Real-time, portable genome sequencing for Ebola surveillance

Research output: Contribution to journalArticle

Standard

Real-time, portable genome sequencing for Ebola surveillance. / Quick, Joshua; Loman, Nicholas J; Duraffour, Sophie; Simpson, Jared T; Severi, Ettore; Cowley, Lauren; Bore, Joseph Akoi; Koundouno, Raymond; Dudas, Gytis; Mikhail, Amy; Ouédraogo, Nobila; Afrough, Babak; Bah, Amadou; Baum, Jonathan H J; Becker-Ziaja, Beate; Boettcher, Jan Peter; Cabeza-Cabrerizo, Mar; Camino-Sánchez, Álvaro; Carter, Lisa L; Doerrbecker, Juliane; Enkirch, Theresa; García-Dorival, Isabel; Hetzelt, Nicole; Hinzmann, Julia; Holm, Tobias; Kafetzopoulou, Liana Eleni; Koropogui, Michel; Kosgey, Abigael; Kuisma, Eeva; Logue, Christopher H; Mazzarelli, Antonio; Meisel, Sarah; Mertens, Marc; Michel, Janine; Ngabo, Didier; Nitzsche, Katja; Pallasch, Elisa; Patrono, Livia Victoria; Portmann, Jasmine; Repits, Johanna Gabriella; Rickett, Natasha Y; Sachse, Andreas; Singethan, Katrin; Vitoriano, Inês; Yemanaberhan, Rahel L; Zekeng, Elsa G; Racine, Trina; Bello, Alexander; Sall, Amadou Alpha; Faye, Ousmane; Faye, Oumar; Magassouba, N'Faly; Williams, Cecelia V; Amburgey, Victoria; Winona, Linda; Davis, Emily; Gerlach, Jon; Washington, Frank; Monteil, Vanessa; Jourdain, Marine; Bererd, Marion; Camara, Alimou; Somlare, Hermann; Camara, Abdoulaye; Gerard, Marianne; Bado, Guillaume; Baillet, Bernard; Delaune, Déborah; Nebie, Koumpingnin Yacouba; Diarra, Abdoulaye; Savane, Yacouba; Pallawo, Raymond Bernard; Gutierrez, Giovanna Jaramillo; Milhano, Natacha; Roger, Isabelle; Williams, Christopher J; Yattara, Facinet; Lewandowski, Kuiama; Taylor, James; Rachwal, Phillip; Turner, Daniel J; Pollakis, Georgios; Hiscox, Julian A; Matthews, David A; O'Shea, Matthew K; Johnston, Andrew McD; Wilson, Duncan; Hutley, Emma; Smit, Erasmus; Di Caro, Antonino; Wölfel, Roman; Stoecker, Kilian; Fleischmann, Erna; Gabriel, Martin; Weller, Simon A; Koivogui, Lamine; Diallo, Boubacar; Keïta, Sakoba; Rambaut, Andrew; Formenty, Pierre; Günther, Stephan; Carroll, Miles W.

In: Nature, Vol. 530, No. 7589, 11.02.2016, p. 228-32.

Research output: Contribution to journalArticle

Harvard

Quick, J, Loman, NJ, Duraffour, S, Simpson, JT, Severi, E, Cowley, L, Bore, JA, Koundouno, R, Dudas, G, Mikhail, A, Ouédraogo, N, Afrough, B, Bah, A, Baum, JHJ, Becker-Ziaja, B, Boettcher, JP, Cabeza-Cabrerizo, M, Camino-Sánchez, Á, Carter, LL, Doerrbecker, J, Enkirch, T, García-Dorival, I, Hetzelt, N, Hinzmann, J, Holm, T, Kafetzopoulou, LE, Koropogui, M, Kosgey, A, Kuisma, E, Logue, CH, Mazzarelli, A, Meisel, S, Mertens, M, Michel, J, Ngabo, D, Nitzsche, K, Pallasch, E, Patrono, LV, Portmann, J, Repits, JG, Rickett, NY, Sachse, A, Singethan, K, Vitoriano, I, Yemanaberhan, RL, Zekeng, EG, Racine, T, Bello, A, Sall, AA, Faye, O, Faye, O, Magassouba, NF, Williams, CV, Amburgey, V, Winona, L, Davis, E, Gerlach, J, Washington, F, Monteil, V, Jourdain, M, Bererd, M, Camara, A, Somlare, H, Camara, A, Gerard, M, Bado, G, Baillet, B, Delaune, D, Nebie, KY, Diarra, A, Savane, Y, Pallawo, RB, Gutierrez, GJ, Milhano, N, Roger, I, Williams, CJ, Yattara, F, Lewandowski, K, Taylor, J, Rachwal, P, Turner, DJ, Pollakis, G, Hiscox, JA, Matthews, DA, O'Shea, MK, Johnston, AM, Wilson, D, Hutley, E, Smit, E, Di Caro, A, Wölfel, R, Stoecker, K, Fleischmann, E, Gabriel, M, Weller, SA, Koivogui, L, Diallo, B, Keïta, S, Rambaut, A, Formenty, P, Günther, S & Carroll, MW 2016, 'Real-time, portable genome sequencing for Ebola surveillance', Nature, vol. 530, no. 7589, pp. 228-32. https://doi.org/10.1038/nature16996

