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- Title
Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis.
- Authors
Greninger, Alexander L.; Naccache, Samia N.; Federman, Scot; Guixia Yu; Mbala, Placide; Bres, Vanessa; Stryke, Doug; Bouquet, Jerome; Somasekar, Sneha; Linnen, Jeffrey M.; Dodd, Roger; Mulembakani, Prime; Schneider, Bradley S.; Muyembe-Tamfum, Jean-Jacques; Stramer, Susan L.; Chiu, Charles Y.
- 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 107-108 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 × 105 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.
- Subjects
METAGENOMICS; MICROBIAL genomics; PATHOGENIC microorganisms; MICROORGANISMS; NANOPORES
- Publication
Genome Medicine, 2015, Vol 7, Issue 1, p1
- ISSN
1756-994X
- Publication type
Article
- DOI
10.1186/s13073-015-0220-9