Genomic surveillance and evolution of co-circulating goose parvovirus and waterfowl circovirus in China.

As the world's largest waterfowl producer, China faces economic losses from Goose Parvovirus (GPV), worsened by waterfowl circovirus co-infections that increase pathogenicity and immunosuppression. However, current surveillance systems for these viruses lack systematization. This study conducted a comprehensive genetic analysis of GPV and waterfowl circovirus to identify genomic characteristics and recombination events. Surveillance analysis of GPV revealed a significant host-associated genotypic divergence from 2018 to 2024 in China. Goose isolates were predominantly the Mutated GPV (MGPV, 87%), while duck isolates were mainly the duck-adapted Novel GPV (NGPV, 88%). This divergence was corroborated by a global analysis, which confirmed high intra-clade similarity but substantial overall genetic diversity. Whole-genome recombination analysis revealed one isolate as a unique NGPV recombinant, with an NGPV strain as the major parent and an Early GPV strain as the minor parent. Furthermore, our study identified a persistent, host-specific co-circulating GPV and waterfowl circovirus: MGPV/GoCV in geese and NGPV/DuCV in ducks. Phylogenetic analysis shows that waterfowl circovirus exhibits significant genetic diversity: GoCV has two lineages (GoCV-I prevalent in China, GoCV-II with cross-species transmission to European Anser anser), while DuCV has three genotypes with distinct geographical distributions and host ranges across Asia and North America. Genomic analysis corroborated these phylogenetic findings and indicated ongoing genetic variation and recombination as key drivers of waterfowl circovirus evolution. In conclusion, this study systematically elucidates the ongoing adaptive evolution and genetic plasticity of GPV and waterfowl circovirus, providing a scientific basis for targeted waterfowl disease prevention strategies.