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Tare DS, Keng SS, Walimbe AM, Pawar SD. Phylogeography and gene pool analysis of highly pathogenic avian influenza H5N1 viruses reported in India from 2006 to 2021. Arch Virol 2024; 169:111. [PMID: 38664271 DOI: 10.1007/s00705-024-06032-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/15/2024] [Indexed: 05/24/2024]
Abstract
India has reported highly pathogenic avian influenza (HPAI) H5N1 virus outbreaks since 2006, with the first human case reported in 2021. These included viruses belonging to the clades 2.2, 2.2.2, 2.2.2.1, 2.3.2.1a, and 2.3.2.1c. There are currently no data on the gene pool of HPAI H5N1 viruses in India. Molecular clock and phylogeography analysis of the HA and NA genes; and phylogenetic analysis of the internal genes of H5N1 viruses from India were carried out. Sequences reported from 2006 to 2015; and sequences from 2021 that were available in online databases were used in the analysis. Five separate introductions of H5N1 viruses into India were observed, via Indonesia or Korea (2002), Bangladesh (2009), Bhutan (2010), and China (2013, 2018) (clades 2.2, 2.2.2, 2.2.2.1, 2.3.2.1a, 2.3.2.1c, and 2.3.4.4b). Phylogenetic analysis revealed eight reassortant genotypes. The H5N1 virus isolated from the human case showed a unique reassortant genotype. Amino acid markers associated with adaptation to mammals were also present. This is the first report of the spatio-temporal origins and gene pool analysis of H5N1 viruses from India, highlighting the need for increased molecular surveillance.
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Affiliation(s)
- Deeksha S Tare
- ICMR-National Institute of Virology, 130/1, Sus Road, Pashan, Pune, 411021, India
| | - Sachin S Keng
- ICMR-National Institute of Virology, 130/1, Sus Road, Pashan, Pune, 411021, India
| | - Atul M Walimbe
- ICMR-National Institute of Virology, 130/1, Sus Road, Pashan, Pune, 411021, India
- ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, 411001, India
| | - Shailesh D Pawar
- ICMR-National Institute of Virology, 130/1, Sus Road, Pashan, Pune, 411021, India.
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2
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Albarnaz JD, Kite J, Oliveira M, Li H, Di Y, Christensen MH, Paulo JA, Antrobus R, Gygi SP, Schmidt FI, Huttlin EL, Smith GL, Weekes MP. Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection. Nat Commun 2023; 14:8134. [PMID: 38065956 PMCID: PMC10709566 DOI: 10.1038/s41467-023-43299-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 11/02/2023] [Indexed: 12/18/2023] Open
Abstract
Modified vaccinia Ankara (MVA) virus does not replicate in human cells and is the vaccine deployed to curb the current outbreak of mpox. Here, we conduct a multiplexed proteomic analysis to quantify >9000 cellular and ~80% of viral proteins throughout MVA infection of human fibroblasts and macrophages. >690 human proteins are down-regulated >2-fold by MVA, revealing a substantial remodelling of the host proteome. >25% of these MVA targets are not shared with replication-competent vaccinia. Viral intermediate/late gene expression is necessary for MVA antagonism of innate immunity, and suppression of interferon effectors such as ISG20 potentiates virus gene expression. Proteomic changes specific to infection of macrophages indicate modulation of the inflammatory response, including inflammasome activation. Our approach thus provides a global view of the impact of MVA on the human proteome and identifies mechanisms that may underpin its abortive infection. These discoveries will prove vital to design future generations of vaccines.
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Affiliation(s)
- Jonas D Albarnaz
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK.
- The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK.
| | - Joanne Kite
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Marisa Oliveira
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Hanqi Li
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Ying Di
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | | | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Florian I Schmidt
- Institute of Innate Immunity, University of Bonn, 53127, Bonn, Germany
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK.
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3
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Abdelwhab EM, Mettenleiter TC. Zoonotic Animal Influenza Virus and Potential Mixing Vessel Hosts. Viruses 2023; 15:980. [PMID: 37112960 PMCID: PMC10145017 DOI: 10.3390/v15040980] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/05/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Influenza viruses belong to the family Orthomyxoviridae with a negative-sense, single-stranded segmented RNA genome. They infect a wide range of animals, including humans. From 1918 to 2009, there were four influenza pandemics, which caused millions of casualties. Frequent spillover of animal influenza viruses to humans with or without intermediate hosts poses a serious zoonotic and pandemic threat. The current SARS-CoV-2 pandemic overshadowed the high risk raised by animal influenza viruses, but highlighted the role of wildlife as a reservoir for pandemic viruses. In this review, we summarize the occurrence of animal influenza virus in humans and describe potential mixing vessel or intermediate hosts for zoonotic influenza viruses. While several animal influenza viruses possess a high zoonotic risk (e.g., avian and swine influenza viruses), others are of low to negligible zoonotic potential (e.g., equine, canine, bat and bovine influenza viruses). Transmission can occur directly from animals, particularly poultry and swine, to humans or through reassortant viruses in "mixing vessel" hosts. To date, there are less than 3000 confirmed human infections with avian-origin viruses and less than 7000 subclinical infections documented. Likewise, only a few hundreds of confirmed human cases caused by swine influenza viruses have been reported. Pigs are the historic mixing vessel host for the generation of zoonotic influenza viruses due to the expression of both avian-type and human-type receptors. Nevertheless, there are a number of hosts which carry both types of receptors and can act as a potential mixing vessel host. High vigilance is warranted to prevent the next pandemic caused by animal influenza viruses.
