Real-time, portable genome sequencing for Ebola surveillance

Joshua Quick, Nicholas J. Loman (), Sophie Duraffour, Jared T. Simpson, Ettore Severi, Lauren Cowley, Joseph Akoi Bore, Raymond Koundouno, Gytis Dudas, Amy Mikhail, Nobila Ouédraogo, Babak Afrough, Amadou Bah, Jonathan H. J. Baum, Beate Becker-Ziaja, Jan Peter Boettcher, Mar Cabeza-Cabrerizo, Álvaro Camino-Sánchez, Lisa L. Carter, Juliane Doerrbecker, Theresa Enkirch, Isabel García- Dorival, Nicole Hetzelt, Julia Hinzmann, Tobias Holm, Liana Eleni Kafetzopoulou, Michel Koropogui, Abigael Kosgey, Eeva Kuisma, Christopher H. Logue, Antonio Mazzarelli, Sarah Meisel, Marc Mertens, Janine Michel, Didier Ngabo, Katja Nitzsche, Elisa Pallasch, Livia Victoria Patrono, Jasmine Portmann, Johanna Gabriella Repits, Natasha Y. Rickett, Andreas Sachse, Katrin Singethan, Inês Vitoriano, Rahel L. Yemanaberhan, Elsa G. Zekeng, Trina Racine, Alexander Bello, Amadou Alpha Sall, Ousmane Faye, Oumar Faye, N’Faly Magassouba, Cecelia V. Williams, Victoria Amburgey, Linda Winona, Emily Davis, Jon Gerlach, Frank Washington, Vanessa Monteil, Marine Jourdain, Marion Bererd, Alimou Camara, Hermann Somlare, Abdoulaye Camara, Marianne Gerard, Guillaume Bado, Bernard Baillet, Déborah Delaune, Koumpingnin Yacouba Nebie, Abdoulaye Diarra, Yacouba Savane, Raymond Bernard Pallawo, Giovanna Jaramillo Gutierrez, Natacha Milhano, Isabelle Roger, Christopher J. Williams, Facinet Yattara, Kuiama Lewandowski, James Taylor, Phillip Rachwal, Daniel J. Turner, Georgios Pollakis, Julian A. Hiscox, David A. Matthews, Matthew K. O’ Shea, Andrew McD. Johnston, Duncan Wilson, Emma Hutley, Erasmus Smit, Antonino Di Caro, Roman Wölfel, Kilian Stoecker, Erna Fleischmann, Martin Gabriel, Simon A. Weller, Lamine Koivogui, Boubacar Diallo, Sakoba Keïta, Andrew Rambaut, Pierre Formenty, Stephan Günther and Miles W. Carroll
Additional contact information
Joshua Quick: Institute of Microbiology and Infection, University of Birmingham
Nicholas J. Loman: Institute of Microbiology and Infection, University of Birmingham
Sophie Duraffour: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Jared T. Simpson: Ontario Institute for Cancer Research
Ettore Severi: European Centre for Disease Prevention and Control (ECDC)
Lauren Cowley: National Infection Service, Public Health England
Joseph Akoi Bore: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Raymond Koundouno: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Gytis Dudas: Institute of Evolutionary Biology, University of Edinburgh
Amy Mikhail: National Infection Service, Public Health England
Nobila Ouédraogo: Postgraduate Training for Applied Epidemiology (PAE, German FETP), Robert Koch Institute
Babak Afrough: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Amadou Bah: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Jonathan H. J. Baum: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Beate Becker-Ziaja: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Jan Peter Boettcher: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Mar Cabeza-Cabrerizo: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Álvaro Camino-Sánchez: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Lisa L. Carter: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Juliane Doerrbecker: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Theresa Enkirch: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Isabel García- Dorival: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Nicole Hetzelt: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Julia Hinzmann: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Tobias Holm: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Liana Eleni Kafetzopoulou: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Michel Koropogui: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Abigael Kosgey: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Eeva Kuisma: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Christopher H. Logue: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Antonio Mazzarelli: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Sarah Meisel: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Marc Mertens: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Janine Michel: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Didier Ngabo: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Katja Nitzsche: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Elisa Pallasch: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Livia Victoria Patrono: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Jasmine Portmann: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Johanna Gabriella Repits: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Natasha Y. Rickett: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Andreas Sachse: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Katrin Singethan: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Inês Vitoriano: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Rahel L. Yemanaberhan: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Elsa G. Zekeng: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Trina Racine: Public Health Agency of Canada
