A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses
Identifieur interne : 000918 ( Main/Exploration ); précédent : 000917; suivant : 000919A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses
Auteurs : Tavis K. Anderson [États-Unis] ; Catherine A. Macken [Nouvelle-Zélande] ; Nicola S. Lewis [Royaume-Uni] ; Richard H. Scheuermann [États-Unis] ; Kristien Van Reeth [Belgique] ; Ian H. Brown [Royaume-Uni] ; Sabrina L. Swenson [États-Unis] ; Gaëlle Simon [France] ; Takehiko Saito [Japon] ; Yohannes Berhane [Canada] ; Janice Ciacci-Zanella [Brésil] ; Ariel Pereda [Argentine] ; C. Todd Davis [États-Unis] ; Ruben O. Donis [États-Unis] ; Richard J. Webby [États-Unis] ; Amy L. Vincent [États-Unis]Source :
- mSphere [ 2379-5042 ] ; 2016.
Abstract
A fundamental goal in the biological sciences is the definition of groups of organisms based on evolutionary history and the naming of those groups. For influenza A viruses (IAVs) in swine, understanding the hemagglutinin (HA) genetic lineage of a circulating strain aids in vaccine antigen selection and allows for inferences about vaccine efficacy. Previous reporting of H1 virus HA in swine relied on colloquial names, frequently with incriminating and stigmatizing geographic toponyms, making comparisons between studies challenging. To overcome this, we developed an adaptable nomenclature using measurable criteria for historical and contemporary evolutionary patterns of H1 global swine IAVs. We also developed a web-accessible tool that classifies viruses according to this nomenclature. This classification system will aid agricultural production and pandemic preparedness through the identification of important changes in swine IAVs and provides terminology enabling discussion of swine IAVs in a common context among animal and human health initiatives.
Url:
DOI: 10.1128/mSphere.00275-16
PubMed: 27981236
PubMed Central: 5156671
Affiliations:
- Argentine, Belgique, Brésil, Canada, France, Japon, Nouvelle-Zélande, Royaume-Uni, États-Unis
- Angleterre, Angleterre de l'Est, Californie, Géorgie (États-Unis), Iowa, Province de Flandre-Orientale, Région flamande, Santa Catarina, Tennessee
- Cambridge, Gand
- Université de Cambridge, Université de Gand
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Swenson</name><affiliation wicri:level="2"><nlm:aff id="aff8">National Veterinary Services Laboratories, USDA-APHIS, Ames, Iowa, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Veterinary Services Laboratories, USDA-APHIS, Ames, Iowa</wicri:regionArea><placeName><region type="state">Iowa</region></placeName></affiliation></author><author><name sortKey="Simon, Gaelle" sort="Simon, Gaelle" uniqKey="Simon G" first="Gaëlle" last="Simon">Gaëlle Simon</name><affiliation wicri:level="1"><nlm:aff id="aff9">ANSES, Ploufragan-Plouzané Laboratory, Swine Virology Immunology Unit, Ploufragan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>ANSES, Ploufragan-Plouzané Laboratory, Swine Virology Immunology Unit, Ploufragan</wicri:regionArea><wicri:noRegion>Ploufragan</wicri:noRegion><wicri:noRegion>Ploufragan</wicri:noRegion></affiliation></author><author><name sortKey="Saito, Takehiko" sort="Saito, Takehiko" uniqKey="Saito T" first="Takehiko" last="Saito">Takehiko Saito</name><affiliation wicri:level="1"><nlm:aff id="aff10">Division of Transboundary Animal Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Division of Transboundary Animal Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki</wicri:regionArea><wicri:noRegion>Ibaraki</wicri:noRegion></affiliation></author><author><name sortKey="Berhane, Yohannes" sort="Berhane, Yohannes" uniqKey="Berhane Y" first="Yohannes" last="Berhane">Yohannes Berhane</name><affiliation wicri:level="1"><nlm:aff id="aff11">Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, Manitoba, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, Manitoba</wicri:regionArea><wicri:noRegion>Manitoba</wicri:noRegion></affiliation></author><author><name sortKey="Ciacci Zanella, Janice" sort="Ciacci Zanella, Janice" uniqKey="Ciacci Zanella J" first="Janice" last="Ciacci-Zanella">Janice Ciacci-Zanella</name><affiliation wicri:level="2"><nlm:aff id="aff12">Embrapa Swine and Poultry, Animal Health and Genetic