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Affiliation(s)
- Elsayed M. Abdelwhab
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Thomas C. Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
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4
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Wickenhagen A, Sugrue E, Lytras S, Kuchi S, Noerenberg M, Turnbull ML, Loney C, Herder V, Allan J, Jarmson I, Cameron-Ruiz N, Varjak M, Pinto RM, Lee JY, Iselin L, Palmalux N, Stewart DG, Swingler S, Greenwood EJD, Crozier TWM, Gu Q, Davies EL, Clohisey S, Wang B, Trindade Maranhão Costa F, Freire Santana M, de Lima Ferreira LC, Murphy L, Fawkes A, Meynert A, Grimes G, Da Silva Filho JL, Marti M, Hughes J, Stanton RJ, Wang ECY, Ho A, Davis I, Jarrett RF, Castello A, Robertson DL, Semple MG, Openshaw PJM, Palmarini M, Lehner PJ, Baillie JK, Rihn SJ, Wilson SJ. A prenylated dsRNA sensor protects against severe COVID-19. Science 2021; 374:eabj3624. [PMID: 34581622 PMCID: PMC7612834 DOI: 10.1126/science.abj3624] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022]
Abstract
Inherited genetic factors can influence the severity of COVID-19, but the molecular explanation underpinning a genetic association is often unclear. Intracellular antiviral defenses can inhibit the replication of viruses and reduce disease severity. To better understand the antiviral defenses relevant to COVID-19, we used interferon-stimulated gene (ISG) expression screening to reveal that 2′-5′-oligoadenylate synthetase 1 (OAS1), through ribonuclease L, potently inhibits severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We show that a common splice-acceptor single-nucleotide polymorphism (Rs10774671) governs whether patients express prenylated OAS1 isoforms that are membrane-associated and sense-specific regions of SARS-CoV-2 RNAs or if they only express cytosolic, nonprenylated OAS1 that does not efficiently detect SARS-CoV-2. In hospitalized patients, expression of prenylated OAS1 was associated with protection from severe COVID-19, suggesting that this antiviral defense is a major component of a protective antiviral response.
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Affiliation(s)
- Arthur Wickenhagen
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Elena Sugrue
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Spyros Lytras
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Srikeerthana Kuchi
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Marko Noerenberg
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Matthew L. Turnbull
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Colin Loney
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Vanessa Herder
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Jay Allan
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Innes Jarmson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Natalia Cameron-Ruiz
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Margus Varjak
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Rute M. Pinto
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Jeffrey Y. Lee
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Louisa Iselin
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Natasha Palmalux
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Douglas G. Stewart
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Simon Swingler
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Edward J. D. Greenwood
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Thomas W. M. Crozier
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Quan Gu
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Emma L. Davies
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Fabio Trindade Maranhão Costa
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paolo, Brazil
| | - Monique Freire Santana
- Department of Education and Research, Oncology Control Centre of Amazonas State (FCECON), Manaus, Amazonas, Brazil
| | - Luiz Carlos de Lima Ferreira
- Postgraduate Program in Tropical Medicine, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Alison Meynert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Graeme Grimes
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - ISARIC4C Investigators
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paolo, Brazil
- Department of Education and Research, Oncology Control Centre of Amazonas State (FCECON), Manaus, Amazonas, Brazil
- Postgraduate Program in Tropical Medicine, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
- Division of Infection & Immunity, Cardiff University, Cardiff, UK
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare, National Health Service Trust London, London, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Joao Luiz Da Silva Filho
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Matthias Marti
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | | | - Eddie C. Y. Wang
- Division of Infection & Immunity, Cardiff University, Cardiff, UK
| | - Antonia Ho
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ruth F. Jarrett
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Alfredo Castello
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - David L. Robertson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, UK
| | - Peter J. M. Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare, National Health Service Trust London, London, UK
| | - Massimo Palmarini
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Paul J. Lehner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - J. Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Suzannah J. Rihn
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Sam J. Wilson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
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5
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Charman M, McFarlane S, Wojtus JK, Sloan E, Dewar R, Leeming G, Al-Saadi M, Hunter L, Carroll MW, Stewart JP, Digard P, Hutchinson E, Boutell C. Constitutive TRIM22 Expression in the Respiratory Tract Confers a Pre-Existing Defence Against Influenza A Virus Infection. Front Cell Infect Microbiol 2021; 11:689707. [PMID: 34621686 PMCID: PMC8490869 DOI: 10.3389/fcimb.2021.689707] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/26/2021] [Indexed: 12/19/2022] Open
Abstract
The induction of antiviral effector proteins as part of a homeostatically controlled innate immune response to infection plays a critical role in limiting the propagation and transmission of respiratory pathogens. However, the prolonged induction of this immune response can lead to lung hyperinflammation, tissue damage, and respiratory failure. We hypothesized that tissues exposed to the constant threat of infection may constitutively express higher levels of antiviral effector proteins to reduce the need to activate potentially harmful innate immune defences. By analysing transcriptomic data derived from a range of human tissues, we identify lung tissue to express constitutively higher levels of antiviral effector genes relative to that of other mucosal and non-mucosal tissues. By using primary cell lines and the airways of rhesus macaques, we show the interferon-stimulated antiviral effector protein TRIM22 (TRIpartite Motif 22) to be constitutively expressed in the lung independently of viral infection or innate immune stimulation. These findings contrast with previous reports that have shown TRIM22 expression in laboratory-adapted cell lines to require interferon stimulation. We demonstrate that constitutive levels of TRIM22 are sufficient to inhibit the onset of human and avian influenza A virus (IAV) infection by restricting the onset of viral transcription independently of interferon-mediated innate immune defences. Thus, we identify TRIM22 to confer a pre-existing (intrinsic) intracellular defence against IAV infection in cells derived from the respiratory tract. Our data highlight the importance of tissue-specific and cell-type dependent patterns of pre-existing immune gene expression in the intracellular restriction of IAV from the outset of infection.
