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Real-time, portable genome sequencing for Ebola surveillance

Author

Listed:
  • 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
    Bernhard-Nocht-Institute for Tropical Medicine)

  • Jared T. Simpson

    (Ontario Institute for Cancer Research
    University of Toronto)

  • 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
    National Infection Service, Public Health England, Porton Down)

  • Amadou Bah

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Swiss Tropical and Public Health Institute)

  • Jonathan H. J. Baum

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Bernhard-Nocht-Institute for Tropical Medicine)

  • Beate Becker-Ziaja

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Bernhard-Nocht-Institute for Tropical Medicine)

  • Jan Peter Boettcher

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Robert Koch Institute)

  • Mar Cabeza-Cabrerizo

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    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
    University College London)

  • Juliane Doerrbecker

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Bernhard-Nocht-Institute for Tropical Medicine)

  • Theresa Enkirch

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Paul-Ehrlich-Institut)

  • Isabel García- Dorival

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Institute of Infection and Global Health, University of Liverpool)

  • Nicole Hetzelt

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Robert Koch Institute)

  • Julia Hinzmann

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Robert Koch Institute)

  • Tobias Holm

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Bernhard-Nocht-Institute for Tropical Medicine)

  • Liana Eleni Kafetzopoulou

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Laboratory for Clinical and Epidemiological Virology)

  • Michel Koropogui

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Ministry of Health Guinea)

  • Abigael Kosgey

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Kenya Medical Research Institute)

  • Eeva Kuisma

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    National Infection Service, Public Health England, Porton Down)

  • Christopher H. Logue

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    National Infection Service, Public Health England, Porton Down)

  • Antonio Mazzarelli

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    National Institute for Infectious Diseases L. Spallanzani)

  • Sarah Meisel

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Bernhard-Nocht-Institute for Tropical Medicine)

  • Marc Mertens

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Friedrich-Loeffler-Institute)

  • Janine Michel

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Robert Koch Institute)

  • Didier Ngabo

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    National Infection Service, Public Health England, Porton Down)

  • Katja Nitzsche

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Bernhard-Nocht-Institute for Tropical Medicine)

  • Elisa Pallasch

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Bernhard-Nocht-Institute for Tropical Medicine)

  • Livia Victoria Patrono

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Bernhard-Nocht-Institute for Tropical Medicine)

  • Jasmine Portmann

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Federal Office for Civil Protection, Spiez Laboratory)

  • Johanna Gabriella Repits

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Janssen-Cilag)

  • Natasha Y. Rickett

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Institute of Infection and Global Health, University of Liverpool
    NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool)

  • Andreas Sachse

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Robert Koch Institute)

  • Katrin Singethan

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Institute of Virology, Technische Universität München)

  • Inês Vitoriano

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    National Infection Service, Public Health England, Porton Down)

  • Rahel L. Yemanaberhan

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Bernhard-Nocht-Institute for Tropical Medicine)

  • Elsa G. Zekeng

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Institute of Infection and Global Health, University of Liverpool
    NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool)

  • 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
    Ratoma Ebola Diagnostic Center)

  • Victoria Amburgey

    (Sandia National Laboratories
    Ratoma Ebola Diagnostic Center)

  • Linda Winona

    (Sandia National Laboratories
    Ratoma Ebola Diagnostic Center)

  • Emily Davis

    (Ratoma Ebola Diagnostic Center
    MRIGlobal, Kansas City)

  • Jon Gerlach

    (Ratoma Ebola Diagnostic Center
    MRIGlobal, Kansas City)

  • Frank Washington

    (Ratoma Ebola Diagnostic Center
    MRIGlobal, Kansas City)

  • 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
    Laboratoire de Biologie - Centre de Traitement des Soignants)

  • 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)
    Norwegian Institute of Public Health, PO Box 4404 Nydalen, 0403 Oslo, Norway)

  • Isabelle Roger

    (World Health Organization)

  • Christopher J. Williams

    (European Centre for Disease Prevention and Control (ECDC)
    Public Health)

  • 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
    NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool)

  • Julian A. Hiscox

    (Institute of Infection and Global Health, University of Liverpool
    NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, 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
    National Institute for Infectious Diseases L. Spallanzani)

  • Roman Wölfel

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Bundeswehr Institute of Microbiology)

  • Kilian Stoecker

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Bundeswehr Institute of Microbiology)

  • Erna Fleischmann

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Bundeswehr Institute of Microbiology)

  • Martin Gabriel

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    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
    Fogarty International Center, National Institutes of Health, Bethesda
    Centre for Immunology, Infection and Evolution, University of Edinburgh)

  • Pierre Formenty

    (World Health Organization)

  • Stephan Günther

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    Bernhard-Nocht-Institute for Tropical Medicine)

  • Miles W. Carroll

    (The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine
    National Infection Service, Public Health England, Porton Down
    University of Southampton, South General Hospital
    NIHR Health Protection Research Unit in Emerging and Zoonotic Infections)

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.

Suggested Citation

  • 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 Afr, 2016. "Real-time, portable genome sequencing for Ebola surveillance," Nature, Nature, vol. 530(7589), pages 228-232, February.
    • Handle: RePEc:nat:nature:v:530:y:2016:i:7589:d:10.1038_nature16996
    DOI: 10.1038/nature16996
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    Citations

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    Cited by:

    1. Yunxi Liu & Joshua Kearney & Medhat Mahmoud & Bryce Kille & Fritz J. Sedlazeck & Todd J. Treangen, 2022. "Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    2. Mariateresa Cesare & Mulenga Mwenda & Anna E. Jeffreys & Jacob Chirwa & Chris Drakeley & Kammerle Schneider & Brenda Mambwe & Karolina Glanz & Christina Ntalla & Manuela Carrasquilla & Silvia Portugal, 2024. "Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    3. Gábor Kemenesi & Gábor E. Tóth & Martin Mayora-Neto & Simon Scott & Nigel Temperton & Edward Wright & Elke Mühlberger & Adam J. Hume & Ellen L. Suder & Brigitta Zana & Sándor A. Boldogh & Tamás Görföl, 2022. "Isolation of infectious Lloviu virus from Schreiber’s bats in Hungary," Nature Communications, Nature, vol. 13(1), pages 1-11, December.

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