Comparative genomic analysis of duck plague virus reveals evolutionary divergence between vaccine and contemporary field isolates in Thailand

Abstract

Duck Plague Virus (DPV), an alphaherpesvirus, causes significant morbidity and mortality in waterfowl and remains a persistent threat to duck farming across Asia. This study reports the first complete genomic characterization of DPV isolates from Thailand including a commercial vaccine strain (DPVac) and two contemporary field isolates (DPV7 and DPV8). Using Oxford Nanopore Technologies (ONT) and hybrid Illumina-ONT sequencing, we successfully assembled complete genomes ranging from 160,511 to 163,789 bp. The assembled genomes showed high sequence identity to the European reference strain DEV 2085. Comparative genomic analysis revealed structural differences in the UL and US regions. Phylogenetic reconstruction based on core genome single-nucleotide polymorphisms (SNPs) placed DPV7 within a clade of recent Chinese field strains, while DPV8 clustered closely with vaccine-associated lineages from Germany, India, and Bangladesh. Notably, SNP analysis identified multiple virulence-associated mutations uniquely present in DPV7. These mutations, absent in DPVac and DPV8, were located within or near genes involved in viral replication (UL54), host immune evasion (UL41, UL14), viral entry (UL44, UL8), intracellular trafficking (US3, US8), and virulence modulation (LORF3). These findings suggest that DPV7 may be undergoing adaptive evolution under immune pressure, potentially compromising vaccine effectiveness. Our results underscore the critical need for continuous molecular surveillance and functional studies to evaluate the impact of emerging DPV variants. The complete genome sequences reported herein provide a valuable resource for future research on DPV evolution, diagnostics, and vaccine development in endemic regions.