Genomic variation and recombination dynamics of duck hepatitis A virus type 3 (DHAV-3) from clinical isolates in 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 Shandong and Anhui Provinces during 2023-2024, from which 84 DHAV-3–positive cases were identified, and the complete genomes of 31 isolates were obtained. Phylogenetic analysis revealed that all isolates clustered within subgenotype GⅠ-a, with some strains exhibiting regional clustering patterns. Amino acid substitutions were mainly concentrated in VP1, 2A2, 2C, and 3A proteins. Notably, VP1 mutations were located within the predicted antigenic epitopes, potentially affecting immune recognition, whereas most variations in the nonstructural proteins 2A2 and 2C occurred in the P-loop domain, suggesting possible impacts on viral replication. Recombination analysis identified six potential events across multiple genomic regions, with evidence of recombination hotspots in specific areas. Histopathological examination revealed strain-specific differences in the severity of tissue damage, indicating a link between genetic variation and pathogenic characteristics. Collectively, this study provides a systematic overview of the molecular characteristics of circulating DHAV-3 strains in China, enhances our understanding of its epidemiology and pathogenesis, and offers valuable insights for vaccine design and targeted prevention strategies.