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

Authors: Anderson, Tavis; ZHANG, YUN - J Craig Venter Institute; MACKEN, CATHERINE - University Of Auckland; OFFLU SWINE, INFLUENZA GROUP - World Organization For Animal Health; SCHEUERMANN, RICHARD - University Of California; Baker, Amy

Submitted to: International Symposium on Neglected Influenza Viruses
Publication Type: Abstract Only
Publication Acceptance Date: 3/1/2018
Publication Date: 4/18/2018
Citation: Anderson, T.K., Zhang, Y., Macken, C.A., Offlu Swine, I., Scheuermann, R.H., Vincent, A.L. 2018. An automated annotation tool and unified nomenclature system for H3 hemagglutinin genes from swine influenza A viruses [abstract].International Symposium on Neglected Influenza Viruses. Abstract No. P2.

Interpretive Summary:

Technical Abstract: Epidemiologic and phylogenetic analyses of influenza A viruses (IAV) provide rational criteria for vaccine strain selection, control strategies, improved diagnostic tests, and may identify strains with pandemic potential. The hemagglutinin (HA) H3 subtype has been circulating in swine since the 1968 human influenza pandemic. Over time, repeated introductions of human seasonal H3, in conjunction with primarily N2 neuraminidases, have resulted in 9 genetically distinct H3 lineages circulating in swine globally. Due to limited global data and regionally restricted circulation, the naming of these genetic clades has lacked a comprehensive framework, resulting in inconsistent regional naming conventions that do not reflect evolutionary history. We proposed phylogenetic criteria for a globally consistent nomenclature of divergent swine H3 viruses. Further, we developed and implemented an annotation tool that assigns these biologically informative lineage categories to observed sequence data. This tool classified 2070 swine H3 HA sequences collected between 1969 and 2017. To provide evolutionary context, these data were combined with 19014 HA H3 virus sequences sampled from the same time period (2701 avian, 11910 human seasonal, 3913 equine, and 490 canine). Our proposed phylogeny-based nomenclature currently designates the nine distinct co-circulating swine clades; an additional 6 decadal clade classifications for human H3-HA to incorporate other minor swine incursions; 5 classifications for avian H3-HA clades; 2 classifications for canine H3-HA; and a single clade classification for equine H3-HA. Our annotation tool assigned swine H3 sequences to the correct clade more than 95% of the time. In addition to the nine contemporary swine H3 clades, these analyses revealed 30 additional human-to-swine transmission events over the past 50 years. However, it remains to be determined if these introductions resulted in onward transmission in the swine population since evidence from current surveillance data was lacking. Our nomenclature and classification tool for swine H3 viruses provides a robust and accurate method for researchers to assign clade designations to publically available or privately generated HA sequences. The classification tool can be updated readily as new clades emerge, assuring its continued relevance. A common global nomenclature facilitates comprehensive comparisons of IAVs infecting mammals and birds, within and between global regions. Importantly, our global nomenclature can ultimately provide insight into the scope of the global diversity and evolutionary patterns of swine H3 influenza virus and the impact on vaccine strain selection and diagnostic capabilities.