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Research Project: Intervention Strategies to Control Influenza A Virus Infection in Swine

Location: Virus and Prion Research

Title: An automated annotation tool and unified nomenclature system for H3 hemagglutinin genes from swine influenza A viruses

Author
item Anderson, Tavis
item ZHANG, YUN - J. CRAIG VENTER INSTITUTE
item MACKEN, CATHERINE - NATIONAL CENTER FOR AGRICULTURE AND FORESTRY TECHNOLOGIES (CENTA)
item SWINE FLU WORK GROUP - WORLD HEALTH ORGANIZATION (WHO) - FRANCE
item SCHEUERMANN, RICHARD - OAK RIDGE INSTITUTE FOR SCIENCE AND EDUCATION (ORISE)
item Vincent, Amy

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/17/2019
Publication Date: 6/24/2019
Citation: Anderson, T.K., Zhang, Y., Macken, C.A., Swine Flu Work Group, Scheuermann, R.H., Vincent, A.L. 1019. An automated annotation tool and unified nomenclature system for H3 hemagglutinin genes from swine influenza A viruses [abstract]. Centers of Excellence for Influenza Research and Surveillance. Abstract No. 42.

Interpretive Summary:

Technical Abstract: Epidemiologic and phylogenetic analyses of influenza A viruses (IAV) provide rational criteria for vaccine strain selection, control strategies, and may identify viruses with pandemic potential. From the 1968 pandemic to date, human seasonal H3 subtype viruses have been repeatedly introduced into swine leading to the circulation of genetically distinct H3 hemagglutinin (HA) lineages. Due to limited data and regionally restricted circulation, the delineation and naming of these genetic clades has lacked a comprehensive framework, resulting in inconsistent naming conventions that do not reflect evolutionary history. We proposed criteria for a globally consistent nomenclature of swine H3 viruses and developed an annotation tool that can be used to assign these biologically informative lineage categories to sequence data. A total of 3,410 swine H3 HA sequences collected from 1968 to 2019 were collated with avian (2,701), human (11,910), equine (3,913), and canine (490) H3 HA sequences. Within these data, we designated 13 co-circulating swine lineages. To facilitate rapid detection of incursions of non-swine IAV into pigs, we incorporated criteria that classifies human H3-HA by decade, avian H3-HA clades, canine H3-HA clades, and an equine H3-HA clade. Our annotation tool assigned swine H3 sequences correctly more than 95% of the time. 33 additional human-to-swine introductions were revealed but it remains to be determined whether these introductions resulted in onward transmission in swine due to lack of contemporary sequences in public databases. A common H3 global nomenclature facilitates comprehensive comparisons of IAVs infecting humans, mammals, and birds within and between species and regions. Common nomenclature can also provide insight into genetic diversity and evolutionary patterns of swine H3 influenza virus in relationship to other H3 host species, and the impact of genetic diversity on vaccine strain selection and diagnostic capabilities.