title: Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study.
abstract: High-throughput sequencing (HTS) provides the means to analyze clinical specimens in unprecedented molecular detail. While this technology has been successfully applied to virus discovery and other related areas of research, HTS methodology has yet to be exploited for use in a clinical setting for routine diagnostics. Here, a bioinformatics pipeline (ezVIR) was designed to process HTS data from any of the standard platforms and to evaluate the entire spectrum of known human viruses at once, providing results that are easy to interpret and customizable. The pipeline works by identifying the most likely viruses present in the specimen given the sequencing data. Additionally, ezVIR can generate optional reports for strain typing, can create genome coverage histograms, and can perform cross-contamination analysis for specimens prepared in series. In this pilot study, the pipeline was challenged using HTS data from 20 clinical specimens representative of those most often collected and analyzed in daily practice. The specimens (5 cerebrospinal fluid, 7 bronchoalveolar lavage fluid, 5 plasma, 2 serum, and 1 nasopharyngeal aspirate) were originally found to be positive for a diverse range of DNA or RNA viruses by routine molecular diagnostics. The ezVIR pipeline correctly identified 14 of 14 specimens containing viruses with genomes of <40,000 bp, and 4 of 6 specimens positive for large-genome viruses. Although further validation is needed to evaluate sensitivity and to define detection cutoffs, results obtained in this pilot study indicate that the overall detection success rate, coupled with the ease of interpreting the analysis reports, makes it worth considering using HTS for clinical diagnostics.
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland Swiss Institute of Bioinformatics, Geneva, Switzerland Thomas.Petty@unige.ch.
authors.forename: Tom J
authors.initials: TJ
authors.lastname: Petty
authors.affiliation: Division of Infectious Diseases, Laboratory of Virology and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva, Switzerland Department of Medicine, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Samuel
authors.initials: S
authors.lastname: Cordey
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland Swiss Institute of Bioinformatics, Geneva, Switzerland.
authors.forename: Ismael
authors.initials: I
authors.lastname: Padioleau
authors.affiliation: University of Geneva Medical School and Genomics Platform, Geneva, Switzerland.
authors.forename: Mylène
authors.initials: M
authors.lastname: Docquier
authors.affiliation: Department of Medicine, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Lara
authors.initials: L
authors.lastname: Turin
authors.affiliation: Laboratory of Immunohematology, Hematology Unit, Department of Genetic and Laboratory Medicine, University Hospitals of Geneva, University of Geneva, Geneva, Switzerland.
authors.forename: Olivier
authors.initials: O
authors.lastname: Preynat-Seauve
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland Swiss Institute of Bioinformatics, Geneva, Switzerland Imperial College London, South Kensington Campus, London, United Kingdom.
authors.forename: Evgeny M
authors.initials: EM
authors.lastname: Zdobnov
authors.affiliation: Division of Infectious Diseases, Laboratory of Virology and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva, Switzerland Department of Medicine, University of Geneva Medical School, Geneva, Switzerland.
authors.forename: Laurent
authors.initials: L
authors.lastname: Kaiser
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002648:Child; D002675:Child, Preschool; D019295:Computational Biology / Q000379:methods*; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D057166:High-Throughput Screening Assays / Q000379:methods; D006801:Humans; D007223:Infant; D008297:Male; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D010865:Pilot Projects; D014777:Virus Diseases / Q000175:diagnosis* / Q000821:virology*; D014780:Viruses / Q000302:isolation & purification*; D055815:Young Adult