Format

Send to

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

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

Author information

1
Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.
2
UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA.
3
Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo, Africa.
4
Metabiota, Inc, San Francisco, CA, 94104, USA.
5
Hologic, Inc, Bedford, MA, 01730, USA.
6
American Red Cross, Gaithersburg, MD, 2087, USA.
7
Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA. charles.chiu@ucsf.edu.
8
UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA. charles.chiu@ucsf.edu.
9
Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA. charles.chiu@ucsf.edu.

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.

PMID:
26416663
PMCID:
PMC4587849
DOI:
10.1186/s13073-015-0220-9
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center