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

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 lapto...

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Main Authors: Greninger, Alexander L., Naccache, Samia N., Federman, Scot, Yu, Guixia, 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.
Format: Online
Language:English
Published: BioMed Central 2015
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4587849/
id pubmed-4587849
recordtype oai_dc
spelling pubmed-45878492015-09-30 Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis Greninger, Alexander L. Naccache, Samia N. Federman, Scot Yu, Guixia 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. Method 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. BioMed Central 2015-09-29 /pmc/articles/PMC4587849/ /pubmed/26416663 http://dx.doi.org/10.1186/s13073-015-0220-9 Text en © Greninger et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Greninger, Alexander L.
Naccache, Samia N.
Federman, Scot
Yu, Guixia
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.
spellingShingle Greninger, Alexander L.
Naccache, Samia N.
Federman, Scot
Yu, Guixia
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.
Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
author_facet Greninger, Alexander L.
Naccache, Samia N.
Federman, Scot
Yu, Guixia
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.
author_sort Greninger, Alexander L.
title Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
title_short Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
title_full Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
title_fullStr Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
title_full_unstemmed Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
title_sort rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
description 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.
publisher BioMed Central
publishDate 2015
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4587849/
_version_ 1613481613954383872

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