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      Temporal and spatial analysis of the 2014–2015 Ebola virus outbreak in West Africa

      research-article
      1 , 2 , 3 , , 4 , 5 , 1 , 5 , 6 , 7 , 8 , 1 , 2 , 9 , 5 , 2 , 10 , 11 , 2 , 10 , 11 , 2 , 12 , 1 , 2 , 2 , 13 , 2 , 13 , 2 , 13 , 1 , 2 , 2 , 14 , 15 , 2 , 16 , 1 , 2 , 2 , 14 , 2 , 15 , 17 , 2 , 14 , 15 , 2 , 18 , 19 , 2 , 20 , 1 , 2 , 5 , 2 , 21 , 2 , 22 , 2 , 22 , 2 , 22 , 1 , 2 , 2 , 22 , 2 , 15 , 23 , 2 , 13 , 2 , 14 , 24 , 2 , 14 , 25 , 2 , 21 , 2 , 26 , 2 , 18 , 27 , 2 , 15 , 28 , 2 , 20 , 2 , 21 , 2 , 21 , 2 , 21 , 2 , 13 , 1 , 2 , 2 , 15 , 17 , 2 , 29 , 2 , 21 , 2 , 21 , 2 , 30 , 2 , 31 , 1 , 2 , 2 , 21 , 2 , 14 , 15 , 1 , 2 , 2 , 15 , 32 , 2 , 24 , 1 , 2 , 2 , 18 , 19 , 2 , 15 , 23 , 2 , 22 , 2 , 15 , 33 , 2 , 21 , 2 , 15 , 28 , 2 , 15 , 32 , 2 , 15 , 33 , 1 , 2 , 1 , 2 , 2 , 14 , 15 , 2 , 13 , 2 , 13 , 2 , 13 , 2 , 13 , 2 , 14 , 15 , 2 , 29 , 2 , 34 , 1 , 2 , 1 , 2 , 2 , 35 , 2 , 22 ,   2 , 36 , 2 , 37 , 2 , 21 , 2 , 14 , 15 , 2 , 21 , 2 , 21 , 2 , 15 , 17 , 2 , 15 , 17 , 1 , 2 ,   1 , 2 , 2 , 13 , 1 , 2 , 2 , 38 , 2 , 12 , 1 , 2 , 2 , 15 , 28 , 2 , 15 , 17 , 2 , 21 , 2 , 22 , 39 , 1 , 40 , 5 , 6 , 41 , 2 , 14 , 15 , 42 , 43 , 1 , 44 , 45 , 46 , 47 , 47 , 47 , 48 , 49 , 50 , 11 , 10 , 2 , 30 , 2 , 21 , 2 , 34 , 2 , 22 , 2 , 15 , 17 , 2 , 15 , 28 , 2 , 14 , 15 , 2 , 19 , 2 , 22 , 2 , 15 , 28 , 45 , 2 , 14 , 15
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      Ebola virus

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          Abstract

          Analysis of 179 new Ebola virus sequences from patient samples collected in Guinea between March 2014 and January 2015 shows how different lineages evolved and spread in West Africa.

          Supplementary information

          The online version of this article (doi:10.1038/nature14594) contains supplementary material, which is available to authorized users.

          Ebola virus lineage evolution

          Miles Carroll and colleagues report describe the genetic evolution of Ebola virus circulating in West Africa, based on 179 new virus sequences from patient samples collected in Guinea between March 2014 and January 2015. Their analysis shows how different lineages evolved and spread in West Africa between Sierra Leone, Guinea and Liberia.

          Supplementary information

          The online version of this article (doi:10.1038/nature14594) contains supplementary material, which is available to authorized users.

          Abstract

          West Africa is currently witnessing the most extensive Ebola virus (EBOV) outbreak so far recorded 1, 2, 3 . 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.

          Supplementary information

          The online version of this article (doi:10.1038/nature14594) contains supplementary material, which is available to authorized users.

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          Fast gapped-read alignment with Bowtie 2.

          As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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            MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

            Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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              Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis.
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                Author and article information

