Nanopore sequencing for rapid diagnostics of salmonid RNA viruses

Michael D Gallagher; Iveta Matejusova; Lien Nguyen; Neil M Ruane; Knut Falk; Daniel MacQueen

doi:10.1038/s41598-018-34464-x

Nanopore sequencing for rapid diagnostics of salmonid RNA viruses

Michael D Gallagher, Iveta Matejusova, Lien Nguyen, Neil M Ruane, Knut Falk, Daniel MacQueen^* (Corresponding Author)

^*Corresponding author for this work

Aberdeen Centre For Environmental Sustainability

Research output: Contribution to journal › Article › peer-review

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Abstract

Analysis of pathogen genome variation is essential for informing disease management and control measures in farmed animals. For farmed fish, the standard approach is to use PCR and Sanger sequencing to study partial regions of pathogen genomes, with second and third-generation sequencing tools yet to be widely applied. Here we demonstrate rapid and accurate sequencing of two disease-causing viruses affecting global salmonid aquaculture, salmonid alphavirus (SAV) and infectious salmon anaemia virus (ISAV), using third-generation nanopore sequencing on the MinION platform (Oxford Nanopore Technologies). Our approach complements PCR from infected material with MinION sequencing to recover genomic information that matches near perfectly to Sanger-verified references. We use this method to present the first SAV subtype-6 genome, which branches as the sister to all other SAV lineages in a genome-wide phylogenetic reconstruction. MinION sequencing offers an effective strategy for fast, genome-wide analysis of fish viruses, with major potential applications for diagnostics and robust investigations into the origins and spread of disease outbreaks.

Original language	English
Article number	16307
Journal	Scientific Reports
Volume	8
DOIs	https://doi.org/10.1038/s41598-018-34464-x
Publication status	Published - 5 Nov 2018

Bibliographical note

This work received support from the Biotechnology and Biological Sciences Research Council (grant BB/M010996/1) and Marine Scotland Science. The authors thank Dr Elena Fringuelli (Agri-Food and Biosciences Institute, Belfast) for providing some of the SAV material used.

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Nanopore sequencing for rapid diagnostics of salmonid RNA viruses
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Cite this

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title = "Nanopore sequencing for rapid diagnostics of salmonid RNA viruses",

abstract = "Analysis of pathogen genome variation is essential for informing disease management and control measures in farmed animals. For farmed fish, the standard approach is to use PCR and Sanger sequencing to study partial regions of pathogen genomes, with second and third-generation sequencing tools yet to be widely applied. Here we demonstrate rapid and accurate sequencing of two disease-causing viruses affecting global salmonid aquaculture, salmonid alphavirus (SAV) and infectious salmon anaemia virus (ISAV), using third-generation nanopore sequencing on the MinION platform (Oxford Nanopore Technologies). Our approach complements PCR from infected material with MinION sequencing to recover genomic information that matches near perfectly to Sanger-verified references. We use this method to present the first SAV subtype-6 genome, which branches as the sister to all other SAV lineages in a genome-wide phylogenetic reconstruction. MinION sequencing offers an effective strategy for fast, genome-wide analysis of fish viruses, with major potential applications for diagnostics and robust investigations into the origins and spread of disease outbreaks.",

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note = "This work received support from the Biotechnology and Biological Sciences Research Council (grant BB/M010996/1) and Marine Scotland Science. The authors thank Dr Elena Fringuelli (Agri-Food and Biosciences Institute, Belfast) for providing some of the SAV material used.",

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AU - Nguyen, Lien

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AU - Falk, Knut

AU - MacQueen, Daniel

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AB - Analysