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Abstract Viruses persist in nature owing to their extreme genetic heterogeneity and large –population sizes, which enable them to evade host immune defenses, escape anti-viral drugs, and adapt to new hosts. The persistence of viruses is challenging to study because mutations affect multiple virus genes, interactions among genes in their impacts on virus growth are seldom known, and measures of viral fitness have yet to be standardized. To address these challenges, we employed a data-driven computational model of cell infection by a virus. The infection model accounted for the kinetics of viral gene expression, functional gene-gene interactions, genome replication, and allocation of host cellular resources to produce progeny of vesicular stomatitis virus (VSV), a prototype RNA virus. We used this model to computationally probe how interactions among genes carrying up to 11 deleterious mutations affect different measures of virus fitness: single-cycle growth yields and multi-cycle rates of infection spread. Individual mutations were implemented by perturbing biophysical parameters associated with individual gene functions of the wild-type model. Our analysis revealed synergistic epistasis among deleterious mutations in their effects on virus yield; so adverse effects of single deleterious mutations were amplified by interaction. For the same mutations, multi-cycle infection spread indicated weak or negligible epistasis, where single mutations act alone in their effects on infection spread. These results were robust to simulation under high and low host resource environments. Our work highlights how different types and magnitudes of epistasis can arise for genetically identical virus variants, depending on the fitness measure. More broadly, gene-gene interactions can differently affect how viruses grow and spread.
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Role of Viral Hemorrhagic Septicemia Virus Matrix (M) Protein in Suppressing Host Transcription
Viral Hemorrhagic Septicemia virus (VHSV) is a pathogenic fish rhabdovirus found in discrete locales throughout the northern hemisphere. VHSV infection of fish cells leads to upregulation of the host's virus detection response, but the virus quickly suppresses interferon (IFN) production and antiviral genes expression. By systematically screening each of the six VHSV structural and nonstructural genes, we have identified matrix protein (M) as its most potent anti-host protein. VHSV-IVb M alone suppressed mitochondrial antiviral signaling protein (MAVS) and type I IFN-induced gene expression in a dose-dependent manner. M also suppressed the constitutively active SV40 promoter and globally decreased cellular RNA levels. Chromatin immunoprecipitation (ChIP) studies illustrated that M inhibited RNA polymerase II (RNAP II) recruitment to gene promoters, and decreased RNAP II CTD Ser2 phosphorylation during VHSV infection. However, transcription directed by RNAP I-III was suppressed by M. To identify regions of functional importance, M proteins from a variety of VHSV strains were tested in cell-based transcriptional inhibition assays. M protein of a particular VHSV-Ia strain, F1, was significantly less potent than -IVb M at inhibiting SV40/luc expression, yet differed by just four amino acids. Mutation of D62 to alanine alone, or in combination with an E181 to alanine mutation (D62A/E181A), dramatically reduced the ability of -IVb M to suppress host transcription. Introducing either M D62A or D62A/E181A mutations into VHSV-IVb via reverse genetics resulted in viruses that replicated efficiently but exhibited less cytotoxicity and reduced anti-transcriptional activities, implicating M as a primary regulator of cytopathicity and host transcriptional suppression. Importance: Viruses must suppress host antiviral responses to replicate and spread between hosts. In these studies, we identified the matrix protein of the deadly fish Novirhabdovirus, VHSV, as a critical mediator of host suppression during infection. Our studies indicated that M alone could block cellular gene expression at very low expression levels. We identified several subtle mutations in M that were less potent at suppressing host transcription. When these mutations were engineered back into recombinant viruses, the resulting viruses replicated well but elicited less toxicity in infected cells and activated host innate immune responses more robustly. These data demonstrated that VHSV M plays an important role in mediating both virus-induced cell toxicity and viral replication. Our data suggest that its roles in these two processes can be separated to design effective attenuated viruses for vaccine candidates.
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- Award ID(s):
- 1354684
- PAR ID:
- 10039452
- Date Published:
- Journal Name:
- Journal of Virology
- ISSN:
- 0022-538X
- Page Range / eLocation ID:
- JVI.00279-17
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1128/JVI.00279-17
