H5nx Panzootic Bird Flu—Influenza's Newest Worldwide Evolutionary Tour
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(HPAI) A/Turkey/Turkey/1/2005 H5N1 in Pekin Ducks (Anas Platyrhynchos) Infected Experimentally Brandon Z
Pathogenesis of Highly Pathogenic Avian Influenza (HPAI) A/turkey/Turkey/1/2005 H5N1 in Pekin ducks (Anas platyrhynchos) infected experimentally Brandon Z. Löndt, Alejandro Nunez, Jill Banks, Hassan Nili, Linda K Johnson, Dennis Alexander To cite this version: Brandon Z. Löndt, Alejandro Nunez, Jill Banks, Hassan Nili, Linda K Johnson, et al.. Pathogenesis of Highly Pathogenic Avian Influenza (HPAI) A/turkey/Turkey/1/2005 H5N1 in Pekin ducks (Anas platyrhynchos) infected experimentally. Avian Pathology, Taylor & Francis, 2008, 37 (06), pp.619-627. 10.1080/03079450802499126. hal-00540137 HAL Id: hal-00540137 https://hal.archives-ouvertes.fr/hal-00540137 Submitted on 26 Nov 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Avian Pathology For Peer Review Only Pathogenesis of Highly Pathogenic Avian Influenza (HPAI) A/turkey/Turkey/1/2005 H5N1 in Pekin ducks ( Anas platyrhynchos ) infected experimentally Journal: Avian Pathology Manuscript ID: CAVP-2008-0107.R1 Manuscript Type: Original Research Paper Date Submitted by the 01-Sep-2008 Author: Complete -
Recent Human-To-Poultry Host Jump, Adaptation, and Pandemic Spread of Staphylococcus Aureus
Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus Bethan V. Lowdera, Caitriona M. Guinanea, Nouri L. Ben Zakoura, Lucy A. Weinertb, Andrew Conway-Morrisc, Robyn A. Cartwrighta, A. John Simpsonc, Andrew Rambautb, Ulrich Nu¨ beld, and J. Ross Fitzgeralda,1 aThe Roslin Institute and Centre for Infectious Diseases, Royal (Dick) School of Veterinary Studies, bInstitute of Evolutionary Biology, and cCentre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH8 9YL, Scotland, United Kingdom; and dRobert Koch Institut, 38855 Wernigerode, Germany Edited by Richard P. Novick, New York University School of Medicine, New York, NY, and approved September 18, 2009 (received for review August 14, 2009) The impact of globalization on the emergence and spread of industry (7, 8). The reasons for the emergence and subsequent pathogens is an important veterinary and public health issue. increase in incidence of BCO among chickens are unknown. Staphylococcus aureus is a notorious human pathogen associated with serious nosocomial and community-acquired infections. In Results and Discussion addition, S. aureus is a major cause of animal diseases including The Majority of S. aureus Isolates from Poultry Belong to a Single skeletal infections of poultry, which are a large economic burden Clonal Complex (CC5) Usually Associated with Humans. To examine on the global broiler chicken industry. Here, we provide evidence the population genetics of S. aureus strains infecting farmed that the majority of S. aureus isolates from broiler chickens are the birds, we carried out multi-locus sequence typing (MLST) of 57 descendants of a single human-to-poultry host jump that occurred S. -
Identification of Combinatorial Host-Specific Signatures with A
Khaliq et al. BMC Genomics (2016) 17:529 DOI 10.1186/s12864-016-2919-4 RESEARCH ARTICLE Open Access Identification of combinatorial host-specific signatures with a potential to affect host adaptation in influenza A H1N1 and H3N2 subtypes Zeeshan Khaliq1, Mikael Leijon2,3, Sándor Belák3,4 and Jan Komorowski1,5* Abstract Background: The underlying strategies used by influenza A viruses (IAVs) to adapt to new hosts while crossing the species barrier are complex and yet to be understood completely. Several studies have been published identifying singular genomic signatures that indicate such a host switch. The complexity of the problem suggested that in addition to the singular signatures, there might be a combinatorial use of such genomic features, in nature, defining adaptation to hosts. Results: We used computational rule-based modeling to identify combinatorial sets of interacting amino acid (aa) residues in 12 proteins of IAVs of H1N1 and H3N2 subtypes. We built highly accurate