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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Virus and Prion Research » Research » Publications at this Location » Publication #362682

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

item Anderson, Tavis
item ZHANG, YUN - J Craig Venter Institute
item MACKEN, CATHERINE - University Of Auckland
item SWINE FLU WORK GROUP - World Organization For Animal Health
item SCHEUERMANN, RICHARD - J Craig Venter Institute
item Baker, Amy

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 6/2/2019
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Introduction: Timely 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. Methods: 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. This tool was applied to 3,410 swine H3 HA sequences collected from 1968 to 2019 and an additional collated 2701 avian, 11,910 human, 3,913 equine, and 490 canine H3 HA sequences. Results: Our proposed phylogeny-based nomenclature designated 13 co-circulating swine lineages. To facilitate 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. Conclusion: 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.