Candidate Genes Associated with Survival Following Highly Pathogenic Avian Influenza Infection in Chickens

Abstract: Highly pathogenic strains of avian influenza (HPAI) devastate poultry flocks and result in significant economic losses to farmers due to high mortality, reduced egg production and mandated euthanization of infected flocks. Within recent years, HPAI outbreaks have affected egg production flocks across the world. The H5N2 outbreak in the US in 2015 resulted in over 99% mortality. Here we analyze sequence data from chickens that survived (42 cases) along with un-infected controls (28 samples) to find genomic regions that differ between these two groups and that, therefore, may encompass prime candidates that infer resistance to HPAI. Blood samples were obtained from survivors of the 2015 HPAI outbreak plus age and genetics-matched non-affected controls. Whole genome sequence was obtained and genetic variants characterized and used in a genome wide association study to identify regions showing significant association with survival. Regions associated with HPAI resistance were indicated on chromosomes 1, 2, 5, 8, 10, 11, 15, 20 and 28, with a number of candidate genes identified. We did not detect a specific locus which could fully explain the difference between survivors and controls. Influenza virus replication depends on multiple components of the host cellular machinery, with many genes involved in the host response.