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Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study

Published in Journal of clinical microbiology. 2014, vol. 52, no. 9, p. 3351-3361
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.
Keywords AdolescentAdultAgedAged, 80 and overChildChild, PreschoolComputational Biology/methodsFemaleHigh-Throughput Nucleotide Sequencing/methodsHigh-Throughput Screening Assays/methodsHumansInfantMaleMiddle AgedMolecular Diagnostic Techniques/methodsPilot ProjectsVirus Diseases/diagnosis/virologyViruses/isolation & purificationYoung Adult
PMID: 25009045
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Article (Published version) (2.8 MB) - public document Free access
Research groups Groupe Laurent Kaiser (virologie clinique) (668)
Génomique Evolutionnaire Computationnelle (830)
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PETTY II, Thomas John et al. Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study. In: Journal of clinical microbiology, 2014, vol. 52, n° 9, p. 3351-3361. doi: 10.1128/JCM.01389-14 https://archive-ouverte.unige.ch/unige:74559

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Deposited on : 2015-08-10

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