ArticleJournal of clinical microbiology2014
Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study.
Article in Journal of clinical microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Medical software for precision diagnostics of infection with immunoprofiling and artificial intelligence.Journal of translational medicine · 2026Review
- Blood Virome After Allogeneic Hematopoietic Stem Cell Transplantation.Open forum infectious diseases · 2025Article
- Towards a Rapid-Turnaround Low-Depth Unbiased Metagenomics Sequencing Workflow on the Illumina Platforms.Bioengineering (Basel, Switzerland) · 2023Article
- Blood virosphere in febrile Tanzanian children.Emerging microbes & infections · 2021Article
- SARS-CoV-2 Evolution among Oncological Population: In-Depth Virological Analysis of a Clinical Cohort.Microorganisms · 2021Article
- Evaluation of targeted next-generation sequencing for detection of equine pathogens in clinical samples.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2021Article
- A streamlined clinical metagenomic sequencing protocol for rapid pathogen identification.Scientific reports · 2021Article
- Article
- Unbiased metagenomic next-generation sequencing of blood from hospitalized febrile children in Gabon.Emerging microbes & infections · 2020Article
- Daily Viral Kinetics and Innate and Adaptive Immune Response Assessment in COVID-19: a Case Series.mSphere · 2020Article
- Article
- Review
- Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in critically ill patients.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2020Article
- Sensitivity and breadth of detection of high-throughput sequencing for adventitious virus detection.NPJ vaccines · 2020Article
- Diagnosis of complication in lung transplantation by TBLB + ROSE + mNGS.Open medicine (Warsaw, Poland) · 2020Article
- Nearly Complete Genome Sequence of a Novel Phlebovirus-Like Virus Detected in a Human Plasma Sample by High-Throughput Sequencing.Microbiology resource announcements · 2019Article
- Article
- Article
- Viral Metagenomics of Blood Donors and Blood-Derived Products Using Next-Generation Sequencing.Transfusion medicine and hemotherapy : offizielles Organ der Deutschen Gesellschaft fur Transfusionsmedizin und Immunhamatologie · 2019Review
- Detection of dicistroviruses RNA in blood of febrile Tanzanian children.Emerging microbes & infections · 2019Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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