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Development of cell culture tools to study fish virus interactions with a focus on fastidious carp viruses

School of Biological Sciences

About the Project

Aquaculture is of major and increasing importance in global food security. Globally, cyprinids represent the highest produced species in aquaculture totalling 26 million tonnes per annum and accounting for almost 50% of total cultured finfish in 2018. The production of all farmed fish is constrained by infectious disease. The pox virus, carp edema virus (CEV) and variants of koi herpesvirus, also known as cyprinid herpesvirus-3 (KHV, CyHV-3), are Eurasian carp viruses of national and international importance. These viruses do not replicate in currently available fish cell lines, which significantly hampers our ability to characterise these viruses, especially in terms of virulence levels. Thus, we are currently unable to assess their risk to the aquatic environment and to develop appropriate control measures.

Fundamental studies are needed to improve virus purification methods and to determine, and/or establish, cell lines that will allow propagation of CEV and CyHV-3 variants. Previous work demonstrates that both viruses have a specific tissue tropism for gills. Few established immortalised cell lines derived from gills of fish currently exist and there are currently no carp gill cell lines available. Primary cell culture from gills represents a potential viable alternative but regular production is time consuming and potentially variable as cells come from different fish. Using state-of-the-art genome editing (CRISPR/CAS9) technology, the knockout of key antiviral immune response pathways or the insertion of key dependence factors for viral replication in cell lines has been carried in supervisor’s labs.

This PhD project will develop new cell lines to enable replication of CEV and CyHV-3, with an emphasis on gill cells. Parallel approaches will use CRISPR/Cas9 genome editing methods on established carp cell lines (e.g. KF, CCB) to target key signal transduction pathways and immune response genes in the host cell antiviral immune response. Effective gene knockout will enable us to develop immune response-deficient cyprinid cell lines to investigate potential viral propagation of CEV and the variant herpesviruses. Finally, from in vivo challenged fish or from in vitro infection of primary gill cell cultures and cell lines, we will study the infected host transcriptome to identify host dependency factors (HDF) critical for entry, replication and transmission of these viruses.

Training and project development:
The student will join UoA’s Scottish Fish Immunology Research Centre and will benefit from in-house training in fully equipped molecular immunology labs, including cell culture facilities and an aquarium with dedicated challenge facilities. The student will also benefit from the onsite Centre for Genome Enabled Biology and Medicine. Training in aquaculture, disease and diagnostics (virology, histopathology and pathogen culture) will be at the International Centre of Excellence for aquatic animal health at Cefas. Time will be spent at both Aberdeen and Cefas, balanced by the needs of the experimental work and skills training. The student will interact with the Fish Health Inspectorate for England and Wales based at Cefas gaining experience in disease surveillance, including opportunities to collaborate with global virus experts on international projects.

This PhD studentship is an exceptional opportunity to gain experience in cutting edge molecular virology and participate in research into an important threat to aquaculture with broad impacts for food security and human health. For further information contact either Prof Sam Martin () or Dr Richard Paley ().

Funding Notes

This project is funded by CEFAS and the University of Aberdeen and is available to UK/EU nationals who meet the RCUK eligibility criteria.

Funding: for tuition fees, stipend and a research training and support grant- subject to eligibility.

Candidates should have (or expect to achieve) a minimum of a 2.1 Honours degree in a relevant subject.


• Apply for Degree of Doctor of Philosophy in Biological Science
• State name of the lead supervisor as ‘Name of Proposed Supervisor’ on application
• State ‘Funded Project' as intended funding source
• Select the ‘Institution Website’ to apply now


Houston, R.D., Bean, T.P., Macqueen, D.J., Gundappa, M.K., Jin, Y.H., Jenkins, T.L., Selly, S.L.C., Martin, S.A.M., Stevens, J.R., Santos, E.M., Davie, A., Robledo, D. 2020. Harnessing genomics to fast-track genetic improvement in aquaculture. Nature Reviews Genetics. 21: 389 – 409

Dehler, C.E., Lester, K., Della Pelle, G., Jouneau, L., Houel, A., Collins, C., Dovgan, T., Machat, R., Zou, J., Boudinot, P., Martin, S.A.M., Collet, B. 2019. Viral resistance and IFN signaling in STAT2 knockout fish cells. Journal of Immunology. 203: 465 – 475

Cano I, Taylor NGH, Bayley A, Gunning S, McCullough R, Bateman K, Nowak BF, Paley R. 2019. In vitro gill cell monolayer successfully reproduces in vivo Atlantic salmon host responses to Neoparamoeba perurans infection. Fish & shellfish immunology 86, 287-300

Dehler, C.E., Boudinot, P., Martin, S.A.M., Collet, B. 2016. Development of an Efficient Genome Editing Method by CRISPR/Cas9 in a Fish Cell Line. Marine Biotechnology. 18: 449 - 452

Gratacap, R.L., Regan, T., Dehler, C.E., Martin, S.A.M., Boudinot, P., Collet, B., Houston, R.D. 2020. Efficient CRISPR/Cas9 genome editing in a salmonid fish cell line using a lentivirus delivery system. BMC Biotechnology. 20: 35

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