rule-based models for each protein that could differentiate between viral aa sequences coming from avian and human hosts. We found 68 host-specific combinations of aa residues, potentially associated to host adaptation on HA, M1, M2, NP, NS1, NEP, PA, PA-X, PB1 and PB2 proteins of the H1N1 subtype and 24 on M1, M2, NEP, PB1 and PB2 proteins of the H3N2 subtypes. In addition to these combinations, we found 132 novel singular aa signatures distributed among allproteins,includingthenewlydiscoveredPA-Xprotein, of both subtypes. We showed that HA, NA, NP, NS1, NEP, PA-X and PA proteins of the H1N1 subtype carry H1N1-specific and HA, NA, PA-X, PA, PB1-F2 and PB1 of the H3N2 subtype carry H3N2-specific signatures. -
Modern-Day SIV Viral Diversity Generated by Extensive Recombination and Cross-Species Transmission. Sidney M. Bell a Thesis Subm
Modern-Day SIV Viral Diversity Generated by Extensive Recombination and Cross-Species Transmission. Sidney M. Bell A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science University of Washington 2017 Committee: Trevor Bedford Anna Wald Michael Emerman Program Authorized to Offer Degree: Epidemiology ©Copyright 2017 Sidney M. Bell 2 University of Washington Abstract Modern-Day SIV Viral Diversity Generated by Extensive Recombination and Cross-Species Transmission. Sidney M. Bell Chair of the Supervisory Committee: Trevor Bedford, PhD, Affiliate Assistant Professor Department of Epidemiology Cross-species transmission (CST) has led to many devastating epidemics, but is still a poorly understood phenomenon. HIV-1 and HIV-2 (human immunodeficiency virus 1 and 2), which have collectively caused over 35 million deaths, are the result of multiple CSTs from chimpanzees, gorillas, and sooty mangabeys. While the immediate history of HIV is known, there are over 45 lentiviruses that infect specific species of primates, and patterns of host switching are not well characterized. We thus took a phylogenetic ap- proach to better understand the natural history of SIV recombination and CST. We modeled host species as a discrete character trait on the viral phylogeny and inferred historical host switches and the pairwise transmission rates between each pair of 24 primate hosts. We identify 14 novel, well-supported, ancient cross-species transmission events. We also find that lentiviral lineages vary widely in their ability to infect new host species: SIVcol (from colobus monkeys) is evolutionarily isolated, while SIVagms (from African green monkeys) frequently move between host subspecies. We also examine the origins of SIVcpz (the predecessor of HIV-1) in greater detail than previous studies, and find that there are still large portions of the genome with unknown origins. -
Host Diversity and Origin of Zoonoses: the Ancient and the New
animals Review Host Diversity and Origin of Zoonoses: The Ancient and the New Judith Recht 1,* , Verena J. Schuenemann 2 and Marcelo R. Sánchez-Villagra 3 1 Independent Consultant, North Bethesda, MD 20817, USA 2 Institute of Evolutionary Medicine, University of Zurich, 8006 Zürich, Switzerland; [email protected] 3 Paleontological Institute and Museum, University of Zurich, 8006 Zürich, Switzerland; [email protected] * Correspondence: [email protected] Received: 5 July 2020; Accepted: 14 September 2020; Published: 17 September 2020 Simple Summary: There is a wide variety of diseases caused by bacteria, viruses, and parasites that are transmitted to humans by different routes from other animals. These diseases, known as zoonoses, represent 75% of new or reemerging infectious diseases. There is a considerable impact of these diseases on the economy and health at local and global levels, including zoonotic diseases caused by the ingestion of food and products derived from animals. The wide range of animal species that host these disease-causing organisms include all groups of mammals. Birds are the second significant animal group to act as hosts for zoonoses. Much progress has been made in understanding disease evolution and animal origin, with important contributions from fields such as paleopathology and analysis of DNA, applied to ancient human bone remains. The study of ancient diseases such as brucellosis and tuberculosis benefits from these approaches. More research is needed as new diseases emerge causing pandemics and some previously eradicated reemerge in some regions. Global efforts are focused, based on evidence generated by research, on the prevention of new pandemics. -
