Infectious diseases cost fisheries and seafood farming operations billions of dollars in lost production per year. For shrimp farming alone, it is estimated that viruses, bacteria, and other microorganisms result in supply and revenue losses amounting to billions of dollars per year globally. Losses of this magnitude make rapid, accurate, and sensitive diagnostics critical for limiting transmission and mitigating outbreaks, thereby protecting farms and their profitability. However, current diagnostic tests require sophisticated equipment, expensive reagents, are time intensive, and cannot be employed in the field. This limits the ability of diagnostic monitoring to translate to immediate and meaningful action to stop disease spread and supply loss.
To address this, we investigated molecular technologies including loop -mediated isothermal amplification (LAMP) and CRISPR collateral cleavage for their potential to be used in a rapid, robust, field-based diagnostic tool for the detection of the common shrimp pathogens White Spot syndrome virus (DNA) and Taura syndrome virus (RNA) . We found LAMP to work robustly, but less specifically than CRISPR alone or CRISPR in combination with LAMP. CRISPR in combination with LAMP worked more sensitively but less quantitatively than CRISPR alone. We found targeting multiple genomic regions through multiplexing guide RNAs increased the sensitivity of CRISPR alone . Overall, CRISPR is a promising technology to adopt in field diagnostics for rapid, inexpensive, user-friendly detection of aquaculture diseases that would aid in mitigating disease outbreaks, reducing supply loss, and increasing productivity and sustainability.