ArticleJournal of clinical virology : the official publication of the Pan American Society for Clinical Virology2017
Application of next generation sequencing for the detection of human viral pathogens in clinical specimens.
Article in Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it.
- 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 characterization of the porcine respiratory virome on farms in northern Kazakhstan.Frontiers in veterinary science · 2026Article
- Multiplex metagenomic sequencing for rapid viral pathogen identification and surveillance in clinical specimens.BMC infectious diseases · 2025Article
- Analysis of tick-borne pathogens using next-generation sequencing in ticks from wild animals in the Republic of Korea.Journal of veterinary science · 2025Article
- Integrating DNA/RNA microbe detection and host response for accurate diagnosis, treatment and prognosis of childhood infectious meningitis and encephalitis.Journal of translational medicine · 2024Article
- Virome Analysis and Association of Positive Coxsackievirus B Serology during Pregnancy with Congenital Heart Disease.Microorganisms · 2023Article
- Etiology of lower respiratory tract in pneumonia based on metagenomic next-generation sequencing: a retrospective study.Frontiers in cellular and infection microbiology · 2023Article
- Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome.Microorganisms · 2022Review
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- Article
- Application of a bioinformatic pipeline to RNA-seq data identifies novel virus-like sequence in human blood.G3 (Bethesda, Md.) · 2021Article
- Assessment of Metagenomic Sequencing and qPCR for Detection of Influenza D Virus in Bovine Respiratory Tract Samples.Viruses · 2020Article
- Applying next-generation sequencing to unravel the mutational landscape in viral quasispecies.Virus research · 2020Review
- Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients.The Journal of molecular diagnostics : JMD · 2020Article
- An Optimized Metagenomic Approach for Virome Detection of Clinical Pharyngeal Samples With Respiratory Infection.Frontiers in microbiology · 2020Article
- Rapid, Unbiased PRRSV Strain Detection Using MinION Direct RNA Sequencing and Bioinformatics Tools.Viruses · 2019Article
- Respiratory viruses identified in western Canadian beef cattle by metagenomic sequencing and their association with bovine respiratory disease.Transboundary and emerging diseases · 2019Article
- Strengthening laboratory surveillance of viral pathogens: Experiences and lessons learned building next-generation sequencing capacity in Ghana.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2019Article
- Identification and genetic characterization of a novel Orthobunyavirus species by a straightforward high-throughput sequencing-based approach.Scientific reports · 2019Article
- Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture.Journal of clinical microbiology · 2018Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundNext generation sequencing (NGS) is a new technology that can be used for broad detection of infectious pathogens and is rapidly becoming an essential platform in clinical laboratories. It is not known how NGS will displace or enhance gold standard methodologies in infectious disease diagnosis.
objectivesTo investigate the feasibility and application of NGS technology in public health laboratories and compare NGS technology with conventional methods. STUDY
designIllumina MiSeq system was used to detect viral pathogens alongside other conventional virology methods using typical clinical specimen matrices. Sixteen clinical specimens and two CDC proficiency panels containing seventeen specimens were analyzed.
resultsKnown pathogenic viral nucleic acid was positively identified in all clinical specimens, correlating and building upon results obtained by more conventional laboratory methods. Sequencing depths ranged from 0.008X to 319 and genome coverage ranged from 0.6% to 99.9%. To substantiate the described methods used to analyze data derived from clinical specimens, the results of a clinical proficiency panel are also presented. DISCUSSION: Our results reveal true scarcity of known pathogenic viral nucleic acids in clinical specimens. NGS outperforms more conventional detection methods in this study by turnaround time as well as the improved depth of knowledge in regards to serotyping and drug resistance.
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