| dc.description.abstract | Viral pathogens are having a significant impact on Tilapia health, threatening global food security. It is critical to increase biosecurity measures, diagnostic testing, and sequencing to better understand their evolution and spread in aquaculture. Yet, this is not feasible or adapted in many countries, as numerous fish farms are situated in resource limited regions with reduced access to diagnostic labs. Delays in turn-around time for results reduces the capacity for timely interventions. One way to avoid devastating outcomes of viral outbreaks in aquaculture is real-time whole genome sequencing (WGS) of isolates, using in-field tools to rapidly resolve chains of transmission and implement control measures.
Here, we investigate the feasibility of a tiled PCR method for genomic surveillance of Infectious spleen and kidney necrosis virus (ISKNV), a powerful tool successfully adapted for genomic surveillance of important human pathogens. We perform a complete phylogeographic analysis on isolates collected from Lake Volta, Ghana, since 2018. ISKNV, a slow evolving double stranded DNA virus has been causing mass mortalities in Ghana, and is capable of infecting a wide range of marine and freshwater fish. In addition, an in-field, non-destructive water sampling method was developed to monitor viruses in tilapia fish cages, by concentrating viral fraction on filters. Challenges were encountered when applying these methods in the field in Ghana, and the technical and economic issues are discussed. We evaluate our developed method on an equally important single stranded RNA virus, known as Tilapia Lake Virus (TiLV), which has been affecting the growth of tilapia for more than a decade. Finally, we highlight the challenges faced during a field -based genomic surveillance campaign performed on Lake Volta. This work is the first of its kind to develop and test a valuable in-field, routine monitoring and detection tool for viral outbreaks impacting the prosperity of aquaculture. | en_GB |
