Isolation, characterization and whole-genome analysis of a potentially novel strain of duck hepatitis A virus type 3 from a vaccinated duck flock in China.

Introduction: Duck viral hepatitis (DVH) is an acute infectious disease caused by duck hepatitis virus. It is characterized by hepatic hemorrhage, hepatomegaly, and opisthotonos in ducklings, posing a significant threat to the global poultry industry. Methods: In this study, a potentially novel duck hepatitis A virus type 3 (DHAV-3) strain, designated HNAY2024, was isolated and purified from an immunized duck farm in Henan Province. The complete genome sequence was obtained through whole-genome sequencing and subjected to phylogenetic analysis. Meanwhile, in-depth analysis of the VP1 gene was performed to determine its genotype, and key mutation sites were identified through amino acid sequence alignment. Results: The HNAY2024 strain demonstrates vaccine-escape potential and breaks the classical pattern where DHAV-3 primarily causes high mortality in ducklings under one week of age. Whole-genome sequencing and phylogenetic analysis revealed that HNAY2024 shares 91.9%-99.9% nucleotide identity with other DHAV-3 reference strains and clusters most closely with the Egyptian strain ZU-ARMY-DHA-36, the Henan strain HNXY23, and the Shandong strain WKX03, indicating its potential dissemination to possibly broader regions. Further analysis of the VP1 gene confirmed that HNAY2024 belongs to genotype I (GI) of DHAV-3. Amino acid alignment identified eight substitutions (V413M, E683Q, V855I, F892S, S1149I, T1151S, E1519G, and K1956E). Conclusion: The eight identified amino acid mutations are predicted to contribute to adaptive changes in viral antigenicity, replication fitness, and host interactions. Such alterations could influence the viral host range or transmission dynamics, thereby posing potential ecological risks for both domestic poultry and wild birds.