Genomic Characterisation of Red Sea Bream Iridovirus (RSIV) Samples Collected in Japan in 2024 Revealed Genotype II and the First Detection of the Intermediate Type in Japan

Abstract

The Megalocytivirus pagrus1 causes serious disease in aquaculture and is classified into three clades: infectious spleen and kidney necrosis virus (ISKNV), turbot reddish body iridovirus (TRBIV), and red sea bream iridovirus (RSIV), further classified as genotype I or II. Several recent studies have reported RSIV strains designated as mixed genotype I/II because they were assigned to different subtypes depending on the gene used for phylogenetic analysis. In 2024, three RSIV samples were collected in Japan, one of which (GT1‐Oita2024) was PCR‐positive but tested negative using an immune fluorescent antibody test (IFAT) with M10 antibodies. Thus, we performed whole genome sequencing and phylogenetic analysis of the IFAT‐negative sample and the two other RSIV samples (GT2‐Oita2024 and Ehime2024). In GT1‐Oita2024, LEGFD, a known antigen of the M10 antibody, was found to harbour several mutations. Based on average nucleotide identity, GT2‐Oita2024 and Ehime2024 were classified as genotype II, showing high homology with KagYT‐96 and RIE12‐1. GT1‐Oita2024 was classified as the intermediate type, showing high homology with SBIV‐VP13 and 17SbTy. GT1‐Oita2024 also contained regions showing homology with genotype I, genotype II and TRBIV. This is the first detection of this genotype in Japan. Further monitoring is warranted to determine the extent of its spread.

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