APA

Quick, J., Loman, N. J., Duraffour, S., Simpson, J. T., Severi, E., Cowley, L., Bore, J. A., Koundouno, R., Dudas, G., Mikhail, A., Ouédraogo, N., Afrough, B., Bah, A., Baum, J. H. J., Becker-Ziaja, B., Boettcher, J. P., Cabeza-Cabrerizo, M., Camino-Sánchez, Á., Carter, L. L., ... Carroll, M. W. (2016). Real-time, portable genome sequencing for Ebola surveillance. Nature, 530(7589), 228-32. https://doi.org/10.1038/nature16996

Vancouver

Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016 Feb 11;530(7589):228-32. https://doi.org/10.1038/nature16996

Author

Quick, Joshua ; Loman, Nicholas J ; Duraffour, Sophie ; Simpson, Jared T ; Severi, Ettore ; Cowley, Lauren ; Bore, Joseph Akoi ; Koundouno, Raymond ; Dudas, Gytis ; Mikhail, Amy ; Ouédraogo, Nobila ; Afrough, Babak ; Bah, Amadou ; Baum, Jonathan H J ; Becker-Ziaja, Beate ; Boettcher, Jan Peter ; Cabeza-Cabrerizo, Mar ; Camino-Sánchez, Álvaro ; Carter, Lisa L ; Doerrbecker, Juliane ; Enkirch, Theresa ; García-Dorival, Isabel ; Hetzelt, Nicole ; Hinzmann, Julia ; Holm, Tobias ; Kafetzopoulou, Liana Eleni ; Koropogui, Michel ; Kosgey, Abigael ; Kuisma, Eeva ; Logue, Christopher H ; Mazzarelli, Antonio ; Meisel, Sarah ; Mertens, Marc ; Michel, Janine ; Ngabo, Didier ; Nitzsche, Katja ; Pallasch, Elisa ; Patrono, Livia Victoria ; Portmann, Jasmine ; Repits, Johanna Gabriella ; Rickett, Natasha Y ; Sachse, Andreas ; Singethan, Katrin ; Vitoriano, Inês ; Yemanaberhan, Rahel L ; Zekeng, Elsa G ; Racine, Trina ; Bello, Alexander ; Sall, Amadou Alpha ; Faye, Ousmane ; Faye, Oumar ; Magassouba, N'Faly ; Williams, Cecelia V ; Amburgey, Victoria ; Winona, Linda ; Davis, Emily ; Gerlach, Jon ; Washington, Frank ; Monteil, Vanessa ; Jourdain, Marine ; Bererd, Marion ; Camara, Alimou ; Somlare, Hermann ; Camara, Abdoulaye ; Gerard, Marianne ; Bado, Guillaume ; Baillet, Bernard ; Delaune, Déborah ; Nebie, Koumpingnin Yacouba ; Diarra, Abdoulaye ; Savane, Yacouba ; Pallawo, Raymond Bernard ; Gutierrez, Giovanna Jaramillo ; Milhano, Natacha ; Roger, Isabelle ; Williams, Christopher J ; Yattara, Facinet ; Lewandowski, Kuiama ; Taylor, James ; Rachwal, Phillip ; Turner, Daniel J ; Pollakis, Georgios ; Hiscox, Julian A ; Matthews, David A ; O'Shea, Matthew K ; Johnston, Andrew McD ; Wilson, Duncan ; Hutley, Emma ; Smit, Erasmus ; Di Caro, Antonino ; Wölfel, Roman ; Stoecker, Kilian ; Fleischmann, Erna ; Gabriel, Martin ; Weller, Simon A ; Koivogui, Lamine ; Diallo, Boubacar ; Keïta, Sakoba ; Rambaut, Andrew ; Formenty, Pierre ; Günther, Stephan ; Carroll, Miles W. / Real-time, portable genome sequencing for Ebola surveillance. In: Nature. 2016 ; Vol. 530, No. 7589. pp. 228-32.

