Identification of novel viruses using VirusHunter--an automated data analysis pipeline
Quick and accurate identification of microbial pathogens is essential for both diagnosis and response to emerging infectious diseases. The advent of next-generation sequencing technology offers an unprecedented platform for rapid sequencing-based identification of novel viruses. We have developed a...
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| Veröffentlicht in: | PloS one 2013-10, Vol.8 (10), p.e78470-e78470 |
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| creator | Zhao, Guoyan Krishnamurthy, Siddharth Cai, Zhengqiu Popov, Vsevolod L Travassos da Rosa, Amelia P Guzman, Hilda Cao, Song Virgin, Herbert W Tesh, Robert B Wang, David |
| description | Quick and accurate identification of microbial pathogens is essential for both diagnosis and response to emerging infectious diseases. The advent of next-generation sequencing technology offers an unprecedented platform for rapid sequencing-based identification of novel viruses. We have developed a customized bioinformatics data analysis pipeline, VirusHunter, for the analysis of Roche/454 and other long read Next generation sequencing platform data. To illustrate the utility of VirusHunter, we performed Roche/454 GS FLX titanium sequencing on two unclassified virus isolates from the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA). VirusHunter identified sequences derived from a novel bunyavirus and a novel reovirus in the two samples respectively. Further sequence analysis demonstrated that the viruses were novel members of the Phlebovirus and Orbivirus genera. Both Phlebovirus and Orbivirus genera include many economic important viruses or serious human pathogens. |
| doi_str_mv | 10.1371/journal.pone.0078470 |
| format | Article |
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The advent of next-generation sequencing technology offers an unprecedented platform for rapid sequencing-based identification of novel viruses. We have developed a customized bioinformatics data analysis pipeline, VirusHunter, for the analysis of Roche/454 and other long read Next generation sequencing platform data. To illustrate the utility of VirusHunter, we performed Roche/454 GS FLX titanium sequencing on two unclassified virus isolates from the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA). VirusHunter identified sequences derived from a novel bunyavirus and a novel reovirus in the two samples respectively. Further sequence analysis demonstrated that the viruses were novel members of the Phlebovirus and Orbivirus genera. Both Phlebovirus and Orbivirus genera include many economic important viruses or serious human pathogens.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0078470</identifier><identifier>PMID: 24167629</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Animals ; Arthropods ; Base Sequence ; Bioinformatics ; Bunyaviridae Infections - diagnosis ; Bunyaviridae Infections - genetics ; Computational Biology ; Data analysis ; Data processing ; Departments ; Drug resistance ; Genomes ; High-Throughput Nucleotide Sequencing - methods ; Humans ; Immunology ; Infectious diseases ; Information management ; Medicine ; Microorganisms ; Molecular Sequence Data ; Orbivirus - genetics ; Pathogens ; Pathology ; Phlebovirus - genetics ; Pipelines ; Reoviridae Infections - diagnosis ; Reoviridae Infections - genetics ; Researchers ; Sequence Analysis, DNA - methods ; Sequence Analysis, RNA - methods ; Viruses</subject><ispartof>PloS one, 2013-10, Vol.8 (10), p.e78470-e78470</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Zhao et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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The advent of next-generation sequencing technology offers an unprecedented platform for rapid sequencing-based identification of novel viruses. We have developed a customized bioinformatics data analysis pipeline, VirusHunter, for the analysis of Roche/454 and other long read Next generation sequencing platform data. To illustrate the utility of VirusHunter, we performed Roche/454 GS FLX titanium sequencing on two unclassified virus isolates from the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA). VirusHunter identified sequences derived from a novel bunyavirus and a novel reovirus in the two samples respectively. Further sequence analysis demonstrated that the viruses were novel members of the Phlebovirus and Orbivirus genera. 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| subjects | Animals Arthropods Base Sequence Bioinformatics Bunyaviridae Infections - diagnosis Bunyaviridae Infections - genetics Computational Biology Data analysis Data processing Departments Drug resistance Genomes High-Throughput Nucleotide Sequencing - methods Humans Immunology Infectious diseases Information management Medicine Microorganisms Molecular Sequence Data Orbivirus - genetics Pathogens Pathology Phlebovirus - genetics Pipelines Reoviridae Infections - diagnosis Reoviridae Infections - genetics Researchers Sequence Analysis, DNA - methods Sequence Analysis, RNA - methods Viruses |
| title | Identification of novel viruses using VirusHunter--an automated data analysis pipeline |
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