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Affiliation(s)
- Matthew Charman
- MRC - University of Glasgow Centre for Virus Research, Glasgow, United Kingdom.,Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Steven McFarlane
- MRC - University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Joanna K Wojtus
- MRC - University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Elizabeth Sloan
- MRC - University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Rebecca Dewar
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Gail Leeming
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Mohammed Al-Saadi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.,Department of Animal Production, University of Al-Qadisiyah, Al-Diwaniyah, Iraq
| | - Laura Hunter
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Miles W Carroll
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - James P Stewart
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Paul Digard
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Edward Hutchinson
- MRC - University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Chris Boutell
- MRC - University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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6
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Evseev D, Magor KE. Molecular Evolution of the Influenza A Virus Non-structural Protein 1 in Interspecies Transmission and Adaptation. Front Microbiol 2021; 12:693204. [PMID: 34671321 PMCID: PMC8521145 DOI: 10.3389/fmicb.2021.693204] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/06/2021] [Indexed: 12/03/2022] Open
Abstract
The non-structural protein 1 (NS1) of influenza A viruses plays important roles in viral fitness and in the process of interspecies adaptation. It is one of the most polymorphic and mutation-tolerant proteins of the influenza A genome, but its evolutionary patterns in different host species and the selective pressures that underlie them are hard to define. In this review, we highlight some of the species-specific molecular signatures apparent in different NS1 proteins and discuss two functions of NS1 in the process of viral adaptation to new host species. First, we consider the ability of NS1 proteins to broadly suppress host protein expression through interaction with CPSF4. This NS1 function can be spontaneously lost and regained through mutation and must be balanced against the need for host co-factors to aid efficient viral replication. Evidence suggests that this function of NS1 may be selectively lost in the initial stages of viral adaptation to some new host species. Second, we explore the ability of NS1 proteins to inhibit antiviral interferon signaling, an essential function for viral replication without which the virus is severely attenuated in any host. Innate immune suppression by NS1 not only enables viral replication in tissues, but also dampens the adaptive immune response and immunological memory. NS1 proteins suppress interferon signaling and effector functions through a variety of protein-protein interactions that may differ from host to host but must achieve similar goals. The multifunctional influenza A virus NS1 protein is highly plastic, highly versatile, and demonstrates a diversity of context-dependent solutions to the problem of interspecies adaptation.
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Affiliation(s)
| | - Katharine E. Magor
- Department of Biological Sciences, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
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7
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Abstract
The abundance, localization, modifications, and protein-protein interactions of many host cell and virus proteins can change dynamically throughout the course of any viral infection. Studying these changes is critical for a comprehensive understanding of how viruses replicate and cause disease, as well as for the development of antiviral therapeutics and vaccines. Previously, we developed a mass spectrometry-based technique called quantitative temporal viromics (QTV), which employs isobaric tandem mass tags (TMTs) to allow precise comparative quantification of host and virus proteomes through a whole time course of infection. In this review, we discuss the utility and applications of QTV, exemplified by numerous studies that have since used proteomics with a variety of quantitative techniques to study virus infection through time. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom;
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8
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Weis S, te Velthuis AJW. Influenza Virus RNA Synthesis and the Innate Immune Response. Viruses 2021; 13:v13050780. [PMID: 33924859 PMCID: PMC8146608 DOI: 10.3390/v13050780] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 04/25/2021] [Accepted: 04/25/2021] [Indexed: 12/25/2022] Open
Abstract
Infection with influenza A and B viruses results in a mild to severe respiratory tract infection. It is widely accepted that many factors affect the severity of influenza disease, including viral replication, host adaptation, innate immune signalling, pre-existing immunity, and secondary infections. In this review, we will focus on the interplay between influenza virus RNA synthesis and the detection of influenza virus RNA by our innate immune system. Specifically, we will discuss the generation of various RNA species, host pathogen receptors, and host shut-off. In addition, we will also address outstanding questions that currently limit our knowledge of influenza virus replication and host adaption. Understanding the molecular mechanisms underlying these factors is essential for assessing the pandemic potential of future influenza virus outbreaks.
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9
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Muñoz-Moreno R, Martínez-Romero C, Blanco-Melo D, Forst CV, Nachbagauer R, Benitez AA, Mena I, Aslam S, Balasubramaniam V, Lee I, Panis M, Ayllón J, Sachs D, Park MS, Krammer F, tenOever BR, García-Sastre A. Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses. Cell Rep 2020; 29:3997-4009.e5. [PMID: 31851929 PMCID: PMC7010214 DOI: 10.1016/j.celrep.2019.11.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/03/2019] [Accepted: 11/15/2019] [Indexed: 12/23/2022] Open
Abstract
Influenza A viruses (IAVs) have a remarkable tropism in their ability to
circulate in both mammalian and avian species. The IAV NS1 protein is a
multifunctional virulence factor that inhibits the type I interferon host
response through a myriad of mechanisms. How NS1 has evolved to enable this
remarkable property across species and its specific impact in the overall
replication, pathogenicity, and host preference remain unknown. Here we analyze
the NS1 evolutionary landscape and host tropism using a barcoded library of
recombinant IAVs. Results show a surprisingly great variety of NS1 phenotypes
according to their ability to replicate in different hosts. The IAV NS1 genes
appear to have taken diverse and random evolutionary pathways within their
multiple phylogenetic lineages. In summary, the high evolutionary plasticity of
this viral protein underscores the ability of IAVs to adapt to multiple hosts
and aids in our understanding of its global prevalence. Muñoz-Moreno et al. report that influenza A virus NS1 undergoes
diverse and unpredictable evolutionary pathways based on its different
phylogenetic lineages. A high-throughput approach using a barcoded library is
used to test the interactions between NS1-recombinant viruses and to study their
preference for specific or multiple hosts.
