title: Transcriptome analysis reveals the host response to Schmallenberg virus in bovine cells and antagonistic effects of the NSs protein.
abstract: BACKGROUND
  Schmallenberg virus (SBV) is a member of the Orthobunyavirus genus (Bunyaviridae family) causing malformations and abortions in ruminants. Although, as for other members of this family/genus, the non-structural protein NSs has been shown to be an interferon antagonist, very little is known regarding the overall inhibitory effects and targets of orthobunyavirus NSs proteins on host gene expression during infection. Therefore, using RNA-seq this study describes changes to the transcriptome of primary bovine cells following infection with Schmallenberg virus (SBV) or with a mutant lacking the non-structural protein NSs (SBVdelNSs) providing a detailed comparison of the effect of NSs expression on the host cell.
  
  
  RESULTS
  The sequence reads from all samples (uninfected cells, SBV and SBVdelNSs) assembled well to the bovine host reference genome (on average 87.43% of the reads). During infection with SBVdelNSs, 649 genes were differentially expressed compared to uninfected cells (78.7% upregulated) and many of these were known antiviral and IFN-stimulated genes. On the other hand, only nine genes were differentially expressed in SBV infected cells compared to uninfected control cells, demonstrating the strong inhibitory effect of NSs on cellular gene expression. However, the majority of the genes that were expressed during SBV infection are involved in restriction of viral replication and spread indicating that SBV does not completely manage to shutdown the host antiviral response.
  
  
  CONCLUSIONS
  In this study we show the effects of SBV NSs on the transcriptome of infected cells as well as the cellular response to wild type SBV. Although NSs is very efficient in shutting down genes of the host innate response, a number of possible antiviral factors were identified. Thus the data from this study can serve as a base for more detailed mechanistic studies of SBV and other orthobunyaviruses.
authors.affiliation: Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden. anne-lie.blomstrom@slu.se.|MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK. anne-lie.blomstrom@slu.se.
authors.forename: Anne-Lie
authors.initials: AL
authors.lastname: Blomström
authors.affiliation: MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK. Quan.Gu@glasgow.ac.uk.
authors.forename: Quan
authors.initials: Q
authors.lastname: Gu
authors.affiliation: MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK. Gerald.Barry@ucd.ie.|UCD Veterinary Science Centre, School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland. Gerald.Barry@ucd.ie.
authors.forename: Gerald
authors.initials: G
authors.lastname: Barry
authors.affiliation: MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK. Gavin.Wilkie@glasgow.ac.uk.
authors.forename: Gavin
authors.initials: G
authors.lastname: Wilkie
authors.affiliation: MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK. js00356@surrey.ac.uk.
authors.forename: Jessica K
authors.initials: JK
authors.lastname: Skelton
authors.affiliation: MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK. Margaret.Baird@glasgow.ac.uk.
authors.forename: Margaret
authors.initials: M
authors.lastname: Baird
authors.affiliation: MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK. Melanie.McDonald@glasgow.ac.uk.
authors.forename: Melanie
authors.initials: M
authors.lastname: McFarlane
authors.affiliation: MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK. Esther.Schnettler@glasgow.ac.uk.
authors.forename: Esther
authors.initials: E
authors.lastname: Schnettler
authors.affiliation: MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK. Richard.Elliott@glasgow.ac.uk.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Elliott
authors.affiliation: MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK. Massimo.Palmarini@glasgow.ac.uk.
authors.forename: Massimo
authors.initials: M
authors.lastname: Palmarini
authors.affiliation: MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK. Alain.Kohl@glasgow.ac.uk.
authors.forename: Alain
authors.initials: A
authors.lastname: Kohl
mesh_terms: D000818:Animals; D001011:Aorta / Q000166:cytology / Q000378:metabolism; D002044:Bunyaviridae Infections / Q000235:genetics* / Q000821:virology; D002417:Cattle; D002478:Cells, Cultured; D007113:Immunity, Innate; D016851:Orthobunyavirus / Q000302:isolation & purification / Q000378:metabolism / Q000502:physiology*; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D015854:Up-Regulation; D017361:Viral Nonstructural Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D017361:Viral Nonstructural Proteins