Influenza A viruses infect and occasionally cause diseases in poultry and other terrestrial and non-terrestrial avian species. Highly pathogenic avian influenza (HPAI), one of the disease phenotypes of avian influenza in poultry, is causing tremendous loss to the poultry industry around the globe annually. Australian black swans (Cygnus atratus) are perhaps the most susceptible wild bird species to HPAI that succumbed to disease within 2-3 days. Death was often peracute, occurring in the absence of clinical signs – a scenario often observed in chickens (Gallus gallus) infected with HPAI-H5N1 viruses. Several reports indicate the species’ high susceptibility to HPAI viruses naturally and experimentally. Like chickens, HPAI-H5N1 viruses in black swans are endotheliotropic.
Here, we aimed to provide the first black swan genome and transcriptome to help understand why this avian species is uniquely susceptible to HPAI viruses. Using PacBio long-read sequencing technology, we established the first genome assembly of the black and mute swan and their full-length transcriptome. We compared the vital immune genes between the species; mute swan (Cygnus olor; a closely related species but comparatively more resistant to HPAI), chicken (highly susceptible to HPAI), and the mallard duck (Anas platyrhynchos; resistant primarily to certain strains of HPAI). We developed a novel method to culture endothelial cells to model HPAI in black swan. These cells were subsequently infected with A/H5N1/0008/2014 HPAI, and differential gene expression analyses and gene set enrichment were performed. Our data suggest that black swans have several underlying genetic susceptibility factors regarding HPAI viruses.