The Experts below are selected from a list of 114 Experts worldwide ranked by ideXlab platform
Edward C. Holmes - One of the best experts on this subject based on the ideXlab platform.
-
Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics.
Viruses, 2019Co-Authors: Ashleigh F. Porter, Mang Shi, John-sebastian Eden, Yong-zhen Zhang, Edward C. HolmesAbstract:DNA Viruses comprise a wide array of genome structures and infect diverse host species. To date, most studies of DNA Viruses have focused on those with the strongest disease associations. Accordingly, there has been a marked lack of sampling of DNA Viruses from Invertebrates. Bulk RNA sequencing has resulted in the discovery of a myriad of novel RNA Viruses, and herein we used this methodology to identify actively transcribing DNA Viruses in meta-transcriptomic libraries of diverse Invertebrate species. Our analysis revealed high levels of phylogenetic diversity in DNA Viruses, including 13 species from the Parvoviridae, Circoviridae, and Genomoviridae families of single-stranded DNA virus families, and six double-stranded DNA virus species from the Nudiviridae, Polyomaviridae, and Herpesviridae, for which few Invertebrate Viruses have been identified to date. By incorporating the sequence of a “blank” experimental control we also highlight the importance of reagent contamination in metagenomic studies. In sum, this work expands our knowledge of the diversity and evolution of DNA Viruses and illustrates the utility of meta-transcriptomic data in identifying organisms with DNA genomes.
-
Meta-transcriptomics and the evolutionary biology of RNA Viruses
Virus Research, 2018Co-Authors: Mang Shi, Yong-zhen Zhang, Edward C. HolmesAbstract:Metagenomics is transforming the study of virus evolution, allowing the full assemblage of virus genomes within a host sample to be determined rapidly and cheaply. The genomic analysis of complete transcriptomes, so-called meta-transcriptomics, is providing a particularly rich source of data on the global diversity of RNA Viruses and their evolutionary history. Herein we review some of the insights that meta-transcriptomics has provided on the fundamental patterns and processes of virus evolution, with a focus on the recent discovery of a multitude of novel Invertebrate Viruses. In particular, meta-transcriptomics shows that the RNA virus world is more fluid than previously realized, with relatively frequent changes in genome length and structure. As well as having a transformative impact on studies of virus evolution, meta-transcriptomics presents major new challenges for virus classification, with the greater sampling of host taxa now filling many of the gaps on virus phylogenies that were previously used to define taxonomic groups. Given that most Viruses in the future will likely be characterized using metagenomics approaches, and that we have evidently only sampled a tiny fraction of the total virosphere, we suggest that proposals for virus classification pay careful attention to the wonders unearthed in this new age of virus discovery.
María D. García-pedrajas - One of the best experts on this subject based on the ideXlab platform.
-
Characterization of a novel single-stranded RNA mycovirus related to Invertebrate Viruses from the plant pathogen Verticillium dahliae
Archives of Virology, 2018Co-Authors: M. Carmen Cañizares, Francisco J. López-escudero, Encarnación Pérez-artés, María D. García-pedrajasAbstract:Fungal Viruses, also known as mycoViruses, are widespread in all major groups of fungi. MycoViruses from plant pathogens can reduce the virulence of their host fungus and have therefore potential as biological control agents. This has spurred the identification of novel mycoViruses in plant pathogens, research which is greatly contributing to our understanding of these organisms. In this work, we report the characterization of a novel monopartite mycovirus from Verticillium dahliae , the main causal agent of Verticillium wilt. This novel mycovirus, which we termed Verticillium dahliae RNA virus 1 (VdRV1), was identified in three different isolates of V. dahliae collected in olive growing areas of the Guadalquivir valley, southern Spain. We determined that the VdRV1 genome is a positive (+) single-stranded (ss) RNA, 2631 nucleotides in length, containing two open reading frames. VdRV1 showed few similarities with known mycoViruses, only with a group of unassigned (+) ssRNA mycoViruses which are related to plant Viruses classified within the family Tombusviridae . However, phylogenetic analysis revealed that VdRV1 and the unassigned (+) ssRNA mycoViruses have a closer relationship with recently reported Invertebrate Viruses. This result indicates that as more viral sequences become available, the relationships of mycoViruses with Viruses from other hosts should be reexamined. Additionally, the work supports the hypothesis of a heterogeneous origin for mycoViruses.
Shouwei Ding - One of the best experts on this subject based on the ideXlab platform.
-
Antiviral RNA silencing in mammals: no news is not good news.
