The Experts below are selected from a list of 22167 Experts worldwide ranked by ideXlab platform
Shouwei Ding - One of the best experts on this subject based on the ideXlab platform.
-
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.
Lia Van Der Hoek - One of the best experts on this subject based on the ideXlab platform.
-
Culturing of respiratory Viruses in well-differentiated pseudostratified human airway epithelium as a tool to detect unknown Viruses
Influenza and Other Respiratory Viruses, 2014Co-Authors: Seyed Mohammad Jazaeri Farsani, Martin Deijs, Ronald Dijkman, Richard Molenkamp, Rienk E. Jeeninga, Margareta Ieven, Herman Goossens, Lia Van Der HoekAbstract:Background Currently, Virus Discovery is mainly based on molecular techniques. Here, we propose a method that relies on Virus culturing combined with state-of-the-art sequencing techniques. The most natural ex vivo culture system was used to enable replication of respiratory Viruses. Method Three respiratory clinical samples were tested on well-differentiated pseudostratified tracheobronchial human airway epithelial (HAE) cultures grown at an air–liquid interface, which resemble the airway epithelium. Cells were stained with convalescent serum of the patients to identify infected cells and apical washes were analyzed by VIDISCA-454, a next-generation sequencing Virus Discovery technique. Results Infected cells were observed for all three samples. Sequencing subsequently indicated that the cells were infected by either human coronaVirus OC43, influenzaVirus B, or influenzaVirus A. The sequence reads covered a large part of the genome (52%, 82%, and 57%, respectively). Conclusion We present here a new method for Virus Discovery that requires a Virus culture on primary cells and an antibody detection. The Virus in the harvest can be used to characterize the viral genome sequence and cell tropism, but also provides progeny Virus to initiate experiments to fulfill the Koch's postulates.
-
Virus Discovery: are we scientists or genome collectors?
Trends in Microbiology, 2014Co-Authors: Marta Canuti, Lia Van Der HoekAbstract:Some scientists now proclaim that future pandemics can be successfully forecasted, allowing the planning of useful intervention strategies for pandemic preparedness. We underline the fundamental importance of performing dedicated investigations when Viruses are discovered, to guarantee public health authorities the availability of nonerroneous information about potential upcoming threats.
-
Metagenomics in Virus Discovery
Isbt Science Series, 2013Co-Authors: S. M. Jazaeri Farsani, Marta Canuti, Bas B. Oude Munnink, Martin Deijs, Lia Van Der HoekAbstract:Virus infections are a continuous threat to the human population. Apart from infections with known Viruses, there is a world of yet unknown Viruses which may cause new emerging diseases, or cause known infectious diseases. Discovery of unknown Viruses requires serious efforts since there is no universal viral genomic sequence to amplify an unknown viral genome, as is the case for bacteria for which 16S rRNA sequences can be used. In the last decennium, next generation sequencing allowed new approaches for Virus Discovery. Our Virus Discovery method is based on cDNA-AFLP (AFLP: Amplified Fragment Length Polymorphism) combined with next generation sequencing techniques (VIDISCA-454). The method supplies thousands of sequence reads with which any RNA or DNA Virus in patient samples can be detected.
-
Random PCR and ultracentrifugation increases sensitivity and throughput of VIDISCA for screening of pathogens in clinical specimens
Journal of Infection in Developing Countries, 2011Co-Authors: Le Van Tan, Lia Van Der Hoek, Maarten F Jebbink, H. Rogier Van Doorn, Vo Minh Hien, Jeremy Farrar, Nguyen Van Vinh Chau, Menno D. De JongAbstract:Introduction: Virus Discovery based on cDNA-AFLP (VIDISCA) is a sequence-independent Virus Discovery method that was recently developed and successfully used to characterize unknown Viruses in cell cultures. Its applicability, however, is limited by its low sensitivity. Methodology: We evaluated whether the introduction of prior amplification of target sequences by random PCR (rPCR) increases the sensitivity of this method to improve its use on clinical specimens. In addition, ultracentrifugation was added to the protocol to allow for pooling of multiple samples, thereby increasing analytical throughput of the VIDSCA. Results: We showed that rPCR enhanced the sensitivity of VIDISCA by 100-fold for two out of four Viruses in different clinical samples, and that the ultracentrifugation step allowed for analyzing samples of large volumes (4 ml) and simultaneous processing of multiple (~40) clinical specimens. Conclusions: We conclude that this modified VIDISCA protocol is a relatively easy method to use for screening of large numbers of clinical samples that are suspected to contain previously unrecognized pathogens, in settings where ultradeep sequencing platforms are not available.
-
Detection of new Viruses by VIDISCA. Virus Discovery based on cDNA-amplified fragment length polymorphism.
