Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Activation of the chicken type I IFN response by infectious bronchitis coronavirus
Kint, J. ; Fernandez Gutierrez, M.M. ; Maier, H.J. ; Britton, P. ; Langereis, M.A. ; Koumans, J. ; Wiegertjes, G.F. ; Forlenza, M. - \ 2015
Journal of Virology 89 (2015)2. - ISSN 0022-538X - p. 1156 - 1167.
mouse hepatitis-virus - singly labeled probes - double-stranded-rna - rig-i - murine coronavirus - innate immunity - receptor activation - viral-rna - cells - induction
Coronaviruses from both the Alpha and Betacoronavirus genera, interfere with the type I interferon (IFN) response in various ways, ensuring limited activation of the IFN response in most cell types. Of Gammacoronaviruses that mainly infect birds, little is known about activation of the host immune response. We show that the prototypical Gammacoronavirus, infectious bronchitis virus (IBV), induces a delayed activation of the IFN response in primary renal cells, tracheal epithelial cells and in a chicken cell line. Ifnß expression in fact, is delayed with respect to the peak of viral replication and accompanying accumulation of dsRNA. In addition, we demonstrate that MDA5 is the primary sensor for Gammacoronavirus infections in chicken cells. Furthermore, we provide evidence that accessory proteins 3a and 3b of IBV modulate the IFN response at the transcriptional and translational level. Finally, we show that, despite the lack of activation of the IFN response during the early phase of IBV infection, signalling of non-self dsRNA through both MDA5 and TLR3 remains intact in IBV-infected cells. Taken together, this study provides the first comprehensive analysis of host-virus interactions of a Gammacoronavirus with avian innate immune responses.
Noncoding subgenomic flavivirus RNA: multiple functions in West Nile virus pathogenesis and modulation of host responses
Roby, J.A. ; Pijlman, G.P. ; Wilusz, J. ; Khromykh, A.A. - \ 2014
Viruses 6 (2014)2. - ISSN 1999-4915 - p. 404 - 427.
japanese encephalitis-virus - double-stranded-rna - la protein binds - innate immune-response - 3 untranslated region - dengue virus - genomic rna - messenger-rna - viral-rna - 3'-untranslated region
Flaviviruses are a large group of positive strand RNA viruses transmitted by arthropods that include many human pathogens such as West Nile virus (WNV), Japanese encephalitis virus (JEV), yellow fever virus, dengue virus, and tick-borne encephalitis virus. All members in this genus tested so far are shown to produce a unique subgenomic flavivirus RNA (sfRNA) derived from the 3' untranslated region (UTR). sfRNA is a product of incomplete degradation of genomic RNA by the cell 5'–3' exoribonuclease XRN1 which stalls at highly ordered secondary RNA structures at the beginning of the 3'UTR. Generation of sfRNA results in inhibition of XRN1 activity leading to an increase in stability of many cellular mRNAs. Mutant WNV deficient in sfRNA generation was highly attenuated displaying a marked decrease in cytopathicity in cells and pathogenicity in mice. sfRNA has also been shown to inhibit the antiviral activity of IFN-a/ß by yet unknown mechanism and of the RNAi pathway by likely serving as a decoy substrate for Dicer. Thus, sfRNA is involved in modulating multiple cellular pathways to facilitate viral pathogenicity; however the overlying mechanism linking all these multiple functions of sfRNA remains to be elucidated.
RNA Elements in Open Reading Frames of the Bluetongue Virus Genome Are Essential for Virus Replication
Feenstra, F. ; Gennip, H.G.P. van; Water, S.G.P. van de; Rijn, P.A. van - \ 2014
PLoS One 9 (2014)3. - ISSN 1932-6203
polymerase-chain-reaction - intragenic recombination - insect cells - protein ns2 - fever virus - vp6 protein - viral-rna - segment - binding - core
Members of the Reoviridae family are non-enveloped multi-layered viruses with a double stranded RNA genome consisting of 9 to 12 genome segments. Bluetongue virus is the prototype orbivirus (family Reoviridae, genus Orbivirus), causing disease in ruminants, and is spread by Culicoides biting midges. Obviously, several steps in the Reoviridae family replication cycle require virus specific as well as segment specific recognition by viral proteins, but detailed processes in these interactions are still barely understood. Recently, we have shown that expression of NS3 and NS3a proteins encoded by genome segment 10 of bluetongue virus is not essential for virus replication. This gave us the unique opportunity to investigate the role of RNA sequences in the segment 10 open reading frame in virus replication, independent of its protein products. Reverse genetics was used to generate virus mutants with deletions in the open reading frame of segment 10. Although virus with a deletion between both start codons was not viable, deletions throughout the rest of the open reading frame led to the rescue of replicating virus. However, all bluetongue virus deletion mutants without functional protein expression of segment 10 contained inserts of RNA sequences originating from several viral genome segments. Subsequent studies showed that these RNA inserts act as RNA elements, needed for rescue and replication of virus. Functionality of the inserts is orientation-dependent but is independent from the position in segment 10. This study clearly shows that RNA in the open reading frame of Reoviridae members does not only encode proteins, but is also essential for virus replication
A Step Forward in Molecular Diagnostics of Lyssaviruses – Results of a Ring Trial among European Laboratories
Fischer, M. ; Wernike, K. ; Freuling, C.M. ; Müller, T. ; Aylan, O. ; Brochier, B. ; Cliquet, F. ; Vázquez-Morón, S. ; Hostnik, P. ; Huovilainen, A. ; Isaksson, M. ; Kooi, E.A. - \ 2013
PLoS One 8 (2013)3. - ISSN 1932-6203 - 9 p.
