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      A brief history of bird flu

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          Abstract

          In 1918, a strain of influenza A virus caused a human pandemic resulting in the deaths of 50 million people. A century later, with the advent of sequencing technology and corresponding phylogenetic methods, we know much more about the origins, evolution and epidemiology of influenza epidemics. Here we review the history of avian influenza viruses through the lens of their genetic makeup: from their relationship to human pandemic viruses, starting with the 1918 H1N1 strain, through to the highly pathogenic epidemics in birds and zoonoses up to 2018. We describe the genesis of novel influenza A virus strains by reassortment and evolution in wild and domestic bird populations, as well as the role of wild bird migration in their long-range spread. The emergence of highly pathogenic avian influenza viruses, and the zoonotic incursions of avian H5 and H7 viruses into humans over the last couple of decades are also described. The threat of a new avian influenza virus causing a human pandemic is still present today, although control in domestic avian populations can minimize the risk to human health.

          This article is part of the theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes’. This issue is linked with the subsequent theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control’.

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          Bayesian Phylogenetics with BEAUti and the BEAST 1.7

          Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk
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            Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

            Abstract The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package has become a primary tool for Bayesian phylogenetic and phylodynamic inference from genetic sequence data. BEAST unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using Markov chain Monte Carlo integration. A convenient, cross-platform, graphical user interface allows the flexible construction of complex evolutionary analyses.
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              Human Infection with a Novel Avian-Origin Influenza A (H7N9) Virus

              New England Journal of Medicine, 368(20), 1888-1897
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                Author and article information

                Journal
                Philos Trans R Soc Lond B Biol Sci
                Philos. Trans. R. Soc. Lond., B, Biol. Sci
                RSTB
                royptb
                Philosophical Transactions of the Royal Society B: Biological Sciences
                The Royal Society
                0962-8436
                1471-2970
                24 June 2019
                6 May 2019
                6 May 2019
                : 374
                : 1775 , Theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes’ compiled and edited by Robin N. Thompson and Ellen Brooks-Pollock
                : 20180257
                Affiliations
                The Roslin Institute, University of Edinburgh , Edinburgh, UK
                Author notes
                Author information
                http://orcid.org/0000-0003-3159-596X
                http://orcid.org/0000-0001-8669-1882
                http://orcid.org/0000-0002-0872-9440
                Article
                rstb20180257
                10.1098/rstb.2018.0257
                6553608
                31056053
                71bf550a-891f-4973-ab07-8b199d6f2f4a
                © 2019 The Authors.

                Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

                History
                : 15 January 2019
                Funding
                Funded by: College of Medicine and Veterinary Medicine, University of Edinburgh, http://dx.doi.org/10.13039/100010949;
                Award ID: Chancellor's Fellowship
                Award ID: Chancellor's Fellowship PhD studentship
                Funded by: Horizon 2020 Framework Programme, http://dx.doi.org/10.13039/100010661;
                Award ID: 727922 - DeltaFlu
                Funded by: Biotechnology and Biological Sciences Research Council, http://dx.doi.org/10.13039/501100000268;
                Award ID: BB/M027163/1
                Award ID: BBS/E/D/20002173
                Funded by: Rural and Environment Science and Analytical Services Division, http://dx.doi.org/10.13039/100011310;
                Award ID: EPIC III
                Categories
                1001
                87
                200
                60
                70
                Articles
                Review Article
                Custom metadata
                June 24, 2019

                Philosophy of science
                avian influenza virus,epidemiology,phylogenetics,pandemic,zoonotic
                Philosophy of science
                avian influenza virus, epidemiology, phylogenetics, pandemic, zoonotic

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