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

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Aquatic Biology

Main article text

 

Introduction

Materials & Methods

Samples

DNA extraction

Droplet digital PCR for viral quantification

Tiled PCR

Library preparation and sequencing

Long read sequencing

a. Water samples:.
b. Tissue samples matching water samples.
c. All tissue samples.

Short read sequencing

Phylogeographic analysis

Results

ISKNV detection and quantification in tissue and water samples

Sequencing and phylogeographic analysis for all samples collected from Ghana—Changes to MinION chemistry do not affect our tiled PCR method

Discussion

Supplemental Information

Supplementary Figures and Tables

DOI: 10.7717/peerj.17605/supp-1

STL 1 for 3d printing of adapter for in-field sampling

DOI: 10.7717/peerj.17605/supp-2

STL 2 for 3d printing of adapter for in-field sampling

DOI: 10.7717/peerj.17605/supp-3

STL 3 for 3d printing of adapter for in-field sampling

DOI: 10.7717/peerj.17605/supp-4

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Shayma Alathari conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Andrew Joseph performed the experiments, authored or reviewed drafts of the article, enabled in-field sampling work and support in Ghana, and approved the final draft.

Luis M. Bolaños analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

David J. Studholme analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Aaron R. Jeffries analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Patrick Appenteng performed the experiments, authored or reviewed drafts of the article, enabled in-field sampling work and support in Ghana, and approved the final draft.

Kwaku A. Duodu performed the experiments, authored or reviewed drafts of the article, enabled in-field sampling work and support in Ghana, and approved the final draft.

Eric B. Sawyerr performed the experiments, authored or reviewed drafts of the article, enabled in-field sampling work and support in Ghana, and approved the final draft.

Richard Paley conceived and designed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Charles R. Tyler conceived and designed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Ben Temperton conceived and designed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

Field experiments were approved by the Fisheries Commission, Ministry of Fisheries and Aquaculture Development, Accra, Ghana.

Data Availability

The following information was supplied regarding data availability:

The raw sequence reads are available at NCBI: PRJNA935699.

Funding

Shayma Alathari was funded on a PhD programme through the centre for Sustainable Aquaculture Futures, a joint partnership between the University of Exeter and the Centre for Environment, Fisheries and Aquaculture Sciences (Cefas). This project used equipment funded by the Wellcome Trust (Multi-User Equipment Grant award number 218247/Z/19/Z) to the Exeter Sequencing Centre. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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