Shayma Alathari from the University of Exeter was the next presenter at the Nanopore Community Meeting 2022 that I watched present. Their five-minute session was very brief, and packed with information. The title of Alathari’s session was “Development and application of genomic tools for tracking viral outbreaks in fish.”Alathari is a Ph.D. student interested in the development of genomic tools to learn about viral outbreaks in fish. They spoke about a 2018 outbreak in Ghana caused by the ISKNV ds DNA virus that caused mass mortalities in tilapia. They noted that Ghana had to suspend production due to the outbreak. Alathari tracked viral outbreaks by designing primers to create 2 kb amplicons to recover the genome and then a combination of primers for tiled PCR. They collected 34 tilapia between 2018 and 2022. After isolating DNA, they performed tiled PCR and sequencing with Nanopore. They then generated a phylogenetic tree with NextStrain. Viral sequences from the 2022 outbreak clustered separately from the 2018 outbreak despite being collected from the same farm. Alathari concluded that variants of ISKNV are host specific and 91 SNPs were identified. They concluded that the PCR tiled approach was successful and can be applied in the field to other samples in the field. Alathari wants to educate others to use this approach. I am also thinking that this outbreak would be a great source of questions and techniques for the class I am teaching.
