Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

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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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Greninger, A. L., Naccache, S. N., Federman, S., Yu, G., Mbala, P., Bres, V., … Chiu, C. Y. (2015). Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Medicine, 7(1). https://doi.org/10.1186/s13073-015-0220-9

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