title: Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis.
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.
authors.affiliation: Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.|UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA.
authors.forename: Alexander L
authors.initials: AL
authors.lastname: Greninger
authors.affiliation: Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.|UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA.
authors.forename: Samia N
authors.initials: SN
authors.lastname: Naccache
authors.affiliation: Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.|UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA.
authors.forename: Scot
authors.initials: S
authors.lastname: Federman
authors.affiliation: Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.|UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA.
authors.forename: Guixia
authors.initials: G
authors.lastname: Yu
authors.affiliation: Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo, Africa.|Metabiota, Inc, San Francisco, CA, 94104, USA.
authors.forename: Placide
authors.initials: P
authors.lastname: Mbala
authors.affiliation: Hologic, Inc, Bedford, MA, 01730, USA.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Bres
authors.affiliation: Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.|UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA.
authors.forename: Doug
authors.initials: D
authors.lastname: Stryke
authors.affiliation: Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.|UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA.
authors.forename: Jerome
authors.initials: J
authors.lastname: Bouquet
authors.affiliation: Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.|UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA.
authors.forename: Sneha
authors.initials: S
authors.lastname: Somasekar
authors.affiliation: Hologic, Inc, Bedford, MA, 01730, USA.
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Linnen
authors.affiliation: American Red Cross, Gaithersburg, MD, 2087, USA.
authors.forename: Roger
authors.initials: R
authors.lastname: Dodd
authors.affiliation: Metabiota, Inc, San Francisco, CA, 94104, USA.
authors.forename: Prime
authors.initials: P
authors.lastname: Mulembakani
authors.affiliation: Metabiota, Inc, San Francisco, CA, 94104, USA.
authors.forename: Bradley S
authors.initials: BS
authors.lastname: Schneider
authors.affiliation: Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo, Africa.
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Muyembe-Tamfum
authors.affiliation: American Red Cross, Gaithersburg, MD, 2087, USA.
authors.forename: Susan L
authors.initials: SL
authors.lastname: Stramer
authors.affiliation: Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA. charles.chiu@ucsf.edu.|UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA. charles.chiu@ucsf.edu.|Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA. charles.chiu@ucsf.edu.
authors.forename: Charles Y
authors.initials: CY
authors.lastname: Chiu
mesh_terms: D065632:Chikungunya Fever / Q000097:blood; D002646:Chikungunya virus / Q000235:genetics*; D019295:Computational Biology; D029043:Ebolavirus / Q000235:genetics*; D019142:Hemorrhagic Fever, Ebola / Q000097:blood; D016174:Hepacivirus / Q000235:genetics*; D006526:Hepatitis C / Q000097:blood; D006801:Humans; D056186:Metagenomics; D058608:Nanopores; D012367:RNA, Viral / Q000097:blood*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012367:RNA, Viral