title: Identification of novel viruses using VirusHunter--an automated data analysis pipeline.
abstract: 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.
authors.affiliation: Departments of Pathology & Immunology, Washington University School of Medicine, and the Midwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, St. Louis, Missouri, United States of America.
authors.forename: Guoyan
authors.initials: G
authors.lastname: Zhao
authors.forename: Siddharth
authors.initials: S
authors.lastname: Krishnamurthy
authors.forename: Zhengqiu
authors.initials: Z
authors.lastname: Cai
authors.forename: Vsevolod L
authors.initials: VL
authors.lastname: Popov
authors.forename: Amelia P
authors.initials: AP
authors.lastname: Travassos da Rosa
authors.forename: Hilda
authors.initials: H
authors.lastname: Guzman
authors.forename: Song
authors.initials: S
authors.lastname: Cao
authors.forename: Herbert W
authors.initials: HW
authors.lastname: Virgin
authors.forename: Robert B
authors.initials: RB
authors.lastname: Tesh
authors.forename: David
authors.initials: D
authors.lastname: Wang
mesh_terms: D000818:Animals; D001483:Base Sequence; D002044:Bunyaviridae Infections / Q000175:diagnosis / Q000235:genetics; D019295:Computational Biology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D018163:Orbivirus / Q000235:genetics*; D016856:Phlebovirus / Q000235:genetics*; D012088:Reoviridae Infections / Q000175:diagnosis / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*