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Title: A phylogeny-based global nomenclature system and automated annotation tool for H1 hemagglutinin genes from swine influenza A viruses

Author
item Anderson, Tavis
item MACKEN, CATHERINE - University Of Auckland
item LEWIS, NICOLA - University Of Cambridge
item SCHEUERMANN, RICHARD - J Craig Venter Institute
item VAN REETH, KRISTIEN - Ghent University
item BROWN, IAN - Animal & Plant Health Agency Apha
item SWENSON, SABRINA - Animal And Plant Health Inspection Service (APHIS)
item SIMON, GAËLLE - French Agency For Food, Environmental And Occupational Health & Safety (ANSES)
item SAITO, TAKEHIKO - National Institute Of Animal Health - Japan (NIAH, NARO)
item BERHANE, YOHANNES - Canadian Food Inspection Agency
item Baker, Amy

Submitted to: mSphere
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/10/2016
Publication Date: 12/14/2016
Citation: Anderson, T.K., Macken, C.A., Lewis, N.S., Scheuermann, R.H., Van Reeth, K., Brown, I.H., Swenson, S.L., Simon, G., Saito, T., Berhane, Y., Ciacci-Zanella, J., Pereda, A., Davis, C.T., Donis, R.O., Webby, R.J., Vincent, A.L. 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:10.1128/mSphere.00275-16.

Interpretive Summary: Many animal species are susceptible to infection with influenza A viruses (IAV). In swine and humans, IAV can cause respiratory disease, and some IAV can transmit between swine and man. Understanding how IAV are changing in swine in a timely manner is critical to reduce disease burden in pigs, and reduce the risk of swine viruses infecting humans. The genetic makeup of IAV continually changes, yet there are no established methods to report significant genetic changes in swine IAV, specifically, in the major viral surface protein gene, hemagglutinin (HA). Previous reporting of new HA genes in swine relied on names and terms used by individual research scientists that provided little insight into the biology of the virus. Using a large dataset of human, avian, and swine HA genetic sequences, we developed an adaptable naming system that uses measurable criteria to define historical and contemporary evolutionary patterns of swine IAV. To enable widespread adoption of this system and to provide rapid identification of swine viruses, we developed a web-accessible tool that automatically classifies and describes swine genetic data into meaningful HA categories. This tool and our approach will aid and improve agricultural production and disease preparedness for humans through the identification of important changes in swine IAV.

Technical Abstract: The H1 subtype of influenza A viruses (IAV) has been circulating in swine since the 1918 human influenza pandemic. Over time, and aided by further introductions from non-swine hosts, swine H1 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 HA evolution. These criteria applied to a dataset of 7070 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 dataset of 7070 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 present had HA's that belonged to 7 contemporary co-circulating clades. Our nomenclature and web-accessible classification tool provides 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, assuring 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, so simplifying communication of such data.