Defective Interfering Viral Particles in Acute Dengue Infections

Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.
PLoS ONE (Impact Factor: 3.23). 04/2011; 6(4):e19447. DOI: 10.1371/journal.pone.0019447
Source: PubMed


While much of the genetic variation in RNA viruses arises because of the error-prone nature of their RNA-dependent RNA polymerases, much larger changes may occur as a result of recombination. An extreme example of genetic change is found in defective interfering (DI) viral particles, where large sections of the genome of a parental virus have been deleted and the residual sub-genome fragment is replicated by complementation by co-infecting functional viruses. While most reports of DI particles have referred to studies in vitro, there is some evidence for the presence of DI particles in chronic viral infections in vivo. In this study, short fragments of dengue virus (DENV) RNA containing only key regulatory elements at the 3' and 5' ends of the genome were recovered from the sera of patients infected with any of the four DENV serotypes. Identical RNA fragments were detected in the supernatant from cultures of Aedes mosquito cells that were infected by the addition of sera from dengue patients, suggesting that the sub-genomic RNA might be transmitted between human and mosquito hosts in defective interfering (DI) viral particles. In vitro transcribed sub-genomic RNA corresponding to that detected in vivo could be packaged in virus like particles in the presence of wild type virus and transmitted for at least three passages in cell culture. DENV preparations enriched for these putative DI particles reduced the yield of wild type dengue virus following co-infections of C6-36 cells. This is the first report of DI particles in an acute arboviral infection in nature. The internal genomic deletions described here are the most extensive defects observed in DENV and may be part of a much broader disease attenuating process that is mediated by defective viruses.

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    • "DIs have been demonstrated to play a role in the pathogenesis of some virus infections, such as in acute dengue virus and influenza virus infections (de Chassey et al., 2013; Li et al., 2011; Saira et al., 2013). Given the relative ease with which HMPV accumulates DIs and the role demonstrated for DIs, the role that DIs may play in the pathogenesis of HMPV is clearly of interest. "
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    ABSTRACT: Type I interferon (IFN) production is one of the hallmarks of host innate immune responses upon virus infection. While most respiratory viruses carry IFN-antagonists, reports on human Metapneumovirus (HMPV) have been conflicting. Using deep sequencing we demonstrate that HMPV particles accumulate excessive amounts of defective interfering RNA (DIs) rapidly upon in-vitro passage, which are associated with IFN induction. Importantly, the DIs were edited extensively; up to 70% of the original A and T residues had mutated to G or C respectively. Such high editing rates of viral RNA have not been reported before. Bioinformatics and PCR assays indicated that Adenosine Deaminase acting on RNA (ADAR) is the most likely editing enzyme. HMPV thus has an unusually high propensity to generate DIs, which are edited at an unprecedented high frequency. The conflicting published data on HMPV IFN induction and antagonism are likely explained by DIs in virus stocks. The interaction of HMPV DIs with the RNA editing machinery and IFN responses warrants further investigation.
    Journal of General Virology 04/2014; 95(Pt 8). DOI:10.1099/vir.0.066100-0 · 3.18 Impact Factor
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    • "The C protein is also a pro-apoptotic factor in various cell lines (Yang et al., 2002, 2008; Oh et al., 2006; Netsawang et al., 2010; Morchang et al., 2011). C of JEV was reported to limit viral neurovirulence (Mori et al., 2005) The C-encoding nucleotide sequence of TBEV contains conserved RNA structures that function as replication enhancer elements (Tuplin et al., 2011) † Precursor membrane (prM) 469–972, 26 kDa, 165 aa ER lumen During virion assembly, the prM forms a heterodimer with the E protein and acts as a chaperone for correct E protein folding (Kuhn et al., 2002; Lorenz et al., 2002; Zhang et al., 2003). In the final step of virion maturation in the trans-Golgi network prior, to viral release, the precursor is cleaved by furin and only the C-terminal region (M) is retained in the viral membrane (Heinz et al., 1994; Elshuber & Mandl, 2005; Lindenbach et al., 2007). "
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    ABSTRACT: In nature, vector-borne flaviviruses are persistently cycled between either the tick or mosquito vector and small mammals such as rodents, skunks, and swine. These viruses account for considerable human morbidity and mortality worldwide. Increasing and substantial evidence of viral persistence in humans, which includes the isolation of RNA by RT-PCR and infectious virus by culture, continues to be reported. Viral persistence can also be established in vitro in various human, animal, arachnid and insect cell lines in culture. Although some research has focused on the potential roles of defective virus particles, evasion of the immune response through the manipulation of autophagy and/or apoptosis, the precise mechanism of flavivirus persistence is still not well understood. We propose additional research for further understanding of how viral persistence is established in different systems. Avenues for additional studies include determining if the multifunctional flavivirus protein NS5 has a role in viral persistence, the development of relevant animal models of viral persistence as well as investigating the host responses that allow vector borne flavivirus replication without detrimental effects on infected cells. Such studies might shed more light on the viral-host relationships, and could be used to unravel the mechanisms for establishment of persistence.This article is protected by copyright. All rights reserved.
    Pathogens and Disease 04/2014; 71(2). DOI:10.1111/2049-632X.12178 · 2.40 Impact Factor
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    • "Non-homologous recombination has the potential to mutate large swathes of the viral genome by deleting large portions to form ‘defective genomes’ or by inserting foreign genetic material from other viruses or from the host. Defective genomes evolve during persistent and acute infections in cell culture (14) as well as during wild infections (15,16). The evolution of defective genomes was proposed to be critical in the transition of acute to chronic viral infections (17) and was found in patients persistently infected with measles virus (18), dengue virus (19) and hepatitis C virus (20). "
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    ABSTRACT: We developed an algorithm named ViReMa (Viral-Recombination-Mapper) to provide a versatile platform for rapid, sensitive and nucleotide-resolution detection of recombination junctions in viral genomes using next-generation sequencing data. Rather than mapping read segments of pre-defined lengths and positions, ViReMa dynamically generates moving read segments. ViReMa initially attempts to align the 5′ end of a read to the reference genome(s) with the Bowtie seed-based alignment. A new read segment is then made by either extracting any unaligned nucleotides at the 3′ end of the read or by trimming the first nucleotide from the read. This continues iteratively until all portions of the read are either mapped or trimmed. With multiple reference genomes, it is possible to detect virus-to-host or inter-virus recombination. ViReMa is also capable of detecting insertion and substitution events and multiple recombination junctions within a single read. By mapping the distribution of recombination events in the genome of flock house virus, we demonstrate that this information can be used to discover de novo functional motifs located in conserved regions of the viral genome.
    Nucleic Acids Research 10/2013; 42(2). DOI:10.1093/nar/gkt916 · 9.11 Impact Factor
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