Virulence During Newcastle Disease Viruses Cross Species Adaptation
viruses Review Virulence during Newcastle Disease Viruses Cross Species Adaptation Claudio L. Afonso Base2bio, LLC, Oshkosh, WI 54905, USA; [email protected]; Tel.: +1-800-817-7160 Abstract: The hypothesis that host adaptation in virulent Newcastle disease viruses (NDV) has been accompanied by virulence modulation is reviewed here. Historical records, experimental data, and phylogenetic analyses from available GenBank sequences suggest that currently circulating NDVs emerged in the 1920–19400s from low virulence viruses by mutation at the fusion protein cleavage site. These viruses later gave rise to multiple virulent genotypes by modulating virulence in opposite directions. Phylogenetic and pathotyping studies demonstrate that older virulent NDVs further evolved into chicken-adapted genotypes by increasing virulence (velogenic-viscerotropic pathotypes with intracerebral pathogenicity indexes [ICPIs] of 1.6 to 2), or into cormorant-adapted NDVs by moderating virulence (velogenic–neurotropic pathotypes with ICPIs of 1.4 to 1.6), or into pigeon-adapted viruses by further attenuating virulence (mesogenic pathotypes with ICPIs of 0.9 to 1.4). Pathogenesis and transmission experiments on adult chickens demonstrate that chicken-adapted velogenic-viscerotropic viruses are more capable of causing disease than older velogenic-neurotropic viruses. Currently circulating velogenic–viscerotropic viruses are also more capable of replicating and of being transmitted in naïve chickens than viruses from cormorants and pigeons. These evolutionary virulence changes are consistent with theories that predict that virulence may evolve in many directions in order to achieve maximum fitness, as determined by genetic and ecologic constraints. Keywords: NDV; evolution; virulence; host adaptation Citation: Afonso, C.L. Virulence during Newcastle Disease Viruses Cross Species Adaptation. -
How Host Cells Defend Against Influenza a Virus Infection
viruses Review Host–Virus Interaction: How Host Cells Defend against Influenza A Virus Infection Yun Zhang 1 , Zhichao Xu and Yongchang Cao * State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; [email protected] (Y.Z.); [email protected] (Z.X.) * Correspondence: [email protected]; Tel.: +86-020-39332938 Received: 28 February 2020; Accepted: 25 March 2020; Published: 29 March 2020 Abstract: Influenza A viruses (IAVs) are highly contagious pathogens infecting human and numerous animals. The viruses cause millions of infection cases and thousands of deaths every year, thus making IAVs a continual threat to global health. Upon IAV infection, host innate immune system is triggered and activated to restrict virus replication and clear pathogens. Subsequently, host adaptive immunity is involved in specific virus clearance. On the other hand, to achieve a successful infection, IAVs also apply multiple strategies to avoid be detected and eliminated by the host immunity. In the current review, we present a general description on recent work regarding different host cells and molecules facilitating antiviral defenses against IAV infection and how IAVs antagonize host immune responses. Keywords: influenza A virus; innate immunity; adaptive immunity 1. Introduction Influenza A virus (IAV) can infect a wide range of warm-blooded animals, including birds, pigs, horses, and humans. In humans, the viruses cause respiratory disease and be transmitted by inhalation of virus-containing dust particles or aerosols [1]. Severe IAV infection can cause lung inflammation and acute respiratory distress syndrome (ARDS), which may lead to mortality. Thus, causing many influenza epidemics and pandemics, IAV has been a threat to public health for decades [2]. -
