In field use of water samples for genomic surveillance of infectious spleen and kidney necrosis virus (ISKNV) infecting tilapia fish in Lake Volta, Ghana

Author:

Alathari Shayma1,Joseph Andrew2,Bolaños Luis M.1,Studholme David J.1,Jeffries Aaron R.1,Appenteng Patrick3,Duodu Kwaku A.3,Sawyerr Eric B.3,Paley Richard2,Tyler Charles R.14,Temperton Ben1

Affiliation:

1. Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom

2. Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, United Kingdom

3. Fisheries Commission, Ministry of Fisheries and Aquaculture Development, Accra, Ghana

4. University of Exeter, Sustainable Aquaculture Futures Centre, Exeter, United Kingdom

Abstract

Viral outbreaks are a constant threat to aquaculture, limiting production for better global food security. A lack of diagnostic testing and monitoring in resource-limited areas hinders the capacity to respond rapidly to disease outbreaks and to prevent viral pathogens becoming endemic in fisheries productive waters. Recent developments in diagnostic testing for emerging viruses, however, offers a solution for rapid in situ monitoring of viral outbreaks. Genomic epidemiology has furthermore proven highly effective in detecting viral mutations involved in pathogenesis and assisting in resolving chains of transmission. Here, we demonstrate the application of an in-field epidemiological tool kit to track viral outbreaks in aquaculture on farms with reduced access to diagnostic labs, and with non-destructive sampling. Inspired by the “lab in a suitcase” approach used for genomic surveillance of human viral pathogens and wastewater monitoring of COVID19, we evaluated the feasibility of real-time genome sequencing surveillance of the fish pathogen, Infectious spleen and kidney necrosis virus (ISKNV) in Lake Volta. Viral fractions from water samples collected from cages holding Nile tilapia (Oreochromis niloticus) with suspected ongoing ISKNV infections were concentrated and used as a template for whole genome sequencing, using a previously developed tiled PCR method for ISKNV. Mutations in ISKNV in samples collected from the water surrounding the cages matched those collected from infected caged fish, illustrating that water samples can be used for detecting predominant ISKNV variants in an ongoing outbreak. This approach allows for the detection of ISKNV and tracking of the dynamics of variant frequencies, and may thus assist in guiding control measures for the rapid isolation and quarantine of infected farms and facilities.

Funder

Sustainable Aquaculture Futures, a joint partnership between the University of Exeter and the Centre for Environment, Fisheries and Aquaculture Sciences

the Wellcome Trust (Multi-User Equipment

Publisher

PeerJ

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