polymerase-chain-reaction - rabies-related viruses - real-time pcr - rt-pcr - cerebrospinal-fluid - saliva samples - viral-rna - bat - assay - infection
Rabies is a lethal and notifiable zoonotic disease for which diagnostics have to meet the highest standards. In recent years, an evolution was especially seen in molecular diagnostics with a wide variety of different detection methods published. Therefore, a first international ring trial specifically designed on the use of reverse transcription polymerase chain reaction (RT-PCR) for detection of lyssavirus genomic RNA was organized. The trial focussed on assessment and comparison of the performance of conventional and real-time assays. In total, 16 European laboratories participated. All participants were asked to investigate a panel of defined lyssavirus RNAs, consisting of Rabies virus (RABV) and European bat lyssavirus 1 and 2 (EBLV-1 and -2) RNA samples, with systems available in their laboratory. The ring trial allowed the important conclusion that conventional RT-PCR assays were really robust assays tested with a high concordance between different laboratories and assays. The real-time RT-PCR system by Wakeley et al. (2005) in combination with an intercalating dye, and the combined version by Hoffmann and co-workers (2010) showed good sensitivity for the detection of all RABV samples included in this test panel. Furthermore, all used EBLV-specific assays, real-time RT-PCRs as well as conventional RT-PCR systems, were shown to be suitable for a reliable detection of EBLVs. It has to be mentioned that differences were seen in the performance between both the individual RT-PCR systems and the laboratories. Laboratories which used more than one molecular assay for testing the sample panel always concluded a correct sample result. Due to the markedly high genetic diversity of lyssaviruses, the application of different assays in diagnostics is needed to achieve a maximum of diagnostic accuracy. To improve the knowledge about the diagnostic performance proficiency testing at an international level is recommended before using lyssavirus molecular diagnostics e.g. for confirmatory testing.
Preferential use of RNA leader sequences during influenza A transcription initiation in vivo
Geerts-Dimitriadou, C. ; Goldbach, R.W. ; Kormelink, R.J.M. - \ 2011
Virology 409 (2011)1. - ISSN 0042-6822 - p. 27 - 32.
b-virus genome - complete nucleotide-sequence - cap-snatching mechanism - open reading frame - messenger-rna - viral-rna - 5' ends - base complementarity - neuraminidase gene - alpha-amanitin
In vitro transcription initiation studies revealed a preference of influenza A virus for capped RNA leader sequences with base complementarity to the viral RNA template. Here, these results were verified during an influenza infection in MDCK cells. Alfalfa mosaic virus RNA3 leader sequences mutated in their base complementarity to the viral template, or the nucleotides 5' of potential base-pairing residues, were tested for their use either singly or in competition. These analyses revealed that influenza transcriptase is able to use leaders from an exogenous mRNA source with a preference for leaders harboring base complementarity to the 3'-ultimate residues of the viral template, as previously observed during in vitro studies. Internal priming at the 3'-penultimate residue, as well as “prime-and-realign” was observed. The finding that multiple base-pairing promotes cap donor selection in vivo, and the earlier observed competitiveness of such molecules in vitro, offers new possibilities for antiviral drug design.
Base-pairing promotes leader selection to prime in vitro influenza genome transcription
Geerts-Dimitriadou, C. ; Zwart, M.P. ; Goldbach, R.W. ; Kormelink, R.J.M. - \ 2011
Virology 409 (2011)1. - ISSN 0042-6822 - p. 17 - 26.
messenger-rna synthesis - cap-snatching mechanism - mosaic-virus rnas - viral-rna - 5' ends - complementary rna - a virus - polymerase - endonuclease - sequences
The requirements for alignment of capped leader sequences along the viral genome during influenza transcription initiation (cap-snatching) have long been an enigma. In this study, competition experiments using an in vitro transcription assay revealed that influenza virus transcriptase prefers leader sequences with base complementarity to the 3'-ultimate residues of the viral template, 10 or 11 nt from the 5' cap. Internal priming at the 3'-penultimate residue, as well as prime-and-realign was observed. The nucleotide identity immediately 5' of the base-pairing residues also affected cap donor usage. Application to the in vitro system of RNA molecules with increased base complementarity to the viral RNA template showed stronger reduction of globin RNA leader initiated influenza transcription compared to those with a single base-pairing possibility. Altogether the results indicated an optimal cap donor consensus sequence of 7mG-(N)7–8-(A/U/G)-(A/U)-AGC-3'.
Tomato spotted wilt virus S-segment mRNAs have overlapping 3'-ends containing a predicted stem-loop structure and conserved sequence motif
Knippenberg, I.C. van; Goldbach, R.W. ; Kormelink, R.J.M. - \ 2005
Virus Research 110 (2005)1-2. - ISSN 0168-1702 - p. 125 - 131.
mosaic-virus - independent translation - uukuniemi virus - punta-toro - viral-rna - termini - transcription - mechanism - protein - initiation
The Tomato spotted wilt virus ambisense M- and S-RNA segments contain an A/U-rich intergenic region predicted to form a stable hairpin structure. The site of transcription termination of S-segment encoded N and NSs mRNAs synthesised in an in vitro transcription system was roughly mapped to the 3¿-end of the intergenic hairpin, i.e. position 1568¿1574 for N and position 1852¿1839 for NSs, as determined by RT-PCR cloning and size estimation on Northern blots. This suggests that these viral transcripts contain a predicted stem-loop structure at their 3¿-end. The potential involvement of the 3¿-end structure in transcription termination is discussed
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