A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses
Identifieur interne : 000325 ( Pmc/Checkpoint ); précédent : 000324; suivant : 000326A 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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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. 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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. 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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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<front><journal-meta><journal-id journal-id-type="nlm-ta">mSphere</journal-id><journal-id journal-id-type="iso-abbrev">mSphere</journal-id><journal-id journal-id-type="hwp">msph</journal-id><journal-id journal-id-type="pmc">msph</journal-id><journal-id journal-id-type="publisher-id">mSphere</journal-id><journal-title-group><journal-title>mSphere</journal-title></journal-title-group><issn pub-type="epub">2379-5042</issn><publisher><publisher-name>American Society for Microbiology</publisher-name><publisher-loc>1752 N St., N.W., Washington, DC</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27981236</article-id><article-id pub-id-type="pmc">5156671</article-id><article-id pub-id-type="publisher-id">mSphere00275-16</article-id><article-id pub-id-type="doi">10.1128/mSphere.00275-16</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject><subj-group><subject>Ecological and Evolutionary Science</subject></subj-group></subj-group></article-categories><title-group><article-title>A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses</article-title><alt-title alt-title-type="running-head">Nomenclature of Swine Influenza H1 Viruses</alt-title><alt-title alt-title-type="short-authors">Anderson et al.</alt-title></title-group><contrib-group><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0002-3138-5535</contrib-id><name><surname>Anderson</surname><given-names>Tavis K.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Macken</surname><given-names>Catherine A.</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lewis</surname><given-names>Nicola S.</given-names></name><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0003-1355-892X</contrib-id><name><surname>Scheuermann</surname><given-names>Richard H.</given-names></name><xref ref-type="aff" rid="aff4"><sup>d</sup></xref><xref ref-type="aff" rid="aff5"><sup>e</sup></xref></contrib><contrib contrib-type="author"><name><surname>Van Reeth</surname><given-names>Kristien</given-names></name><xref ref-type="aff" rid="aff6"><sup>f</sup></xref></contrib><contrib contrib-type="author"><name><surname>Brown</surname><given-names>Ian H.</given-names></name><xref ref-type="aff" rid="aff7"><sup>g</sup></xref></contrib><contrib contrib-type="author"><name><surname>Swenson</surname><given-names>Sabrina L.</given-names></name><xref ref-type="aff" rid="aff8"><sup>h</sup></xref></contrib><contrib contrib-type="author"><name><surname>Simon</surname><given-names>Gaëlle</given-names></name><xref ref-type="aff" rid="aff9"><sup>i</sup></xref></contrib><contrib contrib-type="author"><name><surname>Saito</surname><given-names>Takehiko</given-names></name><xref ref-type="aff" rid="aff10"><sup>j</sup></xref></contrib><contrib contrib-type="author"><name><surname>Berhane</surname><given-names>Yohannes</given-names></name><xref ref-type="aff" rid="aff11"><sup>k</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ciacci-Zanella</surname><given-names>Janice</given-names></name><xref ref-type="aff" rid="aff12"><sup>l</sup></xref></contrib><contrib contrib-type="author"><name><surname>Pereda</surname><given-names>Ariel</given-names></name><xref ref-type="aff" rid="aff13"><sup>m</sup></xref></contrib><contrib contrib-type="author"><name><surname>Davis</surname><given-names>C. Todd</given-names></name><xref ref-type="aff" rid="aff14"><sup>n</sup></xref></contrib><contrib contrib-type="author"><name><surname>Donis</surname><given-names>Ruben O.</given-names></name><xref ref-type="aff" rid="aff14"><sup>n</sup></xref></contrib><contrib contrib-type="author"><name><surname>Webby</surname><given-names>Richard J.</given-names></name><xref ref-type="aff" rid="aff15"><sup>o</sup></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Vincent</surname><given-names>Amy L.