Genotypic Characterization of Infectious Spleen and Kidney Necrosis Virus (ISKNV) in Southeast Asian Aquaculture

Infectious spleen and kidney necrosis virus (ISKNV) is a species within the genus Megalocytivirus (family Iridoviridae), which causes high mortality disease in many freshwater and marine fsh species. ISKNV was frst reported in Asia and is an emerging threat to aquaculture with increasing global distribution, in part due to its presence in ornamental fsh with clinical and subclinical infections. Te species ISKNV includes three genotypes: red seabream iridovirus (RSIV), turbot reddish body iridovirus (TRBIV), and ISKNV. Tere is an increasing overlap in the recognized range of susceptible fsh hosts and the geographic distribution of these distinct genotypes. To better understand the disease caused by ISKNV, a nucleic acid hybridization capture enrichment was used prior to sequencing to characterize whole genomes from archived clinical specimens of aquaculture and ornamental fsh from Southeast Asia (n = 16). Te method was suitable for tissue samples containing 2.50 ×104–4.58 ×109 ISKNV genome copies mg−1. Genome sequences determined using the hybridization capture method were identical to those obtained directly from tissues when there was sufcient viral DNA to sequence without enrichment (n = 2). ISKNV genomes from diverse locations, environments, and hosts had very high similarity and matched established genotype classifcations (14 ISKNV genotype Clade 1 genomes with >98.81 nucleotide similarity). Conversely, two diferent genotypes were obtained at the same time and location (RSIV and ISKNV from grouper, Indonesia with 92.44 nucleotide similarity). Gene-by-gene analysis with representative ISKNV genomes identifed 59 core genes within the species (>95 amino acid identity). Te 14 Clade 1 ISKNV genomes in this study had 100 aa identity for 92–105 of 122 predicted genes. Despite high overall sequence similarity, phylogenetic analyses using single nucleotide polymorphisms diferentiated isolates from diferent host species, country of origin, and time of collection. Whole genome studies of ISKNV and other megalocytiviruses enable genomic epidemiology and will provide information to enhance disease control in aquaculture.