Title |
Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
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Published in |
Genome Medicine, September 2015
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DOI | 10.1186/s13073-015-0220-9 |
Pubmed ID | |
Authors |
Alexander L. Greninger, Samia N. Naccache, Scot Federman, Guixia Yu, Placide Mbala, Vanessa Bres, Doug Stryke, Jerome Bouquet, Sneha Somasekar, Jeffrey M. Linnen, Roger Dodd, Prime Mulembakani, Bradley S. Schneider, Jean-Jacques Muyembe-Tamfum, Susan L. Stramer, Charles Y. Chiu |
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. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United States | 21 | 22% |
United Kingdom | 14 | 15% |
Denmark | 3 | 3% |
Finland | 3 | 3% |
France | 2 | 2% |
Spain | 2 | 2% |
Myanmar | 1 | 1% |
Germany | 1 | 1% |
Australia | 1 | 1% |
Other | 6 | 6% |
Unknown | 41 | 43% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 45 | 47% |
Scientists | 41 | 43% |
Science communicators (journalists, bloggers, editors) | 5 | 5% |
Practitioners (doctors, other healthcare professionals) | 4 | 4% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Brazil | 7 | <1% |
United Kingdom | 6 | <1% |
Germany | 5 | <1% |
United States | 5 | <1% |
Spain | 2 | <1% |
Japan | 2 | <1% |
Korea, Republic of | 2 | <1% |
Sweden | 1 | <1% |
Israel | 1 | <1% |
Other | 7 | <1% |
Unknown | 952 | 96% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 205 | 21% |
Student > Ph. D. Student | 165 | 17% |
Student > Master | 140 | 14% |
Student > Bachelor | 110 | 11% |
Other | 46 | 5% |
Other | 149 | 15% |
Unknown | 175 | 18% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 276 | 28% |
Biochemistry, Genetics and Molecular Biology | 226 | 23% |
Medicine and Dentistry | 73 | 7% |
Immunology and Microbiology | 61 | 6% |
Computer Science | 39 | 4% |
Other | 111 | 11% |
Unknown | 204 | 21% |