Laboratory, Concórdia, SC, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Embrapa Swine and Poultry, Animal Health and Genetic Laboratory, Concórdia, SC</wicri:regionArea><placeName><region type="state">Santa Catarina</region></placeName></affiliation></author><author><name sortKey="Pereda, Ariel" sort="Pereda, Ariel" uniqKey="Pereda A" first="Ariel" last="Pereda">Ariel Pereda</name><affiliation wicri:level="1"><nlm:aff id="aff13">Instituto de Patobiología, CICVyA INTA, Hurlingham, Buenos Aires, Argentina</nlm:aff><country xml:lang="fr">Argentine</country><wicri:regionArea>Instituto de Patobiología, CICVyA INTA, Hurlingham, Buenos Aires</wicri:regionArea><wicri:noRegion>Buenos Aires</wicri:noRegion></affiliation></author><author><name sortKey="Davis, C Todd" sort="Davis, C Todd" uniqKey="Davis C" first="C. 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Anderson</name><affiliation wicri:level="2"><nlm:aff id="aff1">Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa</wicri:regionArea><placeName><region type="state">Iowa</region></placeName></affiliation></author><author><name sortKey="Macken, Catherine A" sort="Macken, Catherine A" uniqKey="Macken C" first="Catherine A." last="Macken">Catherine A. Macken</name><affiliation wicri:level="1"><nlm:aff id="aff2">Bioinformatics Institute, University of Auckland, Auckland, New Zealand</nlm:aff><country xml:lang="fr">Nouvelle-Zélande</country><wicri:regionArea>Bioinformatics Institute, University of Auckland, Auckland</wicri:regionArea><wicri:noRegion>Auckland</wicri:noRegion></affiliation></author><author><name sortKey="Lewis, Nicola S" sort="Lewis, Nicola S" uniqKey="Lewis N" first="Nicola S." last="Lewis">Nicola S. Lewis</name><affiliation wicri:level="4"><nlm:aff id="aff3">Department of Zoology, University of Cambridge, Cambridge, United Kingdom</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Zoology, University of Cambridge, Cambridge</wicri:regionArea><orgName type="university">Université de Cambridge</orgName><placeName><settlement type="city">Cambridge</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Angleterre de l'Est</region></placeName></affiliation></author><author><name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H." last="Scheuermann">Richard H. Scheuermann</name><affiliation wicri:level="2"><nlm:aff id="aff4">J. Craig Venter Institute, La Jolla, California, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>J. Craig Venter Institute, La Jolla, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff5">Department of Pathology, University of California, San Diego, California, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of California, San Diego, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Van Reeth, Kristien" sort="Van Reeth, Kristien" uniqKey="Van Reeth K" first="Kristien" last="Van Reeth">Kristien Van Reeth</name><affiliation wicri:level="4"><nlm:aff id="aff6">Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Merelbeke</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation></author><author><name sortKey="Brown, Ian H" sort="Brown, Ian H" uniqKey="Brown I" first="Ian H." last="Brown">Ian H. Brown</name><affiliation wicri:level="1"><nlm:aff id="aff7">Animal and Plant Health Agency, Weybridge, United Kingdom</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Animal and Plant Health Agency, Weybridge</wicri:regionArea><wicri:noRegion>Weybridge</wicri:noRegion></affiliation></author><author><name sortKey="Swenson, Sabrina L" sort="Swenson, Sabrina L" uniqKey="Swenson S" first="Sabrina L." last="Swenson">Sabrina L. Swenson</name><affiliation wicri:level="2"><nlm:aff id="aff8">National Veterinary Services Laboratories, USDA-APHIS, Ames, Iowa, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Veterinary Services Laboratories, USDA-APHIS, Ames, Iowa</wicri:regionArea><placeName><region type="state">Iowa</region></placeName></affiliation></author><author><name sortKey="Simon, Gaelle" sort="Simon, Gaelle" uniqKey="Simon G" first="Gaëlle" last="Simon">Gaëlle Simon</name><affiliation wicri:level="1"><nlm:aff id="aff9">ANSES, Ploufragan-Plouzané Laboratory, Swine Virology Immunology Unit, Ploufragan, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>ANSES, Ploufragan-Plouzané Laboratory, Swine