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><aff id="aff1"><label>a</label>Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA</aff><aff id="aff2"><label>b</label>Bioinformatics Institute, University of Auckland, Auckland, New Zealand</aff><aff id="aff3"><label>c</label>Department of Zoology, University of Cambridge, Cambridge, United Kingdom</aff><aff id="aff4"><label>d</label>J. Craig Venter Institute, La Jolla, California, USA</aff><aff id="aff5"><label>e</label>Department of Pathology, University of California, San Diego, California, USA</aff><aff id="aff6"><label>f</label>Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium</aff><aff id="aff7"><label>g</label>Animal and Plant Health Agency, Weybridge, United Kingdom</aff><aff id="aff8"><label>h</label>National Veterinary Services Laboratories, USDA-APHIS, Ames, Iowa, USA</aff><aff id="aff9"><label>i</label>ANSES, Ploufragan-Plouzané Laboratory, Swine Virology Immunology Unit, Ploufragan, France</aff><aff id="aff10"><label>j</label>Division of Transboundary Animal Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan</aff><aff id="aff11"><label>k</label>Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, Manitoba, Canada</aff><aff id="aff12"><label>l</label>Embrapa Swine and Poultry, Animal Health and Genetic Laboratory, Concórdia, SC, Brazil</aff><aff id="aff13"><label>m</label>Instituto de Patobiología, CICVyA INTA, Hurlingham, Buenos Aires, Argentina</aff><aff id="aff14"><label>n</label>Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA</aff><aff id="aff15"><label>o</label>Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA</aff></contrib-group><contrib-group><contrib contrib-type="editor"><name><surname>Lowen</surname><given-names>Anice C.</given-names></name><role>Editor</role><aff>Emory University School of Medicine</aff></contrib></contrib-group><author-notes><corresp id="cor1">Address correspondence to Amy L. Vincent, <email>amy.vincent@ars.usda.gov</email>.</corresp><fn fn-type="equal"><p>T.K.A. and C.A.M. contributed equally to this manuscript.</p></fn><fn fn-type="other"><p><bold>Citation</bold> Anderson TK, Macken CA<italic>,</italic> Lewis NS<italic>,</italic> Scheuermann RH<italic>,</italic> Van Reeth K, Brown IH<italic>,</italic> Swenson SL<italic>,</italic> Simon G, Saito T, Berhane Y, Ciacci-Zanella J, Pereda A, Davis CT, Donis RO, Webby RJ, Vincent AL. 2016. A phylogeny-based global nomenclature system and automated annotation tool for H1 hemagglutinin genes from swine influenza A viruses. mSphere 1(6):e00275-16. doi:<ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.1128/mSphere.00275-16">10.1128/mSphere.00275-16</ext-link>.</p></fn></author-notes><pub-date pub-type="epub"><day>14</day><month>12</month><year>2016</year></pub-date><pub-date pub-type="collection"><season>Nov-Dec</season><year>2016</year></pub-date><volume>1</volume><issue>6</issue><elocation-id>e00275-16</elocation-id><history><date date-type="received"><day>19</day><month>9</month><year>2016</year></date><date date-type="accepted"><day>10</day><month>11</month><year>2016</year></date></history><permissions><copyright-statement>Copyright © 2016 Anderson et al.</copyright-statement><copyright-year>2016</copyright-year><copyright-holder>Anderson et al.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International license</ext-link>.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="sph006162204001.pdf"></self-uri><abstract abstract-type="precis"><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></abstract><abstract><title>ABSTRACT</title><p>The H1 subtype of influenza A viruses (IAVs) has been circulating in swine since the 1918 human influenza pandemic. Over time, and aided by further introductions from nonswine hosts, swine H1 viruses have diversified into three genetic lineages. Due to limited global data, these H1 lineages were named based on colloquial context, leading to a proliferation of inconsistent regional naming conventions. In this study, we propose rigorous phylogenetic criteria to establish a globally consistent nomenclature of swine H1 virus hemagglutinin (HA) evolution. These criteria applied to a data set of 7,070 H1 HA sequences led to 28 distinct clades as the basis for the nomenclature. We developed and implemented a web-accessible annotation tool that can assign these biologically informative categories to new sequence data. The annotation tool assigned the combined data set of 7,070 H1 sequences to the correct clade more than 99% of the time. Our analyses indicated that 87% of the swine H1 viruses from 2010 to the present had HAs that belonged to 7 contemporary cocirculating clades. Our nomenclature and web-accessible classification tool provide an accurate method for researchers, diagnosticians, and health officials to assign clade designations to HA sequences. The tool can be updated readily to track evolving nomenclature as new clades emerge, ensuring continued relevance. A common global nomenclature facilitates comparisons of IAVs infecting humans and pigs, within and between regions, and can provide insight into the diversity of swine H1 influenza virus and its impact on vaccine strain selection, diagnostic reagents, and test performance, thereby simplifying communication of such data.