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Volume 22, Number 2—February 2016
Dispatch

Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool

Thomas HoenenComments to Author , Allison Groseth, Kyle Rosenke, Robert J. Fischer, Andreas Hoenen, Seth D. Judson, Cynthia Martellaro, Darryl Falzarano, Andrea Marzi, R. Burke Squires, Kurt R. Wollenberg, Emmie de Wit, Joseph B. Prescott, David Safronetz, Neeltje van Doremalen, Trenton Bushmaker, Friederike Feldmann, Kristin McNally, Fatorma K. Bolay, Barry Fields, Tara Sealy, Mark Rayfield, Stuart T. Nichol, Kathryn C. Zoon, Moses Massaquoi, Vincent J. Munster, and Heinz Feldmann
Author affiliations: Friedrich-Loeffler-Institut, Greifswald–Insel Riems, Germany (T. Hoenen, A. Groseth); National Institutes of Health, Hamilton, Montana, USA (T. Hoenen, A. Groseth, K. Rosenke, R.J. Fischer, S.D. Judson, C. Martellaro, D. Falzarano, A. Marzi, E. de Wit, J. Prescott, D. Safronetz, N. van Doremalen, T. Bushmaker, F. Feldmann, K. McNally, V.J. Munster, H. Feldmann); Independent scholar, Aachen, Germany (A. Hoenen); University of Saskatchewan, Saskatoon, Saskatchewan, Canada (D. Falzarano); National Institutes of Health, Bethesda, Maryland, USA (R.B. Squires, K.R. Wollenberg, K.C. Zoon); The Liberian Institute for Biomedical Research, Charles Ville, Republic of Liberia (F.K. Bolay); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (B. Fields, T. Sealy, M. Rayfield, S.T. Nichol); Ministry of Health and Social Welfare, Monrovia, Republic of Liberia (M. Massaquoi)

Main Article

Figure 1

MinION sequencing. A) Experimental and B) bioinformatics workflows. Times indicated are the approximate duration for each procedure. C) Sequencing results showing Ebola virus load (expressed as Ct value), percentage of the genome with a minimum read depth of <1 or <33, mean read depth, theoretical probability for a miscalled base (TPMB), and GenBank accession numbers of complete and nearly complete genomes. Brackets at left indicate percentage of Ebola virus-positive patient samples below

Figure 1. MinION sequencing. A) Experimental and B) bioinformatics workflows. Times indicated are the approximate duration for each procedure. RT, reverse transcription. C) Sequencing results showing Ebola virus load (expressed as Ct value), percentage of the genome with a minimum read depth of >1 or >33, mean read depth, theoretical probability for a miscalled base (TPMB), and GenBank accession numbers of complete and nearly complete genomes. Brackets at left indicate percentage of Ebola virus-positive patient samples below each of the 3 cutoff cycle threshold (Ct) values used in this study (Ct <21, <24, <31). Sample 8 was from an oral swab; all others were from blood. NA, not available.

Main Article

Page created: January 15, 2016
Page updated: January 15, 2016
Page reviewed: January 15, 2016
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