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Affiliation(s)
- Raquel Muñoz-Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carles Martínez-Romero
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel Blanco-Melo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christian V Forst
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Asiel Arturo Benitez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sadaf Aslam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vinod Balasubramaniam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Malaysia
| | - Ilseob Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maryline Panis
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juan Ayllón
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David Sachs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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10
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Long JS, Mistry B, Haslam SM, Barclay WS. Host and viral determinants of influenza A virus species specificity. Nat Rev Microbiol 2020; 17:67-81. [PMID: 30487536 DOI: 10.1038/s41579-018-0115-z] [Citation(s) in RCA: 308] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Influenza A viruses cause pandemics when they cross between species and an antigenically novel virus acquires the ability to infect and transmit between these new hosts. The timing of pandemics is currently unpredictable but depends on ecological and virological factors. The host range of an influenza A virus is determined by species-specific interactions between virus and host cell factors. These include the ability to bind and enter cells, to replicate the viral RNA genome within the host cell nucleus, to evade host restriction factors and innate immune responses and to transmit between individuals. In this Review, we examine the host barriers that influenza A viruses of animals, especially birds, must overcome to initiate a pandemic in humans and describe how, on crossing the species barrier, the virus mutates to establish new interactions with the human host. This knowledge is used to inform risk assessments for future pandemics and to identify virus-host interactions that could be targeted by novel intervention strategies.
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Affiliation(s)
- Jason S Long
- Department of Medicine, Imperial College London, London, UK
| | - Bhakti Mistry
- Department of Medicine, Imperial College London, London, UK
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, UK
| | - Wendy S Barclay
- Department of Medicine, Imperial College London, London, UK.
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11
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Susceptibility of Chickens to Low Pathogenic Avian Influenza (LPAI) Viruses of Wild Bird- and Poultry-Associated Subtypes. Viruses 2019; 11:v11111010. [PMID: 31683727 PMCID: PMC6893415 DOI: 10.3390/v11111010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 01/01/2023] Open
Abstract
Analysis of low pathogenic avian influenza (LPAI) viruses circulating in the Netherlands in a previous study revealed associations of specific hemagglutinin (HA) and neuraminidase (NA) subtypes with wild bird or poultry hosts. In this study, we identified putative host associations in LPAI virus internal proteins. We show that LPAI viruses isolated from poultry more frequently carried the allele A variant of the nonstructural protein (NS) gene, compared to wild bird viruses. We determined the susceptibility of chickens to wild bird–associated subtypes H3N8 and H4N6 and poultry-associated subtypes H8N4 and H9N2, carrying either NS allele A or B, in an infection experiment. We observed variations in virus shedding and replication patterns, however, these did not correlate with the predicted wild bird- or poultry-associations of the viruses. The experiment demonstrated that LPAI viruses of wild bird-associated subtypes can replicate in chickens after experimental infection, despite their infrequent detection in poultry. Although the NS1 protein is known to play a role in immune modulation, no differences were detected in the limited innate immune response to LPAI virus infection. This study contributes to a better understanding of the infection dynamics of LPAI viruses in chickens.
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12
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Hussain S, Turnbull ML, Pinto RM, McCauley JW, Engelhardt OG, Digard P. Segment 2 from influenza A(H1N1) 2009 pandemic viruses confers temperature-sensitive haemagglutinin yield on candidate vaccine virus growth in eggs that can be epistatically complemented by PB2 701D. J Gen Virol 2019; 100:1079-1092. [PMID: 31169484 DOI: 10.1099/jgv.0.001279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Candidate vaccine viruses (CVVs) for seasonal influenza A virus are made by reassortment of the antigenic virus with an egg-adapted strain, typically A/Puerto Rico/8/34 (PR8). Many 2009 A(H1N1) pandemic (pdm09) high-growth reassortants (HGRs) selected this way contain pdm09 segment 2 in addition to the antigenic genes. To investigate this, we made CVV mimics by reverse genetics (RG) that were either 6 : 2 or 5 : 3 reassortants between PR8 and two pdm09 strains, A/California/7/2009 (Cal7) and A/England/195/2009, differing in the source of segment 2. The 5 : 3 viruses replicated better in MDCK-SIAT1 cells than the 6 : 2 viruses, but the 6 : 2 CVVs gave higher haemagglutinin (HA) antigen yields from eggs. This unexpected phenomenon reflected temperature sensitivity conferred by pdm09 segment 2, as the egg HA yields of the 5 : 3 viruses improved substantially when viruses were grown at 35 °C compared with 37.5 °C, whereas the 6 : 2 virus yields did not. However, the authentic 5 : 3 pdm09 HGRs, X-179A and X-181, were not markedly temperature sensitive despite their PB1 sequences being identical to that of Cal7, suggesting compensatory mutations elsewhere in the genome. Sequence comparisons of the PR8-derived backbone genes identified polymorphisms in PB2, NP, NS1 and NS2. Of these, PB2 N701D affected the temperature dependence of viral transcription and, furthermore, improved and drastically reduced the temperature sensitivity of the HA yield from the 5 : 3 CVV mimic. We conclude that the HA yield of pdm09 CVVs can be affected by an epistatic interaction between PR8 PB2 and pdm09 PB1, but that this can be minimized by ensuring that the backbones used for vaccine manufacture in eggs contain PB2 701D.
