genomic featuresBioinformatics, 2010
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Functions of the ORF9-to-ORF12 Gene Cluster in Varicella-Zoster Virus Replication and in the Pathogenesis of Skin InfectionJournal of Virology, 2008
- Global analysis of alternative splicing differences between humans and chimpanzeesGenes & Development, 2007
- Splitting pairs: the diverging fates of duplicated genesNature Reviews Genetics, 2002