Global dissemination and evolutionary dynamics of duck hepatitis A virus type 3 driven by VP1 gene variation.

Duck hepatitis A virus type 3 (DHAV-3) is a primary causative agent of severe viral hepatitis in ducklings and poses a grave threat to the global duck industry. This study deciphers the genetic evolution and structural features of DHAV-3 via analysis of VP1 gene sequences from a comprehensive datase, which represents the major endemic regions of East Asia, the global primary epidemic area of DHAV-3 worldwide. Integrated phylogenetic, recombination, selection pressure, and structural analyses demonstrate that the VP1 gene segregates into two major genotypes (GⅠ and GⅡ), with GⅠ being the currently dominant genotype and subdivided into multiple sublineages. Bayesian skyline plot revealed a significant expansion in the effective population size of the virus beginning in 2005, followed by a resurgence in viral circulation after 2020, highlighting the persistent epidemiological threat within and beyond East Asia. We identified 79 amino acid variation sites distributed across nine high-frequency mutation regions and six conserved functional domains, reflecting an evolutionary balance between functional constraint and adaptability. Notably, comparative structural analysis revealed a distinctive C-terminal insertion (182T-183P-184 M) in GⅡ strains that may underlie altered antigenicity and enhanced host adaptation. These structural insights provide a foundation for the development of targeted vaccines and improved control strategies against DHAV-3.