</p><p><bold>IMPORTANCE</bold> 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></abstract><kwd-group><title>KEYWORDS:</title><kwd>H1N1</kwd><kwd>H1N2</kwd><kwd>influenza A virus</kwd><kwd>molecular epidemiology</kwd><kwd>nomenclature</kwd><kwd>swine</kwd><kwd>virus evolution</kwd></kwd-group><funding-group><award-group id="award1"><funding-source>HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)
<named-content content-type="funder-id">http://dx.doi.org/10.13039/100000060</named-content></funding-source><award-id>HHSN272201400008C</award-id><principal-award-recipient>Nicola S. Lewis</principal-award-recipient><principal-award-recipient>Amy L. Vincent</principal-award-recipient></award-group><award-group id="award2"><funding-source>HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)
<named-content content-type="funder-id">http://dx.doi.org/10.13039/100000060</named-content></funding-source><award-id>HHSN266200700005C</award-id><award-id>HHSN272201400006C</award-id><principal-award-recipient>Richard J. Webby</principal-award-recipient></award-group><award-group id="award3"><funding-source>HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)
<named-content content-type="funder-id">http://dx.doi.org/10.13039/100000060</named-content></funding-source><award-id>HHSN266200400041C</award-id><award-id>HHSN272201400006C</award-id><principal-award-recipient>Catherine A. Macken</principal-award-recipient><principal-award-recipient>Richard H. Scheuermann</principal-award-recipient></award-group><award-group id="award4"><funding-source>European Commission (EC)
<named-content content-type="funder-id">http://dx.doi.org/10.13039/501100000780</named-content></funding-source><award-id>259949</award-id><principal-award-recipient>Nicola S. Lewis</principal-award-recipient><principal-award-recipient>Kristien Van Reeth</principal-award-recipient><principal-award-recipient>Ian H. Brown</principal-award-recipient><principal-award-recipient>Gaëlle Simon</principal-award-recipient></award-group><award-group id="award5"><funding-source>USDA | Agricultural Research Service (ARS)
<named-content content-type="funder-id">http://dx.doi.org/10.13039/100007917</named-content></funding-source><award-id>58-3625-4-070</award-id><principal-award-recipient>Tavis K. Anderson</principal-award-recipient></award-group><award-group id="award6"><funding-source>USDA | Agricultural Research Service (ARS)
<named-content content-type="funder-id">http://dx.doi.org/10.13039/100007917</named-content></funding-source><award-id>58-3625-2-103F</award-id><principal-award-recipient>Nicola S. Lewis</principal-award-recipient></award-group><award-group id="award7"><funding-source>DOE | LDRD | Oak Ridge Institute for Science and Education (ORISE)
<named-content content-type="funder-id">http://dx.doi.org/10.13039/100006229</named-content></funding-source><award-id>DE-AC05-06OR23100</award-id><principal-award-recipient>Tavis K. Anderson</principal-award-recipient></award-group><award-group id="award8"><funding-source>USDA | Animal and Plant Health Inspection Service (APHIS)
<named-content content-type="funder-id">http://dx.doi.org/10.13039/100009168</named-content></funding-source><principal-award-recipient>Sabrina L. Swenson</principal-award-recipient></award-group><award-group id="award9"><funding-source>USDA | Agricultural Research Service (ARS)
</funding-source><principal-award-recipient>Amy L. Vincent</principal-award-recipient></award-group></funding-group><counts><count count="6" count-type="supplementary-material"></count><fig-count count="2"></fig-count><table-count count="4"></table-count><equation-count count="0"></equation-count><ref-count count="61"></ref-count><page-count count="14"></page-count><word-count count="9636"></word-count></counts><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>November/December 2016</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc><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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