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

Abstract

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 fish species. ISKNV was first reported in Asia and is an emerging threat to aquaculture with increasing global distribution, in part due to its presence in ornamental fish with clinical and subclinical infections. The species ISKNV includes three genotypes: red seabream iridovirus (RSIV), turbot reddish body iridovirus (TRBIV), and ISKNV. There is an increasing overlap in the recognized range of susceptible fish 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 fish from Southeast Asia (n = 16). The 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 sufficient viral DNA to sequence without enrichment (n = 2). ISKNV genomes from diverse locations, environments, and hosts had very high similarity and matched established genotype classifications (14 ISKNV genotype Clade 1 genomes with >98.81% nucleotide similarity). Conversely, two different 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 identified 59 core genes within the species (>95% amino acid identity). The 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 differentiated isolates from different 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.

Genetic characterization of infectious spleen and kidney necrosis virus in Banggai cardinalfish Pterapogon kauderni identified from eight separate cases between 2000 and 2017

“…From the mid-1990s to the present, both ISKNV-C1G and ISKNV-C2G have dominated infections in ornamental fish (de Lucca Maganha et al, 2018;Go & Whittington, 2006;Go et al, 2016;Jeong, Cho, et al, 2008;Jeong, Kim, et al, 2008;Kurita & Nakajima, 2012;Mohr et al, 2015;Nolan et al, 2015;OIE, 2020;Rimmer et al, 2015;Sriwanayos et al, 2013;Subramaniam et al, 2014;Sudthongkong et al, 2002aSudthongkong et al, , 2002bWeber III et al, 2009). All Banggai cardinalfish in this study were confirmed positive by conventional PCR and/or full genome sequencing with either the ISKNV-C1G (two cases) or ISKNV-C2G (six cases).…”

“…Megalocytiviruses (MCV) are large double-stranded DNA viruses that cause mortality in freshwater, brackish and marine teleosts globally, including wild and farmed fish species (Go et al, 2016;Huang et al, 2011;Inouye et al, 1992;Kim et al, 2019;Koda et al, 2018;Song et al, 2008;Subramaniam et al, 2014;Sudthongkong et al, 2002b). The genus currently includes two species, Infectious spleen and kidney necrosis virus (ISKNV) and Scale drop disease virus (SDDV; Chinchar et al, 2017).…”

“…Genetic analyses of ISKNV have revealed three genotypes: infectious spleen and kidney necrosis virus (ISKNV), red seabream iridovirus (RSIV) and turbot reddish body iridovirus (TRBIV). Phylogenetic analyses based on the major capsid protein (MCP) and full genomic sequences have identified that each genotype can further be subdivided into two clades (Go et al, 2016;Kim et al, 2019;Koda et al, 2018Koda et al, , 2019Sriwanayos et al, 2013). Partial sequencing of the previously reported BCIV genome revealed it belongs to the ISKNV clade 2 genotype (hereafter, ISKNV-C2G; Weber III et al, 2009).…”

First report of natural infection with infectious spleen and kidney necrosis virus (ISKNV) associated with disease outbreaks in two gourami species (Trichopodus spp.)

“…The molecular identi cation of ISKNV by sequencing of the MCP and ATPase genes in the current study provides direct evidence for the presence of the virus infecting snakeskin gourami and three spot gourami and its phylogenetic placement in the Megalocytivirus genus. The high degree of sequence identity with known strains of ISKNV suggests a common evolutionary origin and the possibility of a wide distribution of similar genotype of the virus across different sh species and geographical regions (Fusianto et al, 2023). These genetic ndings are crucial for the development of targeted diagnostic tools and understanding the epidemiology of ISKNV infections across many different sh species.…”

“…Additionally, genes encoding adenosine triphosphatase (ATPase), DNA polymerase, and methyltransferase provide complementary genetic information (Kerddee et al, 2021;Kurita & Nakajima, 2012;Whittington et al, 2010). Genetic analyses based on the MCP and ATPase genes of ISKNV have identi ed three main genotypes: ISKNV, red seabream iridovirus (RSIV), and turbot reddish body iridovirus (TRBIV) (Ayiku et al, 2024;Fusianto et al, 2023;Kerddee et al, 2021). Typically, SDDV can be distinguished from other Megalocytivirus infections by its unique external clinical signs (de Groof et al, 2015; Girisha et al, 2021;Senapin et al, 2018).…”