Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
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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.
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In a published research study, mNGS-based detection of Ebola and chikungunya virus infections on a nanopore sequencer was possible in <10 minutes of sequencing time and <6 hours of sample-to-answer turnaround time overall.
“In a published research study126, mNGS-based detection of Ebola and chikungunya virus infections on a nanopore sequencer was possible in <10 minutes of sequencing time and in <6 hours of sample-to-answer turnaround time overall.”
From Clinical metagenomics (2019) · cites this paper as [126]
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- Authors
- Greninger, A. L., Naccache, S. N., Federman, S., Yu, G., Mbala, P., Bres, V., Stryke, D., Bouquet, J., Somasekar, S., Linnen, J. M., Dodd, R., Mulembakani, P., Schneider, B. S., Muyembe-Tamfum, J.-J., Stramer, S. L., & Chiu, C. Y.
- Affiliations
- University of California, San Francisco (US)
- Hologic (United States) (US)
- American Red Cross (US)
- Metabiota (United States) (US)
- ORCID
- Venue
- Genome Medicine
- Published
- 2015-09-29
- Volume
- 7
- Issue
- 1
- Pages
- 99-99
- ISSN
- 1756-994X (ISSN-L)
- PMC
- PMC4587849
- OpenAlex
- W2140466960
- Cited by
- 558
- References
- 39
- Citations by year
- 2026: 39 · 2025: 35 · 2024: 45 · 2023: 52 · 2022: 46 · 2021: 52 · 2020: 48 · 2019: 68 · 2018: 68 · 2017: 58 · 2016: 35 · 2015: 11
- FWCI
- 24.75
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome Medicine (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Abbott Laboratories, Inc.
- National Institutes of Health (R01-HL105704)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Medicine › Infectious Diseases › Viral Infections and Outbreaks Research
- Physical Sciences › Engineering › Biomedical Engineering › Biosensors and Analytical Detection
- Keywords
- viral metagenomics, nanopore sequencing, chikungunya virus, Ebola virus, hepatitis C virus, blood samples, hemorrhagic fever, virus detection, virus strain identification
- MeSH terms
- Chikungunya virus, Hepatitis C, Humans, RNA, Viral, Hepacivirus, Sequence Analysis, RNA, Hemorrhagic Fever, Ebola, Computational Biology, Ebolavirus, Metagenomics, Nanopores, Chikungunya Fever
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