Identification of New Sub-Genotypes of Virulent Newcastle Disease Virus
Infection, Genetics and Evolution 29 (2015) 216–229 Contents lists available at ScienceDirect Infection, Genetics and Evolution journal homepage: www.elsevier.com/locate/meegid Identification of new sub-genotypes of virulent Newcastle disease virus with potential panzootic features Patti J. Miller a, Ruth Haddas b, Luba Simanov b, Avishay Lublin b, Shafqat Fatima Rehmani c, Abdul Wajid c, ⇑ Tasra Bibi c, Taseer Ahmad Khan d, Tahir Yaqub c, Surachmi Setiyaningsih e, Claudio L. Afonso a, a Southeast Poultry Research Laboratory, Agricultural Research Service-United States Department of Agriculture (USDA), Athens, GA 30605, USA b Kimron Veterinary Institute, Bet Dagan 50250, Israel c Quality Operations Laboratory, University of Veterinary and Animal Sciences, Out Fall Road, Lahore, Pakistan d Poultry Research Laboratory, Department of Physiology, University of Karachi, Karachi, Pakistan e Department of Infectious Diseases & Veterinary Public Health, Faculty of Veterinary Medicine-Bogor Agricultural University, Jl. Agatis, IPB Dramaga, Bogor 16680, Indonesia article info abstract Article history: Virulent Newcastle disease virus (NDV) isolates from new sub-genotypes within genotype VII are rapidly Received 29 May 2014 spreading through Asia and the Middle East causing outbreaks of Newcastle disease (ND) characterized Received in revised form 25 October 2014 by significant illness and mortality in poultry, suggesting the existence of a fifth panzootic. These viruses, Accepted 30 October 2014 which belong to the new sub-genotypes VIIh and VIIi, have epizootic characteristics and do not appear to Available online 20 November 2014 have originated directly from other genotype VII NDV isolates that are currently circulating elsewhere, but are related to the present and past Indonesian NDV viruses isolated from wild birds since the 80s. -
Emergence and Resurgence of Zoonotic Infectious Diseases
WellBeing International WBI Studies Repository 2007 The Human/Animal Interface: Emergence and Resurgence of Zoonotic Infectious Diseases Michael Greger The Humane Society of the United States Follow this and additional works at: https://www.wellbeingintlstudiesrepository.org/acwp_tzd Part of the Animal Studies Commons, Other Animal Sciences Commons, and the Veterinary Infectious Diseases Commons Recommended Citation Greger, M. (2007). The human/animal interface: emergence and resurgence of zoonotic infectious diseases. Critical Reviews in Microbiology, 33(4), 243-299. This material is brought to you for free and open access by WellBeing International. It has been accepted for inclusion by an authorized administrator of the WBI Studies Repository. For more information, please contact [email protected]. The Human/Animal Interface: Emergence and Resurgence of Zoonotic Infectious Diseases Michael Greger The Humane Society of the United States CITATION Greger, M. (2007). The human/animal interface: emergence and resurgence of zoonotic infectious diseases. Critical reviews in microbiology, 33(4), 243-299. KEYWORDS agriculture, Avian Influenza, Borrelia burgdorferi, Bovine Spongiform Encephalopathy, bushmeat, Campylobacter; concentrated animal feeding operations, deltaretroviruses, disease ecology, disease evolution, domestic fowl, emerging infectious diseases, Escherichia coli O157, extraintestinal pathogenic Escherichia coli, farm animals, HIV, Influenza A Virus Subtype H5N1, Listeria monocytogenes, multiple drug resistance, Nipah -
Evidence That a Plant Virus Switched Hosts to Infect a Vertebrate and Then Recombined with a Vertebrate-Infecting Virus