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Affiliation(s)
- Saira Hussain
- 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK.,2 The Francis Crick Institute, London, NW1 1AT, UK
| | - Matthew L Turnbull
- 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Rute M Pinto
- 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | | | - Othmar G Engelhardt
- 3 National Institute for Biological Standards and Control, South Mimms, Potters Bar, Hertfordshire, EN6 3QG, UK
| | - Paul Digard
- 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
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13
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Kim JI, Park S, Bae JY, Park MS. Evolutionary relationship analysis of Middle East respiratory syndrome coronavirus 4a and 4b protein coding sequences. J Vet Sci 2019; 20:e1. [PMID: 30944524 PMCID: PMC6441811 DOI: 10.4142/jvs.2019.20.e1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 11/26/2018] [Accepted: 12/16/2018] [Indexed: 02/02/2023] Open
Abstract
The 4a and 4b proteins of the Middle East respiratory syndrome coronavirus (MERS-CoV) have been described for their antagonism on host innate immunity. However, unlike clustering patterns of the complete gene sequences of human and camel MERS-CoVs, the 4a and 4b protein coding regions did not constitute species-specific phylogenetic groups. Moreover, given the estimated evolutionary rates of the complete, 4a, and 4b gene sequences, the 4a and 4b proteins might be less affected by species-specific innate immune pressures. These results suggest that the 4a and 4b proteins of MERS-CoV may function against host innate immunity in a manner independent of host species and/or evolutionary clustering patterns.
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Affiliation(s)
- Jin Il Kim
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Korea
| | - Sehee Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Korea
| | - Joon-Yong Bae
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul 02841, Korea
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14
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Mutation of Influenza A Virus PA-X Decreases Pathogenicity in Chicken Embryos and Can Increase the Yield of Reassortant Candidate Vaccine Viruses. J Virol 2019; 93:JVI.01551-18. [PMID: 30381488 PMCID: PMC6321911 DOI: 10.1128/jvi.01551-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/25/2018] [Indexed: 01/08/2023] Open
Abstract
Influenza A virus is a widespread pathogen that affects both humans and a variety of animal species, causing regular epidemics and sporadic pandemics, with major public health and economic consequences. A better understanding of virus biology is therefore important. The primary control measure is vaccination, which for humans mostly relies on antigens produced in eggs from PR8-based viruses bearing the glycoprotein genes of interest. However, not all reassortants replicate well enough to supply sufficient virus antigen for demand. The significance of our research lies in identifying that mutation of the PA-X gene in the PR8 strain of virus can improve antigen yield, potentially by decreasing the pathogenicity of the virus in embryonated eggs. The PA-X protein of influenza A virus has roles in host cell shutoff and viral pathogenesis. While most strains are predicted to encode PA-X, strain-dependent variations in activity have been noted. We found that PA-X protein from the A/PR/8/34 (PR8) strain had significantly lower repressive activity against cellular gene expression than PA-X proteins from the avian strains A/turkey/England/50-92/91 (H5N1) (T/E) and A/chicken/Rostock/34 (H7N1). Loss of normal PA-X expression, either by mutation of the frameshift site or by truncating the X open reading frame (ORF), had little effect on the infectious virus titer of PR8 or PR8 7:1 reassortants with T/E segment 3 grown in embryonated hens’ eggs. However, in both virus backgrounds, mutation of PA-X led to decreased embryo mortality and lower overall pathology, effects that were more pronounced in the PR8 strain than in the T/E reassortant, despite the low shutoff activity of the PR8 PA-X. Purified PA-X mutant virus particles displayed an increased ratio of hemagglutinin (HA) to nucleoprotein (NP) and M1 compared to values for their wild-type (WT) counterparts, suggesting altered virion composition. When the PA-X gene was mutated in the background of poorly growing PR8 6:2 vaccine reassortant analogues containing the HA and neuraminidase (NA) segments from H1N1 2009 pandemic viruses or from an avian H7N3 strain, HA yield increased up to 2-fold. This suggests that the PR8 PA-X protein may harbor a function unrelated to host cell shutoff and that disruption of the PA-X gene has the potential to improve the HA yield of vaccine viruses. IMPORTANCE Influenza A virus is a widespread pathogen that affects both humans and a variety of animal species, causing regular epidemics and sporadic pandemics, with major public health and economic consequences. A better understanding of virus biology is therefore important. The primary control measure is vaccination, which for humans mostly relies on antigens produced in eggs from PR8-based viruses bearing the glycoprotein genes of interest. However, not all reassortants replicate well enough to supply sufficient virus antigen for demand. The significance of our research lies in identifying that mutation of the PA-X gene in the PR8 strain of virus can improve antigen yield, potentially by decreasing the pathogenicity of the virus in embryonated eggs.