Bibtex

@article{d2ffa005fa0e471e83bda37f14002689,
title = "Real-time, portable genome sequencing for Ebola surveillance",
abstract = "The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is desirable to characterize the infectious agent and determine its evolutionary rate. Genome sequencing also allows the identification of signatures of host adaptation, identification and monitoring of diagnostic targets, and characterization of responses to vaccines and treatments. The Ebola virus (EBOV) genome substitution rate in the Makona strain has been estimated at between 0.87 × 10(-3) and 1.42 × 10(-3) mutations per site per year. This is equivalent to 16-27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions. Genomic surveillance during the epidemic has been sporadic owing to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities. To address this problem, here we devise a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. We present sequence data and analysis of 142 EBOV samples collected during the period March to October 2015. We were able to generate results less than 24 h after receiving an Ebola-positive sample, with the sequencing process taking as little as 15-60 min. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.",
keywords = "Aircraft, Disease Outbreaks, Ebolavirus, Epidemiological Monitoring, Genome, Viral, Guinea, Hemorrhagic Fever, Ebola, Humans, Mutagenesis, Mutation Rate, Sequence Analysis, DNA, Time Factors",
author = "Joshua Quick and Loman, {Nicholas J} and Sophie Duraffour and Simpson, {Jared T} and Ettore Severi and Lauren Cowley and Bore, {Joseph Akoi} and Raymond Koundouno and Gytis Dudas and Amy Mikhail and Nobila Ou{\'e}draogo and Babak Afrough and Amadou Bah and Baum, {Jonathan H J} and Beate Becker-Ziaja and Boettcher, {Jan Peter} and Mar Cabeza-Cabrerizo and {\'A}lvaro Camino-S{\'a}nchez and Carter, {Lisa L} and Juliane Doerrbecker and Theresa Enkirch and Isabel Garc{\'i}a-Dorival and Nicole Hetzelt and Julia Hinzmann and Tobias Holm and Kafetzopoulou, {Liana Eleni} and Michel Koropogui and Abigael Kosgey and Eeva Kuisma and Logue, {Christopher H} and Antonio Mazzarelli and Sarah Meisel and Marc Mertens and Janine Michel and Didier Ngabo and Katja Nitzsche and Elisa Pallasch and Patrono, {Livia Victoria} and Jasmine Portmann and Repits, {Johanna Gabriella} and Rickett, {Natasha Y} and Andreas Sachse and Katrin Singethan and In{\^e}s Vitoriano and Yemanaberhan, {Rahel L} and Zekeng, {Elsa G} and Trina Racine and Alexander Bello and Sall, {Amadou Alpha} and Ousmane Faye and Oumar Faye and N'Faly Magassouba and Williams, {Cecelia V} and Victoria Amburgey and Linda Winona and Emily Davis and Jon Gerlach and Frank Washington and Vanessa Monteil and Marine Jourdain and Marion Bererd and Alimou Camara and Hermann Somlare and Abdoulaye Camara and Marianne Gerard and Guillaume Bado and Bernard Baillet and D{\'e}borah Delaune and Nebie, {Koumpingnin Yacouba} and Abdoulaye Diarra and Yacouba Savane and Pallawo, {Raymond Bernard} and Gutierrez, {Giovanna Jaramillo} and Natacha Milhano and Isabelle Roger and Williams, {Christopher J} and Facinet Yattara and Kuiama Lewandowski and James Taylor and Phillip Rachwal and Turner, {Daniel J} and Georgios Pollakis and Hiscox, {Julian A} and Matthews, {David A} and O'Shea, {Matthew K} and Johnston, {Andrew McD} and Duncan Wilson and Emma Hutley and Erasmus Smit and {Di Caro}, Antonino and Roman W{\"o}lfel and Kilian Stoecker and Erna Fleischmann and Martin Gabriel and Weller, {Simon A} and Lamine Koivogui and Boubacar Diallo and Sakoba Ke{\"i}ta and Andrew Rambaut and Pierre Formenty and Stephan G{\"u}nther and Carroll, {Miles W}",
year = "2016",
month = feb,
day = "11",
doi = "10.1038/nature16996",
language = "English",
volume = "530",
pages = "228--32",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7589",

