ArticleGenome medicine2015
Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis.
Article in Genome medicine, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 308 papers.
What it found
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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.
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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
308 citing papers in PubMed, 578 citations in OpenAlex.
- Metagenomic next-generation sequencing in the diagnosis of viral encephalitis.World journal of virology · 2026Review
- Near-complete genomes from six human coronavirus HKU1-positive samples recovered by metagenomics in coastal Kenya, 2024-2025.Microbiology resource announcements · 2026Article
- Expanded detection of canine enteric viruses in UK dogs with diarrhoea.Microbial genomics · 2026Article
- Computational Genomics for Resistome Characterization: Current Advancements and Future Challenges Under a One Health Perspective.Antibiotics (Basel, Switzerland) · 2026Review
- Small Epidemic Outbreak of Norovirus in the Pediatric Department of Brescia Civic Hospital (Northern Italy): Genomic Characterization and Phylogenetic Analysis.The Pediatric infectious disease journal · 2026Article
- Bacterial screening of platelet donations in England, 2014-2023.Vox sanguinis · 2026Article
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- One health viral metagenomics for pathogen surveillance: robust mNGS workflows for viral detection and genome recovery from swab and tissue specimens.BMC microbiology · 2026Article
- The sequence alignment problem: boundary conditions as the unifying principle.Briefings in bioinformatics · 2026Review
- RPA Combined With CRISPR/Cas12a for Rapid and Ultrasensitive Detection Dual-Gene of Methicillin-Resistant Staphylococcus aureus (MRSA).Journal of molecular recognition : JMR · 2026Article
- Metagenomic profiling unveils the viral diversity in field-collected Aedes larvae from Central India employing nanopore sequencing.Scientific reports · 2026Article
- Review
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- Quantitative metagenomics using a portable protocol.Applied and environmental microbiology · 2026Article
- Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.Nature methods · 2026Article
- Sensitive, flexible, and affordable serum RNA sequencing for pathogen detection on the Oxford Nanopore platform.BMC genomics · 2026Article
- Optimized library preparation, sequencing, and data analysis protocols for the generation of orbivirus consensus sequences.BMC genomics · 2026Article
- Circulating neuron-derived cfDNA for blood-based detection of Alzheimer's and other neurodegenerative conditions.Frontiers in neurology · 2026Article
- Host-Microbe Multiomic Profiling Predicts Mortality in Sepsis.American journal of respiratory and critical care medicine · 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
248 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
16 authors at 7 institutions in 2 countries.
Funding
Abstract
We report unbiased metagenomic detection of chikungunya virus (CHIKV), Ebola virus (EBOV), and hepatitis C virus (HCV) from four human blood samples by MinION nanopore sequencing coupled to a newly developed, web-based pipeline for real-time bioinformatics analysis on a computational server or laptop (MetaPORE). At titers ranging from 10(7)-10(8) copies per milliliter, reads to EBOV from two patients with acute hemorrhagic fever and CHIKV from an asymptomatic blood donor were detected within 4 to 10 min of data acquisition, while lower titer HCV virus (1 × 10(5) copies per milliliter) was detected within 40 min. Analysis of mapped nanopore reads alone, despite an average individual error rate of 24 % (range 8-49 %), permitted identification of the correct viral strain in all four isolates, and 90 % of the genome of CHIKV was recovered with 97-99 % accuracy. Using nanopore sequencing, metagenomic detection of viral pathogens directly from clinical samples was performed within an unprecedented <6 hr sample-to-answer turnaround time, and in a timeframe amenable to actionable clinical and public health diagnostics.
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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.