About: A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses

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About: A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses
Creator	Donis, Ruben Saito, Takehiko Berhane, Yohannes Ciacci-Zanella, Janice Pereda, Ariel Simon, Gaëlle Webby, Richard Anderson, Tavis Brown, Ian Davis, C Lewis, Nicola Reeth, Kristien Scheuermann, Richard Vincent, Amy Macken, Catherine Swenson, Sabrina
Source	PMC
abstract	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. IMPORTANCE 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.
has issue date	2016-12-14(xsd:dateTime)
bibo:doi	10.1128/msphere.00275-16
bibo:pmid	27981236
has license	cc-by
sha1sum (hex)	3455e9fd57dea013498de20c236c15b7bf19b424
schema:url	https://doi.org/10.1128/msphere.00275-16
resource representing a document's title	A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses
has PubMed Central identifier	PMC5156671
has PubMed identifier	27981236
schema:publication	mSphere
resource representing a document's body	covid:3455e9fd57dea013498de20c236c15b7bf19b424#body_text
is schema:about of	named entity 'system' named entity 'The' named entity 'evolving' named entity 'led' named entity 'Hemagglutinin' covid:arg/3455e9fd57dea013498de20c236c15b7bf19b424 named entity 'Vincent' named entity 'aided' named entity 'The' named entity 'Our' named entity 'circulating' named entity 'diagnosticians' named entity 'hemagglutinin' named entity 'clades' named entity 'insight' named entity 'informative' named entity 'test' named entity 'facilitates' named entity 'nomenclature' named entity 'Viruses' named entity 'clade' named entity 'hemagglutinin' named entity 'evolution' named entity 'data set' named entity 'influenza' named entity 'H1 hemagglutinin' named entity 'influenza virus' named entity 'clades' named entity 'swine influenza' named entity 'diagnosticians' named entity 'viruses' named entity 'Swine Influenza' named entity 'clade' named entity 'continued' named entity 'viruses' named entity 'H1N2' named entity 'Brazil' named entity 'Data Set' named entity 'MCMC' named entity 'evolution' named entity 'clade' named entity 'spillovers' named entity 'IAV' named entity 'statistical support' named entity 'H1N1' named entity 'clade' named entity 'clades' named entity 'antigenic drift' named entity 'clade' named entity 'genetic diversity' named entity 'clade' named entity 'data set' named entity 'clades' named entity 'virus' named entity 'posterior probability' named entity 'viruses' named entity 'public health' named entity 'antigenic diversity' named entity 'evolution' named entity 'Brazil' named entity 'human health' named entity 'Swine influenza' named entity 'viruses' named entity 'evolutionary history' named entity '2009 H1N1 pandemic' named entity 'viruses'

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