Molecular detection and phylogenetic characterization of Megalocytivirus pagrus 1 (ISKNV) in ornamental fish imported to the Republic of Korea

A total of 294 pooled samples from ten species were tested for the presence of Megalocytivirus pagrus 1 in a two-year survey. Among them, Megalocytivirus pagrus 1 was detected from 36 samples (pool prevalence of 12.24%) by PCR assay targeting the major capsid protein (MCP) gene. The MCP gene from five representative positives was sequenced. Pairwise identity and maximum-likelihood phylogenetic analyses based on MCP nucleotide sequences indicated close genetic relatedness between the five sequences obtained in this study and ISKNV Clade 1 reference sequences; four sequences exhibited ≥99.68% nucleotide identity to Clade 1 strains, whereas one displayed comparatively lower identity, but was still placed close to the ISKNV Clade 1-associated assemblage. These findings support the use of the MCP gene as a primary marker for distinguishing Megalocytivirus pagrus 1 genotype and clades; however, because the MCP gene constitutes less than 2% of the viral genome, additional loci (e.g., ATPase) or whole-genome sequencing are recommended for higher-resolution phylogenetic analysis. Taken together with additional metadata (host and reported origin), the MCP sequence provides a reference dataset for comparative analysis of Megalocytivirus pagrus 1 diversity. And as the findings here are based on gene sequence, it indicates genetic relatedness rather than a definite diagnosis of an infectious virus. The sequences are available in GenBank, and international cross-study comparison would support future scientific evaluation of the genus Megalocytivirus, in alignment with the World Organisation for Animal Health criteria.