Molecular Epidemiological Survey of Carp Edema Virus Genogroup II from Koi <i>Cyprinus carpio</i> in Japan

In recent years, there have been many publications reporting mass mortality events and genotyping of carp edema virus (CEV) around the world, but molecular phylogenetic knowledge of CEV in Japan is scarce. Therefore, in this study, we performed a comprehensive survey to understand the prevalence and genotypes of CEV in koi fish farms in Japan. PCR was performed to amplify a portion of the p4a gene of CEV from 585 samples collected in 2021 across 96 aquaculture farms in 16 prefectures. The results showed that 62.5% of prefectures and 21.9% of fish farms were found to be positive for CEV. Overall, 42 samples were positive for CEV, and a total of 12 genotypes were detected by sequencing a portion of the p4a gene. Phylogenetic analysis revealed that all of the genotypes obtained in this study belonged to genogroup II. Of the 12 CEV genotypes found in Japan, 10 were identical to CEVs reported in other parts of the world. We speculate that the international koi trade has contributed to the spread of genogroup II. This study represents the first large-scale genetic survey of CEV in koi in Japan.