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

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, Susan L. Stramer, Charles Y. Chiu
doi: https://doi.org/10.1101/020420
Alexander L. Greninger
1Department of Laboratory Medicine, University of California, San Francisco, CA, USA 94107
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA, 91407
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Samia N. Naccache
1Department of Laboratory Medicine, University of California, San Francisco, CA, USA 94107
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA, 91407
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Scot Federman
1Department of Laboratory Medicine, University of California, San Francisco, CA, USA 94107
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA, 91407
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Guixia Yu
1Department of Laboratory Medicine, University of California, San Francisco, CA, USA 94107
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA, 91407
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Placide Mbala
3Institut National de Recherche Biomédicale, Democratic Republic of the Congo, Kinshasa, Africa
6Metabiota, Inc., San Francisco, CA 94104
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Vanessa Bres
4Hologic, Inc., Bedford, MA 01730
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Doug Stryke
1Department of Laboratory Medicine, University of California, San Francisco, CA, USA 94107
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA, 91407
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Jerome Bouquet
1Department of Laboratory Medicine, University of California, San Francisco, CA, USA 94107
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA, 91407
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Sneha Somasekar
1Department of Laboratory Medicine, University of California, San Francisco, CA, USA 94107
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA, 91407
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Jeffrey M. Linnen
4Hologic, Inc., Bedford, MA 01730
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Roger Dodd
5American Red Cross, Gaithersburg, MD 2087
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Prime Mulembakani
6Metabiota, Inc., San Francisco, CA 94104
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Bradley S. Schneider
6Metabiota, Inc., San Francisco, CA 94104
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Jean-Jacques Muyembe
3Institut National de Recherche Biomédicale, Democratic Republic of the Congo, Kinshasa, Africa
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Susan L. Stramer
5American Red Cross, Gaithersburg, MD 2087
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Charles Y. Chiu
1Department of Laboratory Medicine, University of California, San Francisco, CA, USA 94107
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA, 91407
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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 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 minutes of data acquisition, while lower titer HCV virus (1x105 copies per milliliter) was detected within 40 minutes. 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 4 isolates, and 90% of the genome of CHIKV was recovered with >98% accuracy. Using nanopore sequencing, metagenomic detection of viral pathogens directly from clinical samples was performed within an unprecedented <6 hours sample-to-answer turnaround time and in a timeframe amenable for actionable clinical and public health diagnostics.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 03, 2015.
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Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
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, Susan L. Stramer, Charles Y. Chiu
bioRxiv 020420; doi: https://doi.org/10.1101/020420
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Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
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, Susan L. Stramer, Charles Y. Chiu
bioRxiv 020420; doi: https://doi.org/10.1101/020420

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