Cell reports, 2014Co-Authors: Shouwei Ding, Olivier VoinnetAbstract:In plants, fungi, and Invertebrates, antiviral RNAi is activated by processing viral double-stranded RNA (dsRNA) replication intermediates into virus-derived small interfering RNAs (vsiRNAs). Typically of a discrete length of ~22 nt, vsiRNAs form perfect duplexes, with 2 nt 3′ overhangs diagnostic of the Dicer-like RNase III activities that generate them across kingdoms. vsiRNAs are loaded into and guide Argonaute (AGO) nucleases in order to subsequently suppress virus accumulation (Ding and Voinnet, 2007). Attesting to the importance of antiviral RNAi, the virulence of plant and Invertebrate Viruses requires production of virus-encoded suppressors of RNAi (VSRs) that become dispensable for infection in RNAi-defective hosts (Ding and Voinnet, 2007). Comparatively, antiviral RNAi in mammals remains a hotly debated issue: virus-derived small RNAs (vsRNAs, unlike the vsiRNAs evoked above) isolated in numerous infections of mammalian differentiated cell lines do not conform to the definition of siRNAs; their random size-distribution and strong strand bias usually reflect the unspecific degradation of a single, abundant viral RNA strand (Parameswaran et al., 2010). Perhaps unsurprisingly, therefore, the replication of many Viruses is unchanged in differentiated cells in which Dicer function is genetically disabled (Bogerd et al. 2014). This overall uncertainty has led to a hypothesis that the interferon response, which also detects viral dsRNA, may prevent dsRNA recognition by RNAi in mammals. The above premises have led our groups to explore antiviral RNAi in pluripotent mouse embryonic stem cells (ESCs) that lack a potent interferon response (Maillard et al., 2013, Wang et al., 2014). Bona fide siRNAs were significantly enriched in the 5′ terminal genomic RNA regions of two distinct Viruses, but, importantly, their accumulation was strongly attenuated upon ESC differentiation, leading Maillard et al. (2013) to suggest that multipotency might constitute another, and perhaps major, prerequisite to mammalian antiviral RNAi. Focusing on one of these Viruses, Li et al. (2013) showed that highly abundant vsiRNAs, identical to those detected in ESCs, accumulated in systemically infected suckling mice, but only if a VSR inhibiting mammalian Dicer was disabled from the viral genome. vsiRNA accumulation in vivo correlated with the clearance of the VSR-deficient virus, suggesting that antiviral RNAi operates in vivo (Li et al., 2013). Importantly, replication of the VSR-deficient virus was partially restored in mouse ESCs lacking an RNAi response (Maillard et al., 2013). Rescue of VSR-deficient Viruses in RNAi-deficient hosts has been the defining experiment in all model organisms to conclude the antiviral nature of RNAi (Ding and Voinnet 2007), and so it was concluded that RNAi is indeed antiviral, at least in mouse ESCs. Mammalian antiviral RNAi studies are also complicated by the fact that several viral genomes interact directly with host-encoded, Dicer-dependent microRNAs (miRNAs). Specific host miRNAs may either enhance or inhibit virus infection, as shown for hepatitis C virus in hepatocytes and vesicular stomatitis virus (VSV) in murine macrophages, respectively (Jopling et al., 2005; Otsuka et al., 2007). In a recent manuscript focusing on VSV, Backes et al. (2014) concluded that the in vitro and in vivo mammalian responses to infection are independent of silencing by either vsiRNAs or host-encoded miRNAs and that, consequently, RNAi therapies, including their virus-based formulations, should now be considered safe to mammals and humans. However, our analysis shows that these conclusions are not supported by the experiments presented for the following reasons.
-
virus discovery by deep sequencing and assembly of virus derived small silencing rnas
Proceedings of the National Academy of Sciences of the United States of America, 2010Co-Authors: Qingfa Wu, Rui Lu, Wanxiang Li, Shouwei DingAbstract:In response to infection, Invertebrates process replicating viral RNA genomes into siRNAs of discrete sizes to guide virus clearance by RNA interference. Here, we show that viral siRNAs sequenced from fruit fly, mosquito, and nematode cells were all overlapping in sequence, suggesting a possibility of using siRNAs for viral genome assembly and virus discovery. To test this idea, we examined contigs assembled from published small RNA libraries and discovered five previously undescribed Viruses from cultured Drosophila cells and adult mosquitoes, including three with a positive-strand RNA genome and two with a dsRNA genome. Notably, four of the identified Viruses exhibited only low sequence similarities to known Viruses, such that none could be assigned into an existing virus genus. We also report detection of virus-derived PIWI-interacting RNAs (piRNAs) in Drosophila melanogaster that have not been previously described in any other host species and demonstrate viral genome assembly from viral piRNAs in the absence of viral siRNAs. Thus, this study provides a powerful culture-independent approach for virus discovery in Invertebrates by assembling viral genomes directly from host immune response products without prior virus enrichment or amplification. We propose that Invertebrate Viruses discovered by this approach may include previously undescribed human and vertebrate viral pathogens that are transmitted by arthropod vectors.
Bryony C. Bonning - One of the best experts on this subject based on the ideXlab platform.
-
The Dicistroviridae: An emerging family of Invertebrate Viruses
Virologica Sinica, 2009Co-Authors: Bryony C. BonningAbstract:DicistroViruses comprise a newly characterized and rapidly expanding family of small RNA Viruses of Invertebrates. Several features of this virus group have attracted considerable research interest in recent years. In this review I provide an overview of the Dicistroviridae and describe progress made toward the understanding and practical application of dicistroViruses, including (i) construction of the first infectious clone of a dicistrovirus, (ii) use of the baculovirus expression system for production of an infectious dicistrovirus, (iii) the use of Drosophila C virus for analysis of host response to virus infection, and (iv) correlation of the presence of Israeli acute paralysis virus with honey bee colony collapse disorder. The potential use of dicistroViruses for insect pest management is also discussed. The structure, mechanism and practical use of the internal ribosome entry site (IRES) elements has recently been reviewed elsewhere.
