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

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

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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 project, we have developed 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 in the Influenza Research Database 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.

Publications

A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses.
mSphere. 2016-11-01; 1.6:
PMID: 27981236

Funding

This work is funded by the National Institute of Allergy and Infectious Diseases (NIH/DHHS) under contract no. HHSN272201400028C.