Genomic variation and recombination dynamics of duck hepatitis A virus type 3 (DHAV-3) in clinical isolates from Shandong and Anhui, China

Duck hepatitis A virus type 3 (DHAV-3) is a major pathogen that threatens the health of ducklings, and its genetic variation and recombination pose significant challenges for disease control and vaccine development. In this study, clinical samples were collected from selected duck farms in Shandong and Anhui Provinces, China, during 2023–2024, and the complete genome sequences of 31 DHAV-3 isolates were determined. Phylogenetic analysis showed that all isolates belonged to the GI-a genotype and exhibited a certain degree of regional clustering. Sequence comparison suggested that amino acid substitutions were mainly concentrated in regions predicted to be associated with antigenicity in structural proteins and in conserved domains of non-structural proteins. Recombination analysis detected only a small number of credible recombination events, with no evidence of stable inter-subtype recombination, indicating that the genomes of currently circulating DHAV-3 strains are relatively conserved. Histopathological examination further demonstrated differences in pathogenic manifestations among the isolates. Overall, this study provides a molecular characterization of contemporary DHAV-3 strains collected from Shandong and Anhui Provinces, China, and contributes to a better understanding of their genetic evolution, supporting regional epidemiological surveillance and the development of effective control strategies. • Thirty-one DHAV-3 isolates were obtained from duck farms in China (2023–2024). • All isolates belonged to genotype GI-a with evident regional clustering. • Amino acid substitutions mainly occurred in antigenic and functional regions. • Only limited recombination was detected among contemporary DHAV-3 genomes. • Histopathological examination revealed differences in pathogenic manifestations.