Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
Autor(es): 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
Resumo: We report unbiased metagenomic detection of chikungunya virus (CHIKV), Ebola virus (EBOV), - 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 - 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, - 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, - in a timeframe amenable to actionable clinical - public health diagnostics.
Imprenta: Genome Medicine, v. 7, n. 1, p. 99, 2015
Identificador do objeto digital: 10.1186/s13073-015-0220-9
Descritores: Chikungunya virus - Genome ; Chikungunya virus - Infectious diseases ; Chikungunya virus - Viral infections ; Chikungunya Virus - Virus ; Chikungunya virus - Chikungunya fever ; Chikungunya virus - Public health
Data de publicação: 2015
