ArticlePloS one2009
Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers.
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Who cites it
125 citing papers in PubMed.
- Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice.Proceedings of the National Academy of Sciences of the United States of America · 2014Trial
- Detectability of Pathogenic RNA Virus Families in Different Body Sites: A Scoping Review.Viruses · 2026Article
- Metagenomic next-generation sequencing-based characterization of the viral spectrum in clinical pulmonary and peripheral blood samples of patients.Frontiers in cellular and infection microbiology · 2025Article
- Longitudinal and quantitative fecal shedding dynamics of SARS-CoV-2, pepper mild mottle virus, and crAssphage.mSphere · 2023Article
- Shift of human pathogen community composition and their potential human health risk after supply suspension in tap water.Scientific reports · 2023Article
- Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines.Pharmaceutics · 2022Review
- Behavioral-biological surveillance of emerging infectious diseases among a dynamic cohort in Thailand.BMC infectious diseases · 2022Article
- Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples.Cell reports methods · 2021Article
- Complete genome characterization of human noroviruses allows comparison of minor alleles during acute and chronic infections.Access microbiology · 2021Article
- Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing.Wellcome open research · 2021Article
- Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives.Frontiers in microbiology · 2021Review
- Inter-Individual Diversity Scaling Analysis of the Human Virome With Classic Diversity-Area Relationship (DAR) Modeling.Frontiers in genetics · 2021Article
- Detection of Plant Pathogenic Viruses in Commercial Gochujang (Fermented Red Pepper Paste) from Korea.The plant pathology journal · 2020Article
- STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies.The Lancet. Infectious diseases · 2020Review
- Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations.Scientific reports · 2020Article
- Tobamoviruses can be frequently present in the oropharynx and gut of infants during their first year of life.Scientific reports · 2020Article
- A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting.Scientific reports · 2020Article
- Dual infection and recombination of Kaposi sarcoma herpesvirus revealed by whole-genome sequence analysis of effusion samples.Virus evolution · 2020Article
- Coding-Complete Genome Sequence of a Recombinant Human Norovirus Strain Identified as Subtype GII.p12_GII.3.Microbiology resource announcements · 2020Article
- Shotgun-Metagenomics on Positive Blood Culture Bottles Inoculated With Prosthetic Joint Tissue: A Proof of Concept Study.Frontiers in microbiology · 2020Article
65 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
21 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the severe acute respiratory syndrome epidemic of 2003 and renewed attention on avian influenza viral pandemics, new surveillance systems are needed for the earlier detection of emerging infectious diseases. We applied a "next-generation" parallel sequencing platform for viral detection in nasopharyngeal and fecal samples collected during seasonal influenza virus (Flu) infections and norovirus outbreaks from 2005 to 2007 in Osaka, Japan. Random RT-PCR was performed to amplify RNA extracted from 0.1-0.25 ml of nasopharyngeal aspirates (N = 3) and fecal specimens (N = 5), and more than 10 microg of cDNA was synthesized. Unbiased high-throughput sequencing of these 8 samples yielded 15,298-32,335 (average 24,738) reads in a single 7.5 h run. In nasopharyngeal samples, although whole genome analysis was not available because the majority (>90%) of reads were host genome-derived, 20-460 Flu-reads were detected, which was sufficient for subtype identification. In fecal samples, bacteria and host cells were removed by centrifugation, resulting in gain of 484-15,260 reads of norovirus sequence (78-98% of the whole genome was covered), except for one specimen that was under-detectable by RT-PCR. These results suggest that our unbiased high-throughput sequencing approach is useful for directly detecting pathogenic viruses without advance genetic information. Although its cost and technological availability make it unlikely that this system will very soon be the diagnostic standard worldwide, this system could be useful for the earlier discovery of novel emerging viruses and bioterrorism, which are difficult to detect with conventional procedures.
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