}

RIS

TY - JOUR

T1 - Real-time, portable genome sequencing for Ebola surveillance

AU - Quick, Joshua

AU - Loman, Nicholas J

AU - Duraffour, Sophie

AU - Simpson, Jared T

AU - Severi, Ettore

AU - Cowley, Lauren

AU - Bore, Joseph Akoi

AU - Koundouno, Raymond

AU - Dudas, Gytis

AU - Mikhail, Amy

AU - Ouédraogo, Nobila

AU - Afrough, Babak

AU - Bah, Amadou

AU - Baum, Jonathan H J

AU - Becker-Ziaja, Beate

AU - Boettcher, Jan Peter

AU - Cabeza-Cabrerizo, Mar

AU - Camino-Sánchez, Álvaro

AU - Carter, Lisa L

AU - Doerrbecker, Juliane

AU - Enkirch, Theresa

AU - García-Dorival, Isabel

AU - Hetzelt, Nicole

AU - Hinzmann, Julia

AU - Holm, Tobias

AU - Kafetzopoulou, Liana Eleni

AU - Koropogui, Michel

AU - Kosgey, Abigael

AU - Kuisma, Eeva

AU - Logue, Christopher H

AU - Mazzarelli, Antonio

AU - Meisel, Sarah

AU - Mertens, Marc

AU - Michel, Janine

AU - Ngabo, Didier

AU - Nitzsche, Katja

AU - Pallasch, Elisa

AU - Patrono, Livia Victoria

AU - Portmann, Jasmine

AU - Repits, Johanna Gabriella

AU - Rickett, Natasha Y

AU - Sachse, Andreas

AU - Singethan, Katrin

AU - Vitoriano, Inês

AU - Yemanaberhan, Rahel L

AU - Zekeng, Elsa G

AU - Racine, Trina

AU - Bello, Alexander

AU - Sall, Amadou Alpha

AU - Faye, Ousmane

AU - Faye, Oumar

AU - Magassouba, N'Faly

AU - Williams, Cecelia V

AU - Amburgey, Victoria

AU - Winona, Linda

AU - Davis, Emily

AU - Gerlach, Jon

AU - Washington, Frank

AU - Monteil, Vanessa

AU - Jourdain, Marine

AU - Bererd, Marion

AU - Camara, Alimou

AU - Somlare, Hermann

AU - Camara, Abdoulaye

AU - Gerard, Marianne

AU - Bado, Guillaume

AU - Baillet, Bernard

AU - Delaune, Déborah

AU - Nebie, Koumpingnin Yacouba

AU - Diarra, Abdoulaye

AU - Savane, Yacouba

AU - Pallawo, Raymond Bernard

AU - Gutierrez, Giovanna Jaramillo

AU - Milhano, Natacha

AU - Roger, Isabelle

AU - Williams, Christopher J

AU - Yattara, Facinet

AU - Lewandowski, Kuiama

AU - Taylor, James

AU - Rachwal, Phillip

AU - Turner, Daniel J

AU - Pollakis, Georgios

AU - Hiscox, Julian A

AU - Matthews, David A

AU - O'Shea, Matthew K

AU - Johnston, Andrew McD

AU - Wilson, Duncan

AU - Hutley, Emma

AU - Smit, Erasmus

AU - Di Caro, Antonino

AU - Wölfel, Roman

AU - Stoecker, Kilian

AU - Fleischmann, Erna

AU - Gabriel, Martin

AU - Weller, Simon A

AU - Koivogui, Lamine

AU - Diallo, Boubacar

AU - Keïta, Sakoba

AU - Rambaut, Andrew

AU - Formenty, Pierre

AU - Günther, Stephan

AU - Carroll, Miles W

PY - 2016/2/11

Y1 - 2016/2/11

N2 - The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is desirable to characterize the infectious agent and determine its evolutionary rate. Genome sequencing also allows the identification of signatures of host adaptation, identification and monitoring of diagnostic targets, and characterization of responses to vaccines and treatments. The Ebola virus (EBOV) genome substitution rate in the Makona strain has been estimated at between 0.87 × 10(-3) and 1.42 × 10(-3) mutations per site per year. This is equivalent to 16-27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions. Genomic surveillance during the epidemic has been sporadic owing to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities. To address this problem, here we devise a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. We present sequence data and analysis of 142 EBOV samples collected during the period March to October 2015. We were able to generate results less than 24 h after receiving an Ebola-positive sample, with the sequencing process taking as little as 15-60 min. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.

AB - The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is desirable to characterize the infectious agent and determine its evolutionary rate. Genome sequencing also allows the identification of signatures of host adaptation, identification and monitoring of diagnostic targets, and characterization of responses to vaccines and treatments. The Ebola virus (EBOV) genome substitution rate in the Makona strain has been estimated at between 0.87 × 10(-3) and 1.42 × 10(-3) mutations per site per year. This is equivalent to 16-27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions. Genomic surveillance during the epidemic has been sporadic owing to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities. To address this problem, here we devise a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. We present sequence data and analysis of 142 EBOV samples collected during the period March to October 2015. We were able to generate results less than 24 h after receiving an Ebola-positive sample, with the sequencing process taking as little as 15-60 min. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.

KW - Aircraft

KW - Disease Outbreaks

KW - Ebolavirus

KW - Epidemiological Monitoring

KW - Genome, Viral

KW - Guinea

KW - Hemorrhagic Fever, Ebola

KW - Humans

KW - Mutagenesis

KW - Mutation Rate

KW - Sequence Analysis, DNA

KW - Time Factors

U2 - 10.1038/nature16996

DO - 10.1038/nature16996

M3 - Article

C2 - 26840485

VL - 530

SP - 228

EP - 232

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7589

ER -