Genome editing for resistance to white spot syndrome virus in whiteleg shrimp

Shrimp is one of the most important aquaculture groups worldwide, representing 16 % of the world trade of aquatic products in value (FAO 2018, http://www.fao.org/3/I9540EN/i9540en.pdf). In particular, whiteleg shrimp (Litopenaeus vannamei) account for over 50 % of shrimp production worldwide (4.1M tons in 2016; FAO 2018), and is critical for the food security and economic stability of many coastal areas in Southwest Asia and Latin America. Recently, two shrimp farms have opened in UK, one of them in central Scotland.

The largest threat to the sustainability of shrimp aquaculture are infectious diseases, with white spot syndrome (WSS) currently being the biggest concern. This disease causes mortalities up to 100 %, and has led to massive production losses worldwide in recent years (~75 % production reduction in China and Ecuador). WSS remains an unsolved problem for shrimp aquaculture; therefore, improvement of host resistance to the virus is a key goal, and genome editing offers new opportunities to achieve this.

WSS is caused by a circular, double-stranded DNA virus, WSSV. The number of open reading frames (ORF) varies from 500 to 700 depending on the strain, but only ~160 are likely to encode proteins, 60 of which have associated functions so far (Han et al. Vet Res 2017, 48:87). This virus is the only known member of family Nimaviridae and its genome characterization is poor due to a lack of homology with other viruses.

The main aim of this project is to harness CRISPR/Cas9 technology to understand and improve host resistance to WSSV in shrimp. To do so, the PhD student will establish primary cell cultures to perform in vitro WSSV experiments to study the host-virus interaction. Genome-wide in vitro editing of the virus will be used to identify viral genes essential for successful replication. CRISPR/Cas9 and individual guides targeting WSSV ORFs will be transduced into shrimp cells using recombinant baculovirus vectors (Puthumana et al. 2016; Cytotechnology 68:1147-1159), and then infected with WSSV. The effect of each WSSV gene knock-out on the dynamics of viral infection will be assessed, and this information will be leveraged to build a CRISPR-based tool targeting multiple WSSV ORFs fundamental for infection, minimizing the risk of escape mutants. The strategy of equipping the shrimp with the CRISPR/Cas9 machinery will be tested in vivo through collaboration with Mexican colleagues who have extensive experience in genome editing in L. vannamei. The project will develop a method to tackle WSSV in shrimp, but also improve gene editing in crustaceans and expand our knowledge of WSSV and its interaction with host cells, aiding the development of future therapeutic strategies.
This 4-year CASE studentship will provide an excellent inter-disciplinary training opportunity, covering aspects of genomics and genetics, virology and cell biology, and applying a wide variety of techniques. The partnership with Roslin Technologies as part of the CASE studentship offers an exciting opportunity for the PhD student to work on the interface between basic research and commercial application, and to gain first-hand experience outside academia.