Proc. Natl. Acad. Sci. USA Vol. 96, pp. 8022–8027, July 1999 Evolution Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus MARK J. GIBBS* AND GEORG F. WEILLER Bioinformatics, Research School of Biological Sciences, The Australian National University, G.P.O. Box 475, Canberra 2601, Australia Communicated by Bryan D. Harrison, Scottish Crop Research Institute, Dundee, United Kingdom, April 28, 1999 (received for review December 22, 1998) ABSTRACT There are several similarities between the The history of viruses is further complicated by interspecies small, circular, single-stranded-DNA genomes of circoviruses recombination. Distinct viruses have recombined with each that infect vertebrates and the nanoviruses that infect plants. other, producing viruses with new combinations of genes (6, 7); We analyzed circovirus and nanovirus replication initiator viruses have also captured genes from their hosts (8, 9). These protein (Rep) sequences and confirmed that an N-terminal interspecies recombinational events join sequences with dif- region in circovirus Reps is similar to an equivalent region in ferent evolutionary histories; hence, it is important to test viral nanovirus Reps. However, we found that the remaining C- sequence datasets for evidence of recombination before phy- terminal region is related to an RNA-binding protein (protein logenetic trees are inferred. If a set of aligned sequences 2C), encoded by picorna-like viruses, and we concluded that contains regions with significantly different phylogenetic sig- the sequence encoding this region of Rep was acquired from nals and the regions are not delineated, errors may result. one of these single-stranded RNA viruses, probably a calici- Interspecies recombination between viruses has been linked virus, by recombination. -
Evolution of Influenza a Virus by Mutation and Re-Assortment
International Journal of Molecular Sciences Review Evolution of Influenza A Virus by Mutation and Re-Assortment Wenhan Shao 1, Xinxin Li 1, Mohsan Ullah Goraya 1, Song Wang 1,* and Ji-Long Chen 1,2,* 1 Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; [email protected] (W.S.); [email protected] (X.L.); [email protected] (M.U.G.) 2 CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China * Correspondence: [email protected] (S.W.); [email protected] (J.-L.C.); Tel.: +86-591-8375-8852 (S.W.); +86-591-8378-9159 (J.-L.C.) Received: 25 June 2017; Accepted: 24 July 2017; Published: 7 August 2017 Abstract: Influenza A virus (IAV), a highly infectious respiratory pathogen, has continued to be a significant threat to global public health. To complete their life cycle, influenza viruses have evolved multiple strategies to interact with a host. A large number of studies have revealed that the evolution of influenza A virus is mainly mediated through the mutation of the virus itself and the re-assortment of viral genomes derived from various strains. The evolution of influenza A virus through these mechanisms causes worldwide annual epidemics and occasional pandemics. Importantly, influenza A virus can evolve from an animal infected pathogen to a human infected pathogen. The highly pathogenic influenza virus has resulted in stupendous economic losses due to its morbidity and mortality both in human and animals. Influenza viruses fall into a category of viruses that can cause zoonotic infection with stable adaptation to human, leading to sustained horizontal transmission. -
Genomics and Structure/Function Studies of Rhabdoviridae Proteins Involved in Replication and Transcription
Genomics and structure/function studies of Rhabdoviridae proteins involved in replication and transcription. R. Assenberg, O Delmas, B Morin, C Graham, X de Lamballerie, C Laubert, B Coutard, J Grimes, J Neyts, R J Owens, et al. To cite this version: R. Assenberg, O Delmas, B Morin, C Graham, X de Lamballerie, et al.. Genomics and struc- ture/function studies of Rhabdoviridae proteins involved in replication and transcription.. Antivi- ral Research, Elsevier Masson, 2010, 87 (2), pp.149-61. 10.1016/j.antiviral.2010.02.322. pasteur- 01492926 HAL Id: pasteur-01492926 https://hal-pasteur.archives-ouvertes.fr/pasteur-01492926 Submitted on 21 Apr 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - NonCommercial - ShareAlike| 4.0 International License *Manuscript Genomics and structure/function studies of Rhabdoviridae proteins involved in replication and transcription R. Assenberg1, O. Delmas2, B. Morin3, S. C. Graham1, X. De Lamballerie4, C. Laubert5, B. Coutard3, J. M. Grimes1, J. Neyts6, R. J. Owens1,