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15
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Herron LR, Pridans C, Turnbull ML, Smith N, Lillico S, Sherman A, Gilhooley HJ, Wear M, Kurian D, Papadakos G, Digard P, Hume DA, Gill AC, Sang HM. A chicken bioreactor for efficient production of functional cytokines. BMC Biotechnol 2018; 18:82. [PMID: 30594166 PMCID: PMC6311007 DOI: 10.1186/s12896-018-0495-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/18/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The global market for protein drugs has the highest compound annual growth rate of any pharmaceutical class but their availability, especially outside of the US market, is compromised by the high cost of manufacture and validation compared to traditional chemical drugs. Improvements in transgenic technologies allow valuable proteins to be produced by genetically-modified animals; several therapeutic proteins from such animal bioreactors are already on the market after successful clinical trials and regulatory approval. Chickens have lagged behind mammals in bioreactor development, despite a number of potential advantages, due to the historic difficulty in producing transgenic birds, but the production of therapeutic proteins in egg white of transgenic chickens would substantially lower costs across the entire production cycle compared to traditional cell culture-based production systems. This could lead to more affordable treatments and wider markets, including in developing countries and for animal health applications. RESULTS Here we report the efficient generation of new transgenic chicken lines to optimize protein production in eggs. As proof-of-concept, we describe the expression, purification and functional characterization of three pharmaceutical proteins, the human cytokine interferon α2a and two species-specific Fc fusions of the cytokine CSF1. CONCLUSION Our work optimizes and validates a transgenic chicken system for the cost-effective production of pure, high quality, biologically active protein for therapeutics and other applications.
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Affiliation(s)
- Lissa R. Herron
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
- Roslin Technologies Limited, Roslin Innovation Centre, Easter Bush Campus, Midlothian, EH25 9RG UK
| | - Clare Pridans
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
- Centre for Inflammation Research at the University of Edinburgh, The Queen’s Medical Research Institute, Edinburgh, EH16 4TJ UK
| | - Matthew L. Turnbull
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
- Medical Research Council University of Glasgow Centre for Virus Research (CVR), University of Glasgow, Glasgow, G61 1QH UK
| | - Nikki Smith
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Simon Lillico
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Adrian Sherman
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Hazel J. Gilhooley
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Martin Wear
- Edinburgh Protein Production Facility, Wellcome Trust Centre for Cell Biology (WTCCB), University of Edinburgh, Edinburgh, EH9 3JR UK
| | - Dominic Kurian
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Grigorios Papadakos
- Roslin Technologies Limited, Roslin Innovation Centre, Easter Bush Campus, Midlothian, EH25 9RG UK
| | - Paul Digard
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - David A. Hume
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
- Centre for Inflammation Research at the University of Edinburgh, The Queen’s Medical Research Institute, Edinburgh, EH16 4TJ UK
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102 Australia
| | - Andrew C. Gill
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
- School of Chemistry, Joseph Banks Laboratories, University of Lincoln, Lincoln, Lincolnshire LN6 7DL UK
| | - Helen M. Sang
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
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16
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Genetic evidence for the intercontinental movement of avian influenza viruses possessing North American-origin nonstructural gene allele B into South Korea. INFECTION GENETICS AND EVOLUTION 2018; 66:18-25. [PMID: 30196122 DOI: 10.1016/j.meegid.2018.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/16/2018] [Accepted: 09/05/2018] [Indexed: 01/23/2023]
Abstract
Avian influenza viruses (AIVs) are genetically separated by geographical barriers, resulting in the independent evolution of North American and Eurasian lineages. In the present study, to determine whether AIVs possessing the North American-origin nonstructural (NS) gene were previously introduced into South Korea, we performed a genetic analysis of AIVs isolated from fecal samples of migratory birds. We detected seven viruses possessing the North American-origin NS allele B among 413 AIV-positive samples obtained during AI surveillance between 2012 and 2017. We found evidence for the intercontinental transmission of at least three genetically distinct clusters of the B allele of the North American-origin NS gene into Eurasia at a low frequency. The host species of three viruses were identified as the greater white-fronted goose (Anser albifrons) using a DNA barcoding technique. Moreover, we used GPS-CDMA-based telemetry to determine the migration route of the greater white-fronted goose between the Far East of Russia and South Korea and found that this species may play an important role as an intermediate vector in the intercontinental transmission of AIVs. To improve our understanding of the role of wild birds in the ecology of AIVs, advanced AIV surveillance is required in the Far East of Russia as well as in Alaska region of Beringia accompanied by host identification and wild bird tracking.
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17
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Kuo RL, Chen CJ, Tam EH, Huang CG, Li LH, Li ZH, Su PC, Liu HP, Wu CC. Interactome Analysis of NS1 Protein Encoded by Influenza A H7N9 Virus Reveals an Inhibitory Role of NS1 in Host mRNA Maturation. J Proteome Res 2018; 17:1474-1484. [PMID: 29558158 DOI: 10.1021/acs.jproteome.7b00815] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Influenza A virus infections can result in severe respiratory diseases. The H7N9 subtype of avian influenza A virus has been transmitted to humans and caused severe disease and death. Nonstructural protein 1 (NS1) of influenza A virus is a virulence determinant during viral infection. To elucidate the functions of the NS1 encoded by influenza A H7N9 virus (H7N9 NS1), interaction partners of H7N9 NS1 in human cells were identified with immunoprecipitation followed by SDS-PAGE coupled with liquid chromatography-tandem mass spectrometry (GeLC-MS/MS). We identified 36 cellular proteins as the interacting partners of the H7N9 NS1, and they are involved in RNA processing, mRNA splicing via spliceosome, and the mRNA surveillance pathway. Two of the interacting partners, cleavage and polyadenylation specificity factor subunit 2 (CPSF2) and CPSF7, were confirmed to interact with H7N9 NS1 using coimmunoprecipitation and immunoblotting based on the previous finding that the two proteins are involved in pre-mRNA polyadenylation machinery. Furthermore, we illustrate that overexpression of H7N9 NS1, as well as infection by the influenza A H7N9 virus, interfered with pre-mRNA polyadenylation in host cells. This study comprehensively profiled the interactome of H7N9 NS1 in host cells, and the results demonstrate a novel endotype for H7N9 NS1 in inhibiting host mRNA maturation.
