Evolutionary dynamics of endogenous densoviruses NS1 proteins reveal ancient codivergence with their Platyhelminth hosts

ABSTRACT Endogenous viral elements serve as molecular fossils of ancient viral infections, providing valuable evidence for reconstructing the evolutionary history of modern viruses and their hosts. These genomic remnants also provide crucial benchmarks for calibrating viral evolutionary timelines. Here, our flanking sequence analysis reveals that densovirus NS1 sequences are chromosomally integrated in Platyhelminth genomes. Furthermore, their evolutionary dynamics reflect an ancient host-virus codivergence event dating to the Ediacaran-Cambrian transition (approximately 692 million years ago, MYA). Phylogenomic analyses delineate profound divergence between endogenous densovirus sequences in Platyhelminthes and exogenous Parvoviridae sequences, with distinct phylogenetic clustering supporting long-term endogenization. Structural alignments reveal significant global divergence (RMSD: 15.048–36.725 Å) yet striking local conservation in NS1 proteins, with the ATPase (RMSD: 0.271–1.756 Å) and effector domains (RMSD: 2.446–4.775 Å) remaining highly conserved across Platyhelminth hosts. The timescale phylogenetic tree inferred ancient divergence times of 233.51 MYA for Schistosoma-Dicrocoelium and 190.43 MYA for the Clonorchis sinensis , Opisthorchis viverrini , and Paragonimus westermani lineage. Distance matrix analysis revealed pronounced interspecific divergence and intraspecific conservation in NS1 sequences, consistent with a host-virus codivergence model. These findings reveal the preservation of replication-critical domains and the optimization of host-specific adaptation, providing molecular evidence for virus-parasite coevolution over geological timescales. Collectively, our findings reshape our understanding of virus-host coevolution and offer a framework to reconstruct paleoviral dynamics using endogenous “molecular fossils.” IMPORTANCE This study provides evidence of densoviral endogenization in Platyhelminth hosts, advancing understanding of virus-host codivergence and offering a framework for reconstructing paleoviral dynamics using endogenous “molecular fossils.”