Alexander Bello: Public Health Agency of Canada
Amadou Alpha Sall: Institut Pasteur Dakar
Ousmane Faye: Institut Pasteur Dakar
Oumar Faye: Institut Pasteur Dakar
N’Faly Magassouba: Laboratoire de Fièvres Hémorragiques de Guinée
Cecelia V. Williams: Sandia National Laboratories
Victoria Amburgey: Sandia National Laboratories
Linda Winona: Sandia National Laboratories
Emily Davis: Ratoma Ebola Diagnostic Center
Jon Gerlach: Ratoma Ebola Diagnostic Center
Frank Washington: Ratoma Ebola Diagnostic Center
Vanessa Monteil: Expertise France, Laboratoire K-plan de Forecariah en Guinée
Marine Jourdain: Expertise France, Laboratoire K-plan de Forecariah en Guinée
Marion Bererd: Expertise France, Laboratoire K-plan de Forecariah en Guinée
Alimou Camara: Expertise France, Laboratoire K-plan de Forecariah en Guinée
Hermann Somlare: Expertise France, Laboratoire K-plan de Forecariah en Guinée
Abdoulaye Camara: Expertise France, Laboratoire K-plan de Forecariah en Guinée
Marianne Gerard: Expertise France, Laboratoire K-plan de Forecariah en Guinée
Guillaume Bado: Expertise France, Laboratoire K-plan de Forecariah en Guinée
Bernard Baillet: Expertise France, Laboratoire K-plan de Forecariah en Guinée
Déborah Delaune: Fédération des Laboratoires - HIA
Koumpingnin Yacouba Nebie: World Health Organization
Abdoulaye Diarra: World Health Organization
Yacouba Savane: World Health Organization
Raymond Bernard Pallawo: World Health Organization
Giovanna Jaramillo Gutierrez: London School of Hygiene and Tropical Medicine
Natacha Milhano: European Centre for Disease Prevention and Control (ECDC)
Isabelle Roger: World Health Organization
Christopher J. Williams: European Centre for Disease Prevention and Control (ECDC)
Facinet Yattara: Ministry of Health Guinea
Kuiama Lewandowski: National Infection Service, Public Health England, Porton Down
James Taylor: Defence Science and Technology Laboratory (Dstl) Porton Down
Phillip Rachwal: Defence Science and Technology Laboratory (Dstl) Porton Down
Daniel J. Turner: Oxford Nanopore Technologies
Georgios Pollakis: Institute of Infection and Global Health, University of Liverpool
Julian A. Hiscox: Institute of Infection and Global Health, University of Liverpool
David A. Matthews: School of Medical Sciences, University of Bristol
Matthew K. O’ Shea: Royal Centre for Defence Medicine
Andrew McD. Johnston: Royal Centre for Defence Medicine
Duncan Wilson: Royal Centre for Defence Medicine
Emma Hutley: Centre of Defence Pathology, Royal Centre for Defence Medicine
Erasmus Smit: Queen Elizabeth Hospital
Antonino Di Caro: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Roman Wölfel: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Kilian Stoecker: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Erna Fleischmann: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Martin Gabriel: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Simon A. Weller: Defence Science and Technology Laboratory (Dstl) Porton Down
Lamine Koivogui: Institut National de Santé Publique
Boubacar Diallo: World Health Organization
Sakoba Keïta: Ministry of Health Guinea
Andrew Rambaut: Institute of Evolutionary Biology, University of Edinburgh
Pierre Formenty: World Health Organization
Stephan Günther: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
Miles W. Carroll: The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine

Nature, 2016, vol. 530, issue 7589, 228-232

Abstract: A nanopore DNA sequencer is used for real-time genomic surveillance of the Ebola virus epidemic in the field in Guinea; the authors demonstrate that it is possible to pack a genomic surveillance laboratory in a suitcase and transport it to the field for on-site virus sequencing, generating results within 24 hours of sample collection.

Date: 2016
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DOI: 10.1038/nature16996

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