ArticleJournal of clinical virology : the official publication of the Pan American Society for Clinical Virology2015
Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information.
Article in Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
What it found
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The trial behind it
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it, 37 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
- The respiratory tract virome: unravelling the role of viral dark matter in respiratory health and disease.European respiratory review : an official journal of the European Respiratory Society · 2025Review
- The plasma viral communities associate with clinical profiles in a large-scale haematological patients cohort.Microbiome · 2024Article
- Enhanced DNA and RNA pathogen detection via metagenomic sequencing in patients with pneumonia.Journal of translational medicine · 2022Article
- Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients.Clinical microbiology reviews · 2020Review
- Clinical diagnostic application of metagenomic next-generation sequencing in children with severe nonresponding pneumonia.PloS one · 2020Article
- Translating Recent Microbiome Insights in Otitis Media into Probiotic Strategies.Clinical microbiology reviews · 2019Review
- Precisely tailored shell thickness and LnNanoscale advances · 2019Article
- Infectious Disease Transmission in Solid Organ Transplantation: Donor Evaluation, Recipient Risk, and Outcomes of Transmission.Transplantation direct · 2019Article
- Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture.Journal of clinical microbiology · 2018Article
- Critical evaluation of FDA-approved respiratory multiplex assays for public health surveillance.Expert review of molecular diagnostics · 2018Review
- Unbiased Strain-Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol.Scientific reports · 2018Article
- Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015.PloS one · 2018Article
- Review article: the human intestinal virome in health and disease.Alimentary pharmacology & therapeutics · 2017Review
- Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique.Science China. Life sciences · 2017Article
- The Virome of the Human Respiratory Tract.Clinics in chest medicine · 2017Review
- Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome.Genome biology · 2017Article
- An Improved Barcoded Oligonucleotide Primers-based Next-generation Sequencing Approach for Direct Identification of Viral Pathogens in Clinical Specimens.Biomedical and environmental sciences : BES · 2017Article
- Metagenomic analysis of viral genetic diversity in respiratory samples from children with severe acute respiratory infection in China.Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases · 2016Article
- The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae.Frontiers in microbiology · 2016Review
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAcute respiratory tract infections (RTI) cause substantial morbidity during childhood, and are responsible for the majority of pediatric infectious diseases. Although most acute RTI are thought to be of viral origin, viral etiology is still unknown in a significant number of cases.
objectivesMultiplexed whole genome sequencing (WGS) was used for virome determination directly on clinical samples as proof of principle for the use of deep sequencing techniques in clinical diagnosis of viral infections. STUDY
designWGS was performed with nucleic acids from sputum and nasopharyngeal aspirates from four pediatric patients with known respiratory tract infections (two patients with human rhinovirus, one patient with human metapneumovirus and one patient with respiratory syncytial virus), and from four pediatric patients with PCR-negative RTI, and two control samples.
resultsViral infections detected by routine molecular diagnostic methods were confirmed by WGS; in addition, typing information of the different viruses was generated. In three out of four samples from pediatric patients with PCR-negative respiratory tract infections and the two control samples, no causative viral pathogens could be detected. In one sample from a patient with PCR-negative RTI, rhinovirus type-C was detected. Almost complete viral genomes could be assembled and in all cases virus species could be determined.
conclusionsOur study shows that, in a single run, viral pathogens can be detected and characterized, providing information for clinical assessment and epidemiological studies. We conclude that WGS is a powerful tool in clinical virology that delivers comprehensive information on the viral content of clinical samples.
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