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.

DOI: 10.1038/nature16996

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@inproceedings{Quick2016RealtimePG, title={Real-time, portable genome sequencing for Ebola surveillance}, author={Joshua Quick and Nicholas J. Loman and Sophie Duraffour and Jared T. Simpson and Ettore Severi and Lauren A. Cowley and Joseph Akoi Bore and Raymond Koundouno and Gytis Dudas and Amy F W Mikhail and Nobila Ou{\'e}draogo and Babak Afrough and Amadou A. Bah and Jonathan H J Baum and Beate Becker-Ziaja and Jan-Peter Boettcher and Mar Cabeza-Cabrerizo and Alvaro Camino-Sanchez and Lisa L. Carter and Juiliane Doerrbecker and Theresa Enkirch and Isabel Graciela Garc{\'i}a Dorival and Nicole Hetzelt and Julia Hinzmann and Tobias Holm and Liana Eleni Kafetzopoulou and Michel Koropogui and Abigail Kosgey and Eeva Kuisma and Christopher H Logue and Antonio Mazzarelli and Sarah Meisel and Marc Mertens and Janine Michel and Didier Ngabo and Katja Nitzsche and Elisa Pallash and Livia Victoria Patrono and Jasmine Portmann and Johanna Gabriella Repits and Natasha Yasmin Rickett and Andrea Sachse and Katrin Singethan and In{\^e}s Vitoriano and Rahel L Yemanaberhan and Elsa Gayle Zekeng and Racine Trina and Alexander J Bello and Amadou Alpha Sall and Ousmane Faye and Oumar K Faye and N’faly Magassouba and Cecelia V. Williams and Victoria Amburgey and Linda Winona and Emily Faith Davis and Jon Gerlach and Franck Washington and Vanessa Monteil and Marine Jourdain and Marion Bererd and Alimou Camara and Hermann Somlare and Abdoulaye Camara and Marianne G{\'e}rard and Guillaume Bado and Bernard Baillet and D{\'e}borah Delaun{\'e} and Koumpingnin Yacouba Nebie and Abdoulaye Diarra and Yacouba Savane and Raymond Bernard Pallawo and Giovanna Jaramillo Gutierrez and Natacha Milhano and Isabelle Roger and Christopher J.M. Williams and Facinet Yattara and Kuiama S. Lewandowski and Jamie Taylor and Philip Rachwal and Daniel Turner and Georgios P Pollakis and Julian A. Hiscox and David A. Matthews and Matthew K. O’Shea and Andrew McDonald Johnston and Duncan Wilson and Emma J Hutley and Erasmus J. Smit and Antonino Di Caro and Roman Woelfel and Kilian Stoecker and Erna Fleischmann and Martin Gabriel and Simon A. Weller and Lamine Koivogui and Boubacar Djello Diallo and Sakoba Keita and Andrew Rambaut and Pierre B H Formenty and Stephan Gunther and Miles W. Carroll}, booktitle={Nature}, year={2016} }