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Affiliation(s)
- Rei-Lin Kuo
- Department of Medical Biotechnology and Laboratory Science, College of Medicine , Chang Gung University , Taoyuan 33302 , Taiwan.,Research Center for Emerging Viral Infections, College of Medicine , Chang Gung University , Taoyuan 33302 , Taiwan.,Division of Asthma, Allergy, and Rheumatology, Department of Pediatrics , Chang Gung Memorial Hospital , Linkou, Taoyuan 33302 , Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine , Chang Gung University , Taoyuan 33302 , Taiwan
| | - Chi-Jene Chen
- Department of Medical Laboratory Science and Biotechnology , China Medical University , Taichung 40402 , Taiwan.,Research Center for Emerging Viruses , China Medical University Hospital , Taichung 40402 , Taiwan
| | - Ee-Hong Tam
- Department of Medical Biotechnology and Laboratory Science, College of Medicine , Chang Gung University , Taoyuan 33302 , Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine , Chang Gung University , Taoyuan 33302 , Taiwan
| | - Chung-Guei Huang
- Department of Medical Biotechnology and Laboratory Science, College of Medicine , Chang Gung University , Taoyuan 33302 , Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine , Chang Gung University , Taoyuan 33302 , Taiwan.,Department of Laboratory Medicine , Chang Gung Memorial Hospital , Linkou, Taoyuan 33302 , Taiwan
| | - Li-Hsin Li
- Department of Medical Biotechnology and Laboratory Science, College of Medicine , Chang Gung University , Taoyuan 33302 , Taiwan
| | - Zong-Hua Li
- Department of Medical Biotechnology and Laboratory Science, College of Medicine , Chang Gung University , Taoyuan 33302 , Taiwan
| | - Pei-Chia Su
- Department of Medical Biotechnology and Laboratory Science, College of Medicine , Chang Gung University , Taoyuan 33302 , Taiwan
| | - Hao-Ping Liu
- Department of Veterinary Medicine , National Chung Hsing University , Taichung 40227 , Taiwan
| | - Chih-Ching Wu
- Department of Medical Biotechnology and Laboratory Science, College of Medicine , Chang Gung University , Taoyuan 33302 , Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine , Chang Gung University , Taoyuan 33302 , Taiwan.,Department of Otolaryngology-Head & Neck Surgery , Chang Gung Memorial Hospital , Linkou, Taoyuan 33302 , Taiwan
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18
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Petersen H, Mostafa A, Tantawy MA, Iqbal AA, Hoffmann D, Tallam A, Selvakumar B, Pessler F, Beer M, Rautenschlein S, Pleschka S. NS Segment of a 1918 Influenza A Virus-Descendent Enhances Replication of H1N1pdm09 and Virus-Induced Cellular Immune Response in Mammalian and Avian Systems. Front Microbiol 2018; 9:526. [PMID: 29623073 PMCID: PMC5874506 DOI: 10.3389/fmicb.2018.00526] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/08/2018] [Indexed: 12/14/2022] Open
Abstract
The 2009 pandemic influenza A virus (IAV) H1N1 strain (H1N1pdm09) has widely spread and is circulating in humans and swine together with other human and avian IAVs. This fact raises the concern that reassortment between H1N1pdm09 and co-circulating viruses might lead to an increase of H1N1pdm09 pathogenicity in different susceptible host species. Herein, we explored the potential of different NS segments to enhance the replication dynamics, pathogenicity and host range of H1N1pdm09 strain A/Giessen/06/09 (Gi-wt). The NS segments were derived from (i) human H1N1- and H3N2 IAVs, (ii) highly pathogenic- (H5- or H7-subtypes) or (iii) low pathogenic avian influenza viruses (H7- or H9-subtypes). A significant increase of growth kinetics in A549 (human lung epithelia) and NPTr (porcine tracheal epithelia) cells was only noticed in vitro for the reassortant Gi-NS-PR8 carrying the NS segment of the 1918-descendent A/Puerto Rico/8/34 (PR8-wt, H1N1), whereas all other reassortants showed either reduced or comparable replication efficiencies. Analysis using ex vivo tracheal organ cultures of turkeys (TOC-Tu), a species susceptible to IAV H1N1 infection, demonstrated increased replication of Gi-NS-PR8 compared to Gi-wt. Also, Gi-NS-PR8 induced a markedly higher expression of immunoregulatory and pro-inflammatory cytokines, chemokines and interferon-stimulated genes in A549 cells, THP-1-derived macrophages (dHTP) and TOC-Tu. In vivo, Gi-NS-PR8 induced an earlier onset of mortality than Gi-wt in mice, whereas, 6-week-old chickens were found to be resistant to both viruses. These data suggest that the specific characteristics of the PR8 NS segments can impact on replication, virus induced cellular immune responses and pathogenicity of the H1N1pdm09 in different avian and mammalian host species.
