NCM 2022: Development and application of genomic tools for tracking viral outbreaks in fish

Fish losses and food shortages due to the emergence of viruses are commonly seen in countries dependent on aquaculture, posing a threat to fish farmers’ livelihoods and income security. Tilapia farming is one of the most important sectors in aquaculture worldwide. A novel strain of infectious spleen and kidney necrosis virus (ISKNV) has caused mortality (60–90%), threatening tilapia aquaculture in tilapia farms in Lake Volta, Ghana. Losses resulted in the closure of more than 50 farms, loss of over 400 jobs, and disruption to the livelihoods of the communities along the lake. Tiled PCR products have enabled field-based, real-time genomic surveillance of human viral outbreaks. Leveraging similar approaches for tracking ISKNV outbreaks faces several challenges, a much larger genome than previous targets, and slower evolution rates associated with dsDNA viruses. Here, we developed a new protocol to recover near-complete (96%) ISKNV genomes from tissue samples collected from the lake.