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Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of
Tom J Petty1, Samuel Cordey2, Ismael Padioleau3
1Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland Swiss Institute of Bioinformatics, Geneva, Switzerland Thomas.Petty@unige.ch.
Journal of Clinical Microbiology
|July 11, 2014
Summary
A new bioinformatics pipeline, ezVIR, analyzes high-throughput sequencing (HTS) data to detect a wide range of human viruses in clinical samples. This tool shows promise for routine diagnostic use, accurately identifying viruses in a pilot study.
Area of Science:
- Virology
- Bioinformatics
- Clinical Diagnostics
Background:
- High-throughput sequencing (HTS) offers detailed molecular analysis of clinical specimens.
- Current clinical diagnostics rarely utilize HTS for routine viral detection.
- A need exists for efficient and interpretable HTS analysis tools for clinical settings.
Purpose of the Study:
- To develop and evaluate ezVIR, a bioinformatics pipeline for comprehensive human virus detection from HTS data.
- To assess the performance of ezVIR in identifying diverse viruses in various clinical specimen types.
- To determine the potential of HTS, facilitated by ezVIR, for routine clinical viral diagnostics.
Main Methods:
- Designed ezVIR, a bioinformatics pipeline to process HTS data from standard platforms.
- ezVIR identifies potential human viruses, offers strain typing, genome coverage histograms, and cross-contamination analysis.
- The pipeline was tested on 20 clinical specimens previously diagnosed with various DNA or RNA viruses.
Main Results:
- ezVIR correctly identified 14 out of 14 specimens with small-genome viruses (<40,000 bp).
- The pipeline identified 4 out of 6 specimens containing large-genome viruses.
- The ezVIR pipeline demonstrated a high detection success rate and provided easy-to-interpret reports.
Conclusions:
- The ezVIR pipeline is a promising tool for analyzing HTS data for comprehensive viral detection in clinical samples.
- While further validation is required, ezVIR's performance suggests HTS could be integrated into routine clinical diagnostics.
- The ease of use and interpretation of ezVIR reports support its consideration for clinical applications.
