Background: Red Seabream Iridovirus (RSIV) is a causative agent of Red Seabream Iridoviral Disease (RSIVD). RSIV causes mass mortality in more than 30 species of cultured marine fish in Japan. This virus is a member of the genus Megalocytivirus belongs to the family Iridoviridae. The comparative genomic analysis to classify Megalocytiviruses based on the major capsid protein (MCP), ATPase and DNA polymerase gene sequences were showed that RSIV-type Megalocytivirus can be divided into two subclusters: genotype I and genotype II. RSIV Ehime-1, the type strain of RSIV isolated in Japan, belongs to genotype I. RSIV genotype II is recently predominates, and includes other major RSIV strains isolated in Japan, East and Southeast Asia. In addition, other isolates such as rock bream iridovirus (RBIV), orange-spotted grouper iridovirus (OSGIV) giant seaperch iridovirus (GSIV) are also classified into the genotype II of RSIV clade. The objective of the present study is to obtain deeply insights on the comparative variations of Megalocytivirus by comparing whole genome sequences of RSIV isolates in Japan.
Methods: In this study, we sequenced the whole genome of 20 RSIV-type Megalocytivirus isolated from infected fishes in Oita and Ehime prefecture in 2008-2019 by next generation sequencer MiSeq (Illumina) and analyzed these genomic relationships with representative Megalocytiviruses from Genbank.
Results and Discussion: The complete genome sequence of 20 isolates had lengths of 112-113 Kbp. The comparative genome analysis of RSIV isolates with representative Megalocytiviruses members showed that the Japanese isolates categorized as the RSIV genotype II cluster. The phylogenetic network showed relationship of 18 haplotypes of RSIV whole genomes of 7 isolates from Ehime and 13 isolates from Oita. The number of polymorphic sites were detected as 3,577 sites. Whole genome sequence information is a helpful tool to identify genetic variations and provide more precise knowledges in RSIV-type Megalocytivirus in Japan. In future, the relationship between the individual RSIV isolates with their host species, culturing situation, and so on, might help in a better understanding of transmission and prevention of RSIV disease.