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

Genome Med. 2015 Sep 29;7:99. doi: 10.1186/s13073-015-0220-9.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chikungunya Fever / blood
  • Chikungunya virus / genetics*
  • Computational Biology
  • Ebolavirus / genetics*
  • Hemorrhagic Fever, Ebola / blood
  • Hepacivirus / genetics*
  • Hepatitis C / blood
  • Humans
  • Metagenomics
  • Nanopores
  • RNA, Viral / blood*
  • Sequence Analysis, RNA / methods*

Substances

  • RNA, Viral