-
The Dicistroviridae: An emerging family of Invertebrate Viruses
Virologica Sinica, 2009Co-Authors: Bryony C. BonningAbstract:DicistroViruses comprise a newly characterized and rapidly expanding family of small RNA Viruses of Invertebrates. Several features of this virus group have attracted considerable research interest in recent years. In this review I provide an overview of the Dicistroviridae and describe progress made toward the understanding and practical application of dicistroViruses, including (i) construction of the first infectious clone of a dicistrovirus, (ii) use of the baculovirus expression system for production of an infectious dicistrovirus, (iii) the use of Drosophila C virus for analysis of host response to virus infection, and (iv) correlation of the presence of Israeli acute paralysis virus with honey bee colony collapse disorder. The potential use of dicistroViruses for insect pest management is also discussed. The structure, mechanism and practical use of the internal ribosome entry site (IRES) elements has recently been reviewed elsewhere.
-
infectious genomic rna of rhopalosiphum padi virus transcribed in vitro from a full length cdna clone
Virology, 2008Co-Authors: Sandhya Boyapalle, Randy J Beckett, Narinder Pal, Allen W Miller, Bryony C. BonningAbstract:Availability of a cloned genome from which infectious RNA can be transcribed is essential for investigating RNA virus molecular mechanisms. To date, no such clones have been reported for the Dicistroviridae, an emerging family of Invertebrate Viruses. Previously we demonstrated baculovirus-driven expression of a cloned Rhopalosiphum padi virus (RhPV; Dicistroviridae) genome that was infectious to aphids, and we identified a cell line (GWSS-Z10) from the glassy-winged sharpshooter, that supports RhPV replication. Here we report that RNA transcribed from a full-length cDNA clone is infectious. Transfection of GWSS-Z10 cells with the RhPV transcript resulted in cytopathic effects, ultrastructural changes, and accumulation of progeny virions, consistent with virus infection. Virions from transcript-infected cells were infectious in aphids. This infectious transcript of a cloned RhPV genome provides a valuable tool, and a more tractable system without interference from baculovirus infection, for investigating replication and pathogenesis of dicistroViruses.
Mang Shi - One of the best experts on this subject based on the ideXlab platform.
-
Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics.
Viruses, 2019Co-Authors: Ashleigh F. Porter, Mang Shi, John-sebastian Eden, Yong-zhen Zhang, Edward C. HolmesAbstract:DNA Viruses comprise a wide array of genome structures and infect diverse host species. To date, most studies of DNA Viruses have focused on those with the strongest disease associations. Accordingly, there has been a marked lack of sampling of DNA Viruses from Invertebrates. Bulk RNA sequencing has resulted in the discovery of a myriad of novel RNA Viruses, and herein we used this methodology to identify actively transcribing DNA Viruses in meta-transcriptomic libraries of diverse Invertebrate species. Our analysis revealed high levels of phylogenetic diversity in DNA Viruses, including 13 species from the Parvoviridae, Circoviridae, and Genomoviridae families of single-stranded DNA virus families, and six double-stranded DNA virus species from the Nudiviridae, Polyomaviridae, and Herpesviridae, for which few Invertebrate Viruses have been identified to date. By incorporating the sequence of a “blank” experimental control we also highlight the importance of reagent contamination in metagenomic studies. In sum, this work expands our knowledge of the diversity and evolution of DNA Viruses and illustrates the utility of meta-transcriptomic data in identifying organisms with DNA genomes.
-
Meta-transcriptomics and the evolutionary biology of RNA Viruses
Virus Research, 2018Co-Authors: Mang Shi, Yong-zhen Zhang, Edward C. HolmesAbstract:Metagenomics is transforming the study of virus evolution, allowing the full assemblage of virus genomes within a host sample to be determined rapidly and cheaply. The genomic analysis of complete transcriptomes, so-called meta-transcriptomics, is providing a particularly rich source of data on the global diversity of RNA Viruses and their evolutionary history. Herein we review some of the insights that meta-transcriptomics has provided on the fundamental patterns and processes of virus evolution, with a focus on the recent discovery of a multitude of novel Invertebrate Viruses. In particular, meta-transcriptomics shows that the RNA virus world is more fluid than previously realized, with relatively frequent changes in genome length and structure. As well as having a transformative impact on studies of virus evolution, meta-transcriptomics presents major new challenges for virus classification, with the greater sampling of host taxa now filling many of the gaps on virus phylogenies that were previously used to define taxonomic groups. Given that most Viruses in the future will likely be characterized using metagenomics approaches, and that we have evidently only sampled a tiny fraction of the total virosphere, we suggest that proposals for virus classification pay careful attention to the wonders unearthed in this new age of virus discovery.
