Phylodynamic analysis provides insights into genotype displacement of duck hepatitis A virus in China

Duck viral hepatitis, caused by the duck hepatitis A virus (DHAV), poses a significant threat to the global duck industry, particularly in China.

This study examined the evolutionary mechanisms driving the genotype displacement of DHAV-1 by DHAV-3 in China using phylodynamic analysis.

The vp1 genes of 9 DHAV-1 and 17 DHAV-3 strains were sequenced and combined with 82 DHAV-1 and 86 DHAV-3 sequences from GenBank. Bayesian phylogenetic, demographic, and phylogeographic analyses were performed using BEAST v1.10.

The substitution rate for DHAV-1 vp1 was 4.89 × 10⁻⁴ substitutions/site/year (95% highest posterior density [HPD]: 3.072 × 10⁻⁴ to 6.83 × 10⁻⁴), and for DHAV-3 was 2.125 × 10⁻⁴ substitutions/site/year (95% HPD: 1.686 × 10⁻⁴ to 2.567 × 10⁻⁴). The time to the most recent common ancestor for DHAV-1 was estimated at ~1911 and for DHAV-3 at ~1992. The demographic trends showed a decline in DHAV-1 after 2003 and a resurgence of DHAV-3 in ~2010. Phylogeography identified China as the hub for DHAV-3 spread to South Korea, Vietnam, and Egypt.

DHAV-3 has a higher evolutionary rate, and adaptive mutations drive its dominance, informing vaccine design and control strategies.