Methods of Molecular Biology, 2008Co-Authors: Krzysztof Pyrc, Ben Berkhout, Maarten F Jebbink, Lia Van Der HoekAbstract:Virus Discovery based on cDNA-AFLP (amplified fragment length polymorphism) (VIDISCA) is a novel approach that provides a fast and effective tool for amplification of unknown genomes, e.g., of human pathogenic Viruses. The VIDISCA method is based on double restriction enzyme processing of a target sequence and ligation of oligonucleotide adaptors that subsequently serve as priming sites for amplification. As the method is based on the common presence of restriction sites, it results in the generation of reproducible, species-specific amplification patterns. The method allows amplification and identification of viral RNA/DNA, with a lower cutoff value of 10(5) copies/ml for DNA Viruses and 10(6) copies/ml for the RNA Viruses. Previously, we described the identification of a novel human coronaVirus, HCoV-NL63, with the use of the VIDISCA method.
M. Poornima - One of the best experts on this subject based on the ideXlab platform.
-
Viral Metagenomics: A Tool for Virus Discovery and Diversity in Aquaculture
Indian Journal of Virology, 2012Co-Authors: S. V. Alavandi, M. PoornimaAbstract:Viruses are abundant biological entities on earth and the emergence of viral pathogens has become a serious threat to aquaculture and fisheries worldwide. However, our response to viral pathogens has been largely reactive, in the sense that a new pathogen is usually not discovered until it has already reached epidemic proportions. Current diagnostic methods such as PCR, immunological assays and pan-viral microarrays are limited in their ability to identify novel Viruses. In this context, the knowledge on the diversity of Viruses in healthy and disease situations becomes important for understanding their role on the health of animals in aquaculture species. Viral metagenomics, which involves viral purification and shotgun sequencing, has proven to be useful for understanding viral diversity and describing novel Viruses in new diseases and has been recognized as an important tool for discovering novel Viruses in human and veterinary medicine. With the advancements in sequencing technology and development of bioinformatics tools for nucleic acid sequence assembly and annotation, information on novel Viruses and diversity of Viruses in marine ecosystems has been rapidly expanding through viral metagenomics. Novel circoViruses and RNA Viruses in Tampa bay pink shrimp, anneloVirus in sea lion, picornaVirus in ringed seals and several new Viruses of marine animals have been recently described using viral metagenomics and this tool has been also recently used in describing viral diversity in aquaculture ponds. Further, a large amount of information has been generated on the diversity of Viruses in the marine environment using viral metagenomics during the last decade. There exists a great potential with viral metagenomics for discovering novel Viruses in asymptomatic marine candidate animals of aquaculture/mariculture, some of which may assume pathogenic status under high density culture and stress. Additionally, viral metagenomics can help our understanding of Viruses present in aquaculture/mariculture settings and routine pathogen surveillance programmes.
Qingfa Wu - One of the best experts on this subject based on the ideXlab platform.
-
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.
Ronald P. Van Rij - One of the best experts on this subject based on the ideXlab platform.
-
Insect Virus Discovery by Metagenomic and Cell Culture-Based Approaches
Methods of Molecular Biology, 2018Co-Authors: Finny S Varghese, Ronald P. Van RijAbstract:Insects are the most abundant and diverse group of animals on earth, but our knowledge of their Viruses is biased toward insect-borne Viruses that cause disease in plants, animals, or humans. Recent metagenomic studies and systematic surveys of Viruses in wild-caught insects have identified an unanticipated large repertoire of novel Viruses and viral sequences. These include new members of existing clades, new clades, and even entirely new Virus families. These studies greatly expand the known virosphere in insects, provide opportunities to study Virus-host interactions, and generate new insights into Virus evolution. In this chapter, we discuss the methods used to identify novel Viruses in insects and highlight some notable surprises arising from these studies.
-
Mosquito-specific and mosquito-borne Viruses: evolution, infection, and host defense.
Current opinion in insect science, 2017Co-Authors: Rebecca Halbach, Sandra Junglen, Ronald P. Van RijAbstract:Recent Virus Discovery programs have identified an extensive reservoir of Viruses in arthropods. It is thought that arthropod Viruses, including mosquito-specific Viruses, are ancestral to vertebrate-pathogenic arboViruses. Mosquito-specific Viruses are restricted in vertebrate cells at multiple levels, including entry, RNA replication, assembly, and by the inability to replicate at high temperatures. Moreover, it is likely that the vertebrate immune system suppresses replication of these Viruses. The evolution from single to dual-host tropism may also require changes in the course of infection in the mosquito host. In this review we explore the adaptive changes required for a switch from a mosquito-specific to a mosquito-borne transmission cycle.
-
Small Silencing RNAs: Piecing Together a Viral Genome
Cell Host & Microbe, 2010Co-Authors: Joël T. Van Mierlo, Koen W. R. Van Cleef, Ronald P. Van RijAbstract:Virus-derived small interfering RNAs (siRNAs) are the hallmark of RNAi-based antiviral immunity. Wu and colleagues demonstrate how viral genomes can be assembled from these small RNA sequences. Their results provide an approach for Virus Discovery as well as important insights into how these siRNAs mediate antiviral defense.
