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 Ouedraogo, Babak Afrough, Amadou Bah, Jonathon HJ Baum, Beate Becker-Ziaja, Jan Peter Boettcher, Mar Cabeza-Cabrerizo, Alvaro Camino-Sanchez, Lisa L Carter, Julianne DoerrbeckerTheresa Enkirch, Isabel Garcia-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 Reptis, Natasha Y Rickett, Andreas Sachse, Katrin Singethan, Ines Vitoriano, Rachel 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, Deborah Delaune, Koumpingnin Yacouba Nebie, Abdoulaye Diarra, Yacouba Savane, Raymond Bernard Pallawo, Giovanna Jaramillo Guitierrez, 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, Antonio Di Caro, Roman Wolfel, Kilian Stoecker, Erna Fleischmann, Martin Gabriel, Simon A Weller, Lamine Koivogui, Boubacar Diallo, Sakoba Keita, Andrew Rambaut, Pierre Formenty, Stephan Gunther, Miles W Carroll

Research output: Contribution to journalLetter

515 Citations (Scopus)

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 deaths1. 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 epidemic2,3,4,5,6,7. 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 interventions8. 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 facilities9. 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.
Original languageEnglish
Pages (from-to)228-232
Number of pages17
JournalNature
Volume530
Issue number7589
Early online date3 Feb 2016
DOIs
Publication statusPublished - 11 Feb 2016

Keywords

  • Microbial genetics
  • Microbiology
  • Molecular evolution
  • Next-generation sequencing
  • Viral infection

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