Comparative Investigation of Coincident Single Nucleotide Polymorphisms Underlying Avian Influenza Viruses in Chickens and Ducks

Simple Summary: Avian influenza is a serious threat to chickens in comparison to ducks which are more resilient to most virus strains. Today, it is still not completely understood why ducks have more effective inflammatory immune responses. To this extent, the consideration of coincident SNPs (coSNPs) is crucial to unravel genetic programs underlying the susceptibility/resistance of both species to avian influenza. Therefore, our aim is to investigate the differing causal effects of coSNPs on avian-influenza-induced genes, thereby revealing the effector molecules and signaling pathways that mediate an effective immune response after viral infection in ducks and that lead to the disease in chickens. Avian influenza is a severe viral infection that has the potential to cause human pandemics. In particular, chickens are susceptible to many highly pathogenic strains of the virus, resulting in significant losses. In contrast, ducks have been reported to exhibit rapid and effective innate immune responses to most avian influenza virus (AIV) infections. To explore the distinct genetic programs that potentially distinguish the susceptibility/resistance of both species to AIV, the investigation of coincident SNPs (coSNPs) and their differing causal effects on gene functions in both species is important to gain novel insight into the varying immune-related responses of chickens and ducks. By conducting a pairwise genome alignment between these species, we identified coSNPs and their respective effect on AIV-related differentially expressed genes (DEGs) in this study. The examination of these genes (e.g., CD74, RUBCN, and SHTN1 for chickens and ABCA3, MAP2K6, and VIPR2 for ducks) reveals their high relevance to AIV. Further analysis of these genes provides promising effector molecules (such as IkB alpha, STAT1/STAT3, GSK-3 beta, or p53) and related key signaling pathways (such as NF-kB, JAK/STAT, or Wnt) to elucidate the complex mechanisms of immune responses to AIV infections in both chickens and ducks.