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

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 minutes of data acquisition, while lower titer HCV virus (1×105 copies per milliliter) was detected within 40 minutes. 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 4 isolates, and 90% of the genome of CHIKV was recovered with >98% accuracy. Using nanopore sequencing, metagenomic detection of viral pathogens directly from clinical samples was performed within an unprecedented <6 hours sample-to-answer turnaround time and in a timeframe amenable for actionable clinical and public health diagnostics.