Virology Immunology Unit, Ploufragan</wicri:regionArea><wicri:noRegion>Ploufragan</wicri:noRegion><wicri:noRegion>Ploufragan</wicri:noRegion></affiliation></author><author><name sortKey="Saito, Takehiko" sort="Saito, Takehiko" uniqKey="Saito T" first="Takehiko" last="Saito">Takehiko Saito</name><affiliation wicri:level="1"><nlm:aff id="aff10">Division of Transboundary Animal Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Division of Transboundary Animal Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki</wicri:regionArea><wicri:noRegion>Ibaraki</wicri:noRegion></affiliation></author><author><name sortKey="Berhane, Yohannes" sort="Berhane, Yohannes" uniqKey="Berhane Y" first="Yohannes" last="Berhane">Yohannes Berhane</name><affiliation wicri:level="1"><nlm:aff id="aff11">Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, Manitoba, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, Manitoba</wicri:regionArea><wicri:noRegion>Manitoba</wicri:noRegion></affiliation></author><author><name sortKey="Ciacci Zanella, Janice" sort="Ciacci Zanella, Janice" uniqKey="Ciacci Zanella J" first="Janice" last="Ciacci-Zanella">Janice Ciacci-Zanella</name><affiliation wicri:level="2"><nlm:aff id="aff12">Embrapa Swine and Poultry, Animal Health and Genetic Laboratory, Concórdia, SC, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Embrapa Swine and Poultry, Animal Health and Genetic Laboratory, Concórdia, SC</wicri:regionArea><placeName><region type="state">Santa Catarina</region></placeName></affiliation></author><author><name sortKey="Pereda, Ariel" sort="Pereda, Ariel" uniqKey="Pereda A" first="Ariel" last="Pereda">Ariel Pereda</name><affiliation wicri:level="1"><nlm:aff id="aff13">Instituto de Patobiología, CICVyA INTA, Hurlingham, Buenos Aires, Argentina</nlm:aff><country xml:lang="fr">Argentine</country><wicri:regionArea>Instituto de Patobiología, CICVyA INTA, Hurlingham, Buenos Aires</wicri:regionArea><wicri:noRegion>Buenos Aires</wicri:noRegion></affiliation></author><author><name sortKey="Davis, C Todd" sort="Davis, C Todd" uniqKey="Davis C" first="C. Todd" last="Davis">C. Todd Davis</name><affiliation wicri:level="2"><nlm:aff id="aff14">Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia</wicri:regionArea><placeName><region type="state">Géorgie (États-Unis)</region></placeName></affiliation></author><author><name sortKey="Donis, Ruben O" sort="Donis, Ruben O" uniqKey="Donis R" first="Ruben O." last="Donis">Ruben O. Donis</name><affiliation wicri:level="2"><nlm:aff id="aff14">Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia</wicri:regionArea><placeName><region type="state">Géorgie (États-Unis)</region></placeName></affiliation></author><author><name sortKey="Webby, Richard J" sort="Webby, Richard J" uniqKey="Webby R" first="Richard J." last="Webby">Richard J. Webby</name><affiliation wicri:level="2"><nlm:aff id="aff15">Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Vincent, Amy L" sort="Vincent, Amy L" uniqKey="Vincent A" first="Amy L." last="Vincent">Amy L. Vincent</name><affiliation wicri:level="2"><nlm:aff id="aff1">Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa</wicri:regionArea><placeName><region type="state">Iowa</region></placeName></affiliation></author></analytic><series><title level="j">mSphere</title><idno type="eISSN">2379-5042</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>A fundamental goal in the biological sciences is the definition of groups of organisms based on evolutionary history and the naming of those groups. For influenza A viruses (IAVs) in swine, understanding the hemagglutinin (HA) genetic lineage of a circulating strain aids in vaccine antigen selection and allows for inferences about vaccine efficacy. Previous reporting of H1 virus HA in swine relied on colloquial names, frequently with incriminating and stigmatizing geographic toponyms, making comparisons between studies challenging. To overcome this, we developed an adaptable nomenclature using measurable criteria for historical and contemporary evolutionary patterns of H1 global swine IAVs. We also developed a web-accessible tool that classifies viruses according to this nomenclature. This classification system will aid agricultural production and pandemic preparedness through the identification of important changes in swine IAVs and provides terminology enabling discussion of swine IAVs in a common context among animal and human health initiatives.