                Contributors
                miles.carroll@phe.gov.uk
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                17 June 2015
                17 June 2015
                2015
                : 524
                : 7563
                : 97-101
                Affiliations
                [1 ]GRID grid.271308.f, ISNI 0000 0004 5909 016X, Public Health England, ; Porton Down, SP4 0JG Wiltshire UK
                [2 ]The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, ( https://ror.org/01evwfd48) Hamburg, D-20359 Germany
                [3 ]University of Southampton, South General Hospital, ( https://ror.org/01ryk1543) Southampton, SO16 6YD UK
                [4 ]Department of Cellular and Molecular Medicine, School of Medical Sciences, University of Bristol, ( https://ror.org/0524sp257) Bristol, BS8 1TD UK
                [5 ]Institute of Infection and Global Health, University of Liverpool, ( https://ror.org/04xs57h96) Liverpool, L69 2BE UK
                [6 ]Institute of Evolutionary Biology, University of Edinburgh, ( https://ror.org/01nrxwf90) Edinburgh, EH9 2FL UK
                [7 ]Fogarty International Center, National Institutes of Health, ( https://ror.org/02xey9a22) Bethesda, 20892 Maryland USA
                [8 ]Centre for Immunology, Infection and Evolution, University of Edinburgh, ( https://ror.org/01nrxwf90) Edinburgh, EH9 2FL UK
                [9 ]London School of Hygiene and Tropical Medicine, ( https://ror.org/00a0jsq62) Keppel Street, London, WC1E 7HT UK
                [10 ]Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, ( https://ror.org/002g4yr42) Conakry, Guinea
                [11 ]Institut National de Santé Publique, ( https://ror.org/04zpbyn04) Conakry, Guinea
                [12 ]Institute of Tropical Medicine, ( https://ror.org/03xq4x896) Antwerp, B-2000 Belgium
                [13 ]Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, ( https://ror.org/04em8c151) Irrua, Edo State Nigeria
                [14 ]Bernhard Nocht Institute for Tropical Medicine, ( https://ror.org/01evwfd48) Hamburg, D-20359 Germany
                [15 ]German Centre for Infection Research (DZIF), ( https://ror.org/028s4q594) Braunschweig, 38124 Germany
                [16 ]GRID grid.416786.a, ISNI 0000 0004 0587 0574, Swiss Tropical and Public Health Institute, University of Basel, ; Basel, CH-4002 Switzerland
                [17 ]Institute of Virology, Philipps University Marburg, ( https://ror.org/01rdrb571) Marburg, 35043 Germany
                [18 ]National Reference Center for Viral Hemorrhagic Fevers, Lyon, 69365 France
                [19 ]Laboratoire P4 Inserm-Jean Mérieux, US003 Inserm, ( https://ror.org/02hmsgf06) Lyon, 69365 France
                [20 ]Department of Biology, University of Antwerp, ( https://ror.org/008x57b05) Antwerp, B-2020 Belgium
                [21 ]Robert Koch Institute, ( https://ror.org/01k5qnb77) Berlin, 13353 Germany
                [22 ]National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
                [23 ]Friedrich Loeffler Institute, Federal Research Institute for Animal Health, ( https://ror.org/025fw7a54) Greifswald, 17493 Insel Riems Germany
                [24 ]KU Leuven Rega institute, ( https://ror.org/05f950310) Leuven, B-3000 Belgium
                [25 ]Redeemer’s University, ( https://ror.org/01v0we819) Osun State Nigeria
                [26 ]Centro Nacional de Microbiologia, Instituto de Salud Carlos III, ( https://ror.org/00ca2c886) Madrid, 28029 Spain
                [27 ]Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, ( https://ror.org/0495fxg12) Lyon, 69365 France
                [28 ]Bundeswehr Institute of Microbiology, ( https://ror.org/00qay8a95) Munich, 80937 Germany
                [29 ]National Center for Epidemiology, National Biosafety Laboratory, ( https://ror.org/05drnnd98) Budapest, H-1097 Hungary
                [30 ]Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, ( https://ror.org/05njb9z20) Ljubljana, SI-1000 Slovenia
                [31 ]Public Health Agency of Sweden, ( https://ror.org/05x4m5564) Solna, 171 82 Sweden
                [32 ]Heinrich Pette Institute – Leibniz Institute for Experimental Virology, ( https://ror.org/02r2q1d96) Hamburg, 20251 Germany
                [33 ]Institute of Virology, University of Bonn, ( https://ror.org/041nas322) Bonn, 53127 Germany
                [34 ]Federal Office for Civil Protection, Spiez Laboratory, ( https://ror.org/00zb6nk96) Spiez, CH-3700 Switzerland
                [35 ]Bundeswehr Hospital, ( https://ror.org/01wept116) Hamburg, 22049 Germany
                [36 ]GRID grid.438536.f, Institute of Virology and Immunology, ; Mittelhäusern, CH-3147 Switzerland
                [37 ]Janssen-Cilag, Sollentuna, SE-192 07 Sweden
                [38 ]Thünen Institute, Hamburg, D-22767 Germany
                [39 ]Eurice - European Research and Project Office GmbH, Berlin, 10115 Germany
                [40 ]Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, ( https://ror.org/04xs57h96) Liverpool, L69 7ZB UK
                [41 ]Department of Infection and Population Health, University College London, ( https://ror.org/02jx3x895) London, WC1E 6JB UK
                [42 ]Research IT, University of Bristol, ( https://ror.org/0524sp257) Bristol, BS8 1HH UK
                [43 ]Advanced Computing Research Centre, University of Bristol, ( https://ror.org/0524sp257) Bristol, BS8 1HH UK
                [44 ]Ministry of Health Guinea, ( https://ror.org/03v6x9115) Conakry, Guinea
                [45 ]World Health Organization, ( https://ror.org/01f80g185) Geneva 27, 1211 Switzerland
                [46 ]World Health Organization, Conakry, Guinea
                [47 ]Médecins Sans Frontières, ( https://ror.org/03rfn9b75) Brussels, B-1050 Belgium
                [48 ]Section Prévention et Lutte contre la Maladie à la Direction Préfectorale de la Santé de Guéckédou, Guéckédou, Guinea
                [49 ]Université Gamal Abdel Nasser de Conakry, CHU Donka, ( https://ror.org/002g4yr42) Conakry, Guinea
                [50 ]Health and Sustainable Development Foundation, ( https://ror.org/04691az61) Conakry, Guinea
                Article
                BFnature14594
                10.1038/nature14594
                10601607
                26083749
                62d48487-ba48-4362-8685-2b856f101fb8
                © The Author(s) 2015

                This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported licence. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons licence, users will need to obtain permission from the licence holder to reproduce the material. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-sa/3.0/.

                History
                : 9 April 2015
                : 1 June 2015
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