West Africa is currently witnessing the most extensive Ebola virus (EBOV) outbreak so far recorded. Until now, there have been 27,013 reported cases and 11,134 deaths. The origin of the virus is thought to have been a zoonotic transmission from a bat to a two-year-old boy in December 2013 (ref. 2). From this index case the virus was spread by human-to-human contact throughout Guinea, Sierra Leone and Liberia. However, the origin of the particular virus in each country and time of transmission is not known and currently relies on epidemiological analysis, which may be unreliable owing to the difficulties of obtaining patient information. Here we trace the genetic evolution of EBOV in the current outbreak that has resulted in multiple lineages. Deep sequencing of 179 patient samples processed by the European Mobile Laboratory, the first diagnostics unit to be deployed to the epicentre of the outbreak in Guinea, reveals an epidemiological and evolutionary history of the epidemic from March 2014 to January 2015. Analysis of EBOV genome evolution has also benefited from a similar sequencing effort of patient samples from Sierra Leone. Our results confirm that the EBOV from Guinea moved into Sierra Leone, most likely in April or early May. The viruses of the Guinea/Sierra Leone lineage mixed around June/July 2014. Viral sequences covering August, September and October 2014 indicate that this lineage evolved independently within Guinea. These data can be used in conjunction with epidemiological information to test retrospectively the effectiveness of control measures, and provides an unprecedented window into the evolution of an ongoing viral haemorrhagic fever outbreak.
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Acknowledgements The authors would like to acknowledge that the EMLab response and the subsequent EBOV genome sequencing study would not have been possible without the extensive support from the many different agencies and organisations working in the West African EBOV disease outbreak region. EMLab worked with WHO, MSF and the Guinean authorities to tackle the outbreak in the Guéckédou area where the samples from this study were collected. We thank those who helped make this possible and the Guinean authorities for their decision to release the diagnostic samples to EMLab for shipment to Europe to undergo further analysis, including sequencing. We acknowledge Air France, Brussels Airlines and Virgin Airlines for transporting EMLab personnel and equipment in and out of West Africa during the outbreak period; World Courier for shipping our EBOV-positive samples out of Guinea toEurope;andthe logisticssupportunits andpilotsanddriversofWHO/UnitedNations in West Africa for transporting our people and equipment throughout the region, and especially the drivers whomade the 28 h roundtrip journey fromConakry to enable the EMLab unit to be established and resupplied in Guéckédou. We appreciate the work of the numerous European Embassies operating in West Africa who provided emergency support to our personnel at times of need. We thank M. Bull, J. Lewis, P. Payne and S. Leach from the Microbial Risk Assessment and Behavioural Science Team, Emergency Response Department, Public Health England; J. Tree from Public Health England for help with GenBank submission; and S. Price and I. Stewart for helping with the running of our software on BlueCrystal, University of Bristol. We thank the people of West Africa for their gratitude and optimism, and for their positive attitude to our presence that we encountered on the daily journey to the Ebola Treatment Centre in Guéckédou. We acknowledge the efforts of the late Dr Lamine Ouendeno, who was one of the first healthcare workers to die during the current EBVD outbreak. We also thank Isabel and Maurice Ouendeno for providing us with food and shelter whilst delivering our Ebola response duties. This work was carried out in the context of the project EVIDENT (Ebola virus disease: correlates of protection, determinants of outcome, and clinical management) that received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 666100 and in the context of service contract IFS/2011/272-372 funded by Directorate-General for International Cooperation and Development. The EMLab is a technical partner in the WHO Emerging and Dangerous Pathogens Laboratory Network (EDPLN), and the Global Outbreak Alert and Response Network (GOARN) and the deployments in West Africa have been coordinated andsupported bythe GOARN OperationalSupport Team at WHO/HQ.
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