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      The Evolution of Ebola virus: Insights from the 2013–2016 Epidemic

      research-article
      Author(s):   1 , 2 , 3 , 3 , 4 , 5 , 6 , 7 , 8 , 9
      Publication date PMC-release:
      Journal: Nature

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          Preface

          The 2013–2016 epidemic of Ebola virus disease in West Africa was of unprecedented magnitude and changed our perspective on this lethal but sporadically emerging virus. This outbreak also marked the beginning of large-scale real-time molecular epidemiology. Herein, we show how evolutionary analyses of Ebola virus genome sequences provided key insights into virus origins, evolution, and spread during the epidemic. We provide basic scientists, epidemiologists, medical practitioners, and other outbreak responders with an enhanced understanding of the utility and limitations of pathogen genomic sequencing. This will be crucially important in our attempts to track and control future infectious disease outbreaks.

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          Influenza: lessons from past pandemics, warnings from current incidents.

          Taisuke Horimoto, Yoshihiro Kawaoka (2005)
          Recent outbreaks of highly pathogenic avian influenza A virus infections (H5 and H7 subtypes) in poultry and in humans (through direct contact with infected birds) have had important economic repercussions and have raised concerns that a new influenza pandemic will occur in the near future. The eradication of pathogenic avian influenza viruses seems to be the most effective way to prevent influenza pandemics, although this strategy has not proven successful so far. Here, we review the molecular factors that contribute to the emergence of pandemic strains.
          Article 0 comments Cited 217 times – based on 0 reviews     Review now
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            Next-generation sequencing platforms.

            Elaine R. Mardis (2013)
            Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.
            Article 0 comments Cited 161 times – based on 0 reviews     Review now
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              The population genetics and evolutionary epidemiology of RNA viruses

              Andrés Moya, Fernando González-Candelas, Fernando González-Candelas (2004)
              Key Points The authors discuss the main mechanisms of RNA virus evolution — mutation, recombination, natural selection, genetic drift and migration, and how these interact to shape the genetic structure of populations. The quasispecies model of RNA virus evolution is explained and the question of whether this model provides an accurate description of RNA virus evolution is discussed. Experiments that can be carried out to test the basic principles of evolutionary theory are briefly described. The authors review what such experiments have told us about virus evolution and, more widely, what these experiments have revealed in terms of general evolutionary principles. RNA viruses evolve quickly, so a detailed reconstruction of their epidemiological history can be undertaken. The authors show how epidemiological patterns of viruses result from their evolution at two different levels: within individual hosts (and vectors) and among hosts at the population level. Using several examples, including HIV and SARS, the authors describe how studying RNA virus evolution could be used to understand virus emergence. Finally, the important topics of the evolution of virulence and resistance to drugs are discussed.
              Article 0 comments Cited 150 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-journal-id): 0410462
                Journal ID (pubmed-jr-id): 6011
                Journal ID (nlm-ta): Nature
                Journal ID (iso-abbrev): Nature
                Title: Nature
                ISSN (Print): 0028-0836
                ISSN (Electronic): 1476-4687
                Publication date Nihms-submitted: 24 August 2017
                Publication date (Print): 13 October 2016
                Publication date PMC-release: 01 September 2017
                Volume: 538
                Issue: 7624
                Pages: 193-200
                Affiliations
                [1 ]Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
                [2 ]Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
                [3 ]Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH9 3FL, UK
                [4 ]Centre for Immunology, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3FL, UK
                [5 ]Fogarty International Center, National Institutes of Health, MSC 2220 Bethesda, MD 20892, USA
                [6 ]The Scripps Research Institute, Department of Immunology and Microbial Science, La Jolla, CA 92037, USA
                [7 ]The Scripps Research Institute, Department of Integrative Structural and Computational Biology, La Jolla, CA 92037, USA
                [8 ]Scripps Translational Science Institute, La Jolla, CA 92037, USA
                [9 ]The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
                Author notes
                [* ]To whom correspondence should be addressed: ECH: edward.holmes@ 123456sydney.edu.au ; KGA: kristian@ 123456andersen-lab.com
                Article
                Accession ID: PMC5580494 Pmcid ID: PMC5580494 Pmc-uid ID: 5580494 Manuscript ID: nihpa900851
                DOI: 10.1038/nature19790
                PMC ID: 5580494
                PubMed ID: 27734858
                SO-VID: 343b8b01-fb98-4c6b-bf74-fb06efca84f1
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