Authors: Anderson, Tavis K.; Macken, Catherine A.; Lewis, Nicola S.; Scheuermann, Richard H.; Van Reeth, Kristien; Brown, Ian H.; Swenson, Sabrina L.; Simon, Gaëlle; Saito, Takehiko; Berhane, Yohannes; Ciacci Zanella, Janice; Pereda, Ariel Julián; Davis, C. Todd; Donis, Ruben O.; Webby, Richard J.; Vincent, Amy L.
Publication Date: 2016.
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.
Author affiliation: Anderson, Tavis K.. United States Department of Agriculture; Estados Unidos
Author affiliation: Macken, Catherine A.. The University of Auckland; Nueva Zelanda
Author affiliation: Lewis, Nicola S.. University of Cambridge; Reino Unido
Author affiliation: Scheuermann, Richard H.. University of California at San Diego; Estados Unidos
Author affiliation: Van Reeth, Kristien. University of Ghent; Bélgica
Author affiliation: Brown, Ian H.. Animal And Plant Health Agency; Reino Unido
Author affiliation: Swenson, Sabrina L.. United States Department of Agriculture; Estados Unidos
Author affiliation: Simon, Gaëlle. Agence Française de Sécurité Sanitaire Anses; Francia
Author affiliation: Saito, Takehiko. National Agriculture And Food Research Organization; Japón
Author affiliation: Berhane, Yohannes. Canadian Food Inspection Agency; Canadá
Author affiliation: Ciacci Zanella, Janice. Ministerio da Agricultura Pecuaria e Abastecimento de Brasil. Empresa Brasileira de Pesquisa Agropecuaria; Brasil
Author affiliation: Pereda, Ariel Julián. Instituto Nacional de Tecnología Agropecuaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Author affiliation: Davis, C. Todd. Centers for Disease Control and Prevention; Estados Unidos
Author affiliation: Donis, Ruben O.. Centers for Disease Control and Prevention; Estados Unidos
Author affiliation: Webby, Richard J.. St. Jude Childrens Research Hospital; Estados Unidos
Author affiliation: Vincent, Amy L.. United States Department of Agriculture; Estados Unidos
Repository: CONICET Digital (CONICET). Consejo Nacional de Investigaciones Científicas y Técnicas