Molecular Evidence for the Homologous Strains of Infectious Spleen and Kidney Necrosis Virus (ISKNV) Genotype I Infecting the Inland Freshwater Cultured Asian Sea Bass (Lates Calcarifer) in Thailand

Abstract Infectious spleen and kidney necrosis virus (ISKNV) is the fish pathogenic virus belonging to the genus Megalocytivirus of the family Iridoviridae. In 2018, disease occurrences (40–50% cumulative mortality) associated with ISKNV infection have been reported in grown-out Asian sea bass (Lates calcarifer) cultured in the inland freshwater system in Thailand. Clinical samples were collected from seven distinct farms located in the eastern and central regions of Thailand. The moribund fish showed various abnormal signs including lethargy, pale gill, darkened body, and skin hemorrhage, while the basophilic hypertrophied cell in gill, liver, and kidney tissue was observed microscopically. ISKNV infection was confirmed in 6 out of 7 farms using virus-specific semi-nested PCR. MCP and ATPase genes showed 100% identity among virus isolates which also classified the virus into ISKNV genotype I clade. Koch’s postulates were later confirmed by challenge assay and the mortality of the experimentally infected fish at 21 days post-challenge was 50–90% depending on the challenge dose. The complete genome of two ISKNV isolates, namely KU1 and KU2, was recovered directly from the infected specimens using the shotgun metagenomics approach. The genome length of ISKNV KU1 and KU2 were 111,487 and 111,610 bp, respectively. In comparison to the closely related ISKNV strains, the ISKNV KU1 and KU2 harbored nine unique genes, including caspase recruitment domain-containing protein potentially involved in apoptosis inhibition. Collectively, this study indicated the homologous ISKNV strains affecting the inland cultured Asian sea bass which emphasized that the ISKNV genotype I should be prioritized for future vaccine research.