Abstract

1Infectious Spleen and Kidney Necrosis Virus (ISKNV) is increasingly gaining more attention globally, due to its highly significant economic impact on the aquaculture industry. In late 2018, unusually high levels of mortality (60-90%) was reported in some intensive tilapia cage culture systems in Ghana. Preliminary investigations confirmed the involvement of ISKNV, a viral pathogen noted for fatal systemic infections in many fish species. As a follow-up on the outbreak situation, and post-mass vaccination of affected fish farms, the need to investigate further the molecular epidemiology and phylogeography of the virus across Lake Volta became paramount. In this study, a multiplexed PCR assay and MinION nanopore sequencing of the Major Capsid Protein (MCP) were performed to investigate the presence and genotype of ISKNV in tilapia collected from 30 randomly selected farms spread across Lake Volta. Fish with and without clinical signs were included in the molecular detection of the virus from brain, kidney and spleen tissues. ISKNV was detected at 80% prevalence with fry and juvenile fish being most affected. Phylogenetic analysis of the MCP revealed that all 35 isolates from 14 different farms were ISKNV genotype I with near- 100% homology to the 2018 outbreak strain. Vaccination and heat shock treatment; the main specific interventions currently employed to control the viral pathogen have not achieved much success and ISKNV remains a threat to the growth of the aquaculture industry in Ghana. The outcome of this study can be useful in improving fish health management and biosecurity policies in the aquaculture industry.