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Affiliation(s)
- Henning Petersen
- Clinic for Poultry, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Ahmed Mostafa
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany.,Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
| | - Mohamed A Tantawy
- Institute for Experimental Infection Research, TWINCORE Centre for Experimental and Clinical Infection Research, Hanover, Germany.,Department of Hormones, Medical Research Division, National Research Centre, Cairo, Egypt
| | - Azeem A Iqbal
- Institute for Experimental Infection Research, TWINCORE Centre for Experimental and Clinical Infection Research, Hanover, Germany.,Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Aravind Tallam
- Institute for Experimental Infection Research, TWINCORE Centre for Experimental and Clinical Infection Research, Hanover, Germany
| | - Balachandar Selvakumar
- Max-Planck Laboratory for Heart and Lung Research, Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Frank Pessler
- Institute for Experimental Infection Research, TWINCORE Centre for Experimental and Clinical Infection Research, Hanover, Germany.,Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Silke Rautenschlein
- Clinic for Poultry, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
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Comparison of the efficacy of a commercial inactivated influenza A/H1N1/pdm09 virus (pH1N1) vaccine and two experimental M2e-based vaccines against pH1N1 challenge in the growing pig model. PLoS One 2018; 13:e0191739. [PMID: 29381710 PMCID: PMC5790244 DOI: 10.1371/journal.pone.0191739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/10/2018] [Indexed: 01/05/2023] Open
Abstract
Swine influenza A viruses (IAV-S) found in North American pigs are diverse and the lack of cross-protection among heterologous strains is a concern. The objective of this study was to compare a commercial inactivated A/H1N1/pdm09 (pH1N1) vaccine and two novel subunit vaccines, using IAV M2 ectodomain (M2e) epitopes as antigens, in a growing pig model. Thirty-nine 2-week-old IAV negative pigs were randomly assigned to five groups and rooms. At 3 weeks of age and again at 5 weeks of age, pigs were vaccinated intranasally with an experimental subunit particle vaccine (NvParticle/M2e) or a subunit complex-based vaccine (NvComplex/M2e) or intramuscularly with a commercial inactivated vaccine (Inact/pH1N1). At 7 weeks of age, the pigs were challenged with pH1N1 virus or sham-inoculated. Necropsy was conducted 5 days post pH1N1 challenge (dpc). At the time of challenge one of the Inact/pH1N1 pigs had seroconverted based on IAV nucleoprotein-based ELISA, Inact/pH1N1 pigs had significantly higher pdm09H1N1 hemagglutination inhibition (HI) titers compared to all other groups, and M2e-specific IgG responses were detected in the NvParticle/M2e and the NvComplex/M2e pigs with significantly higher group means in the NvComplex/M2e group compared to SHAMVAC-NEG pigs. After challenge, nasal IAV RNA shedding was significantly reduced in Inact/pH1N1 pigs compared to all other pH1N1 infected groups and this group also had reduced IAV RNA in oral fluids. The macroscopic lung lesions were characterized by mild-to-severe, multifocal-to-diffuse, cranioventral dark purple consolidated areas typical of IAV infection and were similar for NvParticle/M2e, NvComplex/M2e and SHAMVAC-IAV pigs. Lesions were significantly less severe in the SHAMVAC-NEG and the Inact/pH1N1pigs. Under the conditions of this study, a commercial Inact/pH1N1 specific vaccine effectively protected pigs against homologous challenge as evidenced by reduced clinical signs, virus shedding in nasal secretions and oral fluids and reduced macroscopic and microscopic lesions whereas intranasal vaccination with experimental M2e epitope-based subunit vaccines did not. The results further highlight the importance using IAV-S type specific vaccines in pigs.
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Hydrogen Bond Variations of Influenza A Viruses During Adaptation in Human. Sci Rep 2017; 7:14295. [PMID: 29085020 PMCID: PMC5662722 DOI: 10.1038/s41598-017-14533-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/11/2017] [Indexed: 01/12/2023] Open
Abstract
Many host specific mutations have been detected in influenza A viruses (IAVs). However, their effects on hydrogen bond (H-bond) variations have rarely been investigated. In this study, 60 host specific sites were identified in the internal proteins of avian and human IAVs, 27 of which contained mutations with effects on H-bonds. Besides, 30 group specific sites were detected in HA and NA. Twenty-six of 36 mutations existing at these group specific sites caused H-bond loss or formation in at least one subtype. The number of mutations in isolations of 2009 pandemic H1N1, human-infecting H5N1 and H7N9 varied. The combinations of mutations and H-bond changes in these three subtypes of IAVs were also different. In addition, the mutations in isolations of H5N1 distributed more scattered than those in 2009 pandemic H1N1 and H7N9. Eight wave specific mutations in isolations of the fifth H7N9 wave were also identified. Three of them, R140K in HA, Y170H in NA, and R340K in PB2, were capable of resulting in H-bond loss. As mentioned above, these host or group or wave specific H-bond variations provide us with a new field of vision for understanding the changes of structural features in the human adaptation of IAVs.
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Barba M, Daly JM. The Influenza NS1 Protein: What Do We Know in Equine Influenza Virus Pathogenesis? Pathogens 2016; 5:pathogens5030057. [PMID: 27589809 PMCID: PMC5039437 DOI: 10.3390/pathogens5030057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 08/24/2016] [Accepted: 08/27/2016] [Indexed: 12/22/2022] Open
Abstract
Equine influenza virus remains a serious health and potential economic problem throughout most parts of the world, despite intensive vaccination programs in some horse populations. The influenza non-structural protein 1 (NS1) has multiple functions involved in the regulation of several cellular and viral processes during influenza infection. We review the strategies that NS1 uses to facilitate virus replication and inhibit antiviral responses in the host, including sequestering of double-stranded RNA, direct modulation of protein kinase R activity and inhibition of transcription and translation of host antiviral response genes such as type I interferon. Details are provided regarding what it is known about NS1 in equine influenza, especially concerning C-terminal truncation. Further research is needed to determine the role of NS1 in equine influenza infection, which will help to understand the pathophysiology of complicated cases related to cytokine imbalance and secondary bacterial infection, and to investigate new therapeutic and vaccination strategies.
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Affiliation(s)
- Marta Barba
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA.
| | - Janet M Daly
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington LE12 5RD, UK.
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