ArticleJournal of clinical microbiology2016
Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel.
Article in Journal of clinical microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 121 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
121 citing papers in PubMed, 2 syntheses or guidelines pooled it, 211 citations in OpenAlex.
- Detection of respiratory viruses directly from clinical samples using next-generation sequencing: A literature review of recent advances and potential for routine clinical use.Reviews in medical virology · 2022Pooled it
- Metagenomic Sequencing as a Pathogen-Agnostic Clinical Diagnostic Tool for Infectious Diseases: a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies.Journal of clinical microbiology · 2021Pooled it
- The Value of Combined Radial Endobronchial Ultrasound-Guided Transbronchial Lung Biopsy and Metagenomic Next-Generation Sequencing for Peripheral Pulmonary Infectious Lesions.Canadian respiratory journal · 2020Trial
- Activity and Abundance of Nitrous Oxide Reducing Bacteria in Platismatia glauca: An Epiphytic Lichen in the Boreal Spruce Forest.Environmental microbiology · 2026Article
- Diagnostic sensitivity and specificity of metagenomic sequencing and qPCR for detection of viruses associated with bovine respiratory disease estimated using Bayesian latent class models.Frontiers in veterinary science · 2026Article
- Admission-time immunologic patterns in hospitalized children withFrontiers in pediatrics · 2026Article
- Integrative analysis of pathogen detection, antimicrobial resistance, virulence, and host response in severe infections using metagenomic next-generation sequencing.Frontiers in cellular and infection microbiology · 2026Article
- Case Report: Sequential mNGS captures fatal HSV-1 reactivation after intestinal obstruction-associated ARDS in a 91-year-old.Frontiers in medicine · 2026Article
- Acute Respiratory Infections (ARIs): Current Etiological Perspectives and Advances in Viral Metagenomics-A Review.Viruses · 2025Review
- Targeted next-generation sequencing characterization of respiratory pathogens in children with acute respiratory infection.BMC infectious diseases · 2025Article
- Metatranscriptomic profiling reveals pathogen and host response signatures of pediatric acute sinusitis and upper respiratory infection.Genome medicine · 2025Article
- HPD-Kit: a comprehensive toolkit for pathogen detection and analysis.Frontiers in cellular and infection microbiology · 2025Article
- Respiratory virus infection dynamics and genomic surveillance to detect seasonal influenza subtypes in wastewater: A longitudinal study in Bengaluru, India.PLOS global public health · 2025Article
- Characteristics of adults with influenza A virus pneumonia and co-infections identified by mNGS in Jilin, China during 2024-2025.Frontiers in cellular and infection microbiology · 2025Article
- The application status of sequencing technology in global respiratory infectious disease diagnosis.Infection · 2024Review
- Harnessing the Power of Next-Generation Sequencing in Wastewater-Based Epidemiology and Global Disease Surveillance.Food and environmental virology · 2024Review
- Empirical assessment of the enrichment-based metagenomic methods in identifying diverse respiratory pathogens.Scientific reports · 2024Article
- VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization.Molecular biology and evolution · 2024Article
- Universal Identification of Pathogenic Viruses by Liquid Chromatography Coupled with Tandem Mass Spectrometry Proteotyping.Molecular & cellular proteomics : MCP · 2024Article
- Epstein-Barr Virus BARF1 Is Expressed in Lung Cancer and Is Associated with Cancer Progression.Cells · 2024Article
61 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 4 institutions in 1 country.
Funding
Abstract
Current infectious disease molecular tests are largely pathogen specific, requiring test selection based on the patient's symptoms. For many syndromes caused by a large number of viral, bacterial, or fungal pathogens, such as respiratory tract infections, this necessitates large panels of tests and has limited yield. In contrast, next-generation sequencing-based metagenomics can be used for unbiased detection of any expected or unexpected pathogen. However, barriers for its diagnostic implementation include incomplete understanding of analytical performance and complexity of sequence data analysis. We compared detection of known respiratory virus-positive (n= 42) and unselected (n= 67) pediatric nasopharyngeal swabs using an RNA sequencing (RNA-seq)-based metagenomics approach and Taxonomer, an ultrarapid, interactive, web-based metagenomics data analysis tool, with an FDA-cleared respiratory virus panel (RVP; GenMark eSensor). Untargeted metagenomics detected 86% of known respiratory virus infections, and additional PCR testing confirmed RVP results for only 2 (33%) of the discordant samples. In unselected samples, untargeted metagenomics had excellent agreement with the RVP (93%). In addition, untargeted metagenomics detected an additional 12 viruses that were either not targeted by the RVP or missed due to highly divergent genome sequences. Normalized viral read counts for untargeted metagenomics correlated with viral burden determined by quantitative PCR and showed high intrarun and interrun reproducibility. Partial or full-length viral genome sequences were generated in 86% of RNA-seq-positive samples, allowing assessment of antiviral resistance, strain-level typing, and phylogenetic relatedness. Overall, untargeted metagenomics had high agreement with a sensitive RVP, detected viruses not targeted by the RVP, and yielded epidemiologically and clinically valuable sequence information.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.