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Brown, Ih" uniqKey="Brown I">IH Brown</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Reeth, K" uniqKey="Van Reeth K">K Van Reeth</name></author><author><name sortKey="Nauwynck, H" uniqKey="Nauwynck H">H Nauwynck</name></author><author><name sortKey="Pensaert, M" uniqKey="Pensaert M">M Pensaert</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thacker, El" uniqKey="Thacker E">EL Thacker</name></author><author><name sortKey="Thacker, Bj" uniqKey="Thacker B">BJ Thacker</name></author><author><name sortKey="Janke, Bh" uniqKey="Janke B">BH 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Hay</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Argentine</li><li>Belgique</li><li>Brésil</li><li>Canada</li><li>France</li><li>Japon</li><li>Nouvelle-Zélande</li><li>Royaume-Uni</li><li>États-Unis</li></country><region><li>Angleterre</li><li>Angleterre de l'Est</li><li>Californie</li><li>Géorgie (États-Unis)</li><li>Iowa</li><li>Province de Flandre-Orientale</li><li>Région flamande</li><li>Santa Catarina</li><li>Tennessee</li></region><settlement><li>Cambridge</li><li>Gand</li></settlement><orgName><li>Université de Cambridge</li><li>Université de Gand</li></orgName></list><tree><country name="États-Unis"><region name="Iowa"><name sortKey="Anderson, Tavis K" sort="Anderson, Tavis K" uniqKey="Anderson T" first="Tavis K." last="Anderson">Tavis K. Anderson</name></region><name sortKey="Davis, C Todd" sort="Davis, C Todd" uniqKey="Davis C" first="C. Todd" last="Davis">C. Todd Davis</name><name sortKey="Donis, Ruben O" sort="Donis, Ruben O" uniqKey="Donis R" first="Ruben O." last="Donis">Ruben O. Donis</name><name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H." last="Scheuermann">Richard H. Scheuermann</name><name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H." last="Scheuermann">Richard H. Scheuermann</name><name sortKey="Swenson, Sabrina L" sort="Swenson, Sabrina L" uniqKey="Swenson S" first="Sabrina L." last="Swenson">Sabrina L. Swenson</name><name sortKey="Vincent, Amy L" sort="Vincent, Amy L" uniqKey="Vincent A" first="Amy L." last="Vincent">Amy L. Vincent</name><name sortKey="Webby, Richard J" sort="Webby, Richard J" uniqKey="Webby R" first="Richard J." last="Webby">Richard J. Webby</name></country><country name="Nouvelle-Zélande"><noRegion><name sortKey="Macken, Catherine A" sort="Macken, Catherine A" uniqKey="Macken C" first="Catherine A." last="Macken">Catherine A. Macken</name></noRegion></country><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Lewis, Nicola S" sort="Lewis, Nicola S" uniqKey="Lewis N" first="Nicola S." last="Lewis">Nicola S. Lewis</name></region><name sortKey="Brown, Ian H" sort="Brown, Ian H" uniqKey="Brown I" first="Ian H." last="Brown">Ian H. Brown</name></country><country name="Belgique"><region name="Région flamande"><name sortKey="Van Reeth, Kristien" sort="Van Reeth, Kristien" uniqKey="Van Reeth K" first="Kristien" last="Van Reeth">Kristien Van Reeth</name></region></country><country name="France"><noRegion><name sortKey="Simon, Gaelle" sort="Simon, Gaelle" uniqKey="Simon G" first="Gaëlle" last="Simon">Gaëlle Simon</name></noRegion></country><country name="Japon"><noRegion><name sortKey="Saito, Takehiko" sort="Saito, Takehiko" uniqKey="Saito T" first="Takehiko" last="Saito">Takehiko Saito</name></noRegion></country><country name="Canada"><noRegion><name sortKey="Berhane, Yohannes" sort="Berhane, Yohannes" uniqKey="Berhane Y" first="Yohannes" last="Berhane">Yohannes Berhane</name></noRegion></country><country name="Brésil"><region name="Santa Catarina"><name sortKey="Ciacci Zanella, Janice" sort="Ciacci Zanella, Janice" uniqKey="Ciacci Zanella J" first="Janice" last="Ciacci-Zanella">Janice Ciacci-Zanella</name></region></country><country name="Argentine"><noRegion><name sortKey="Pereda, Ariel" sort="Pereda, Ariel" uniqKey="Pereda A" first="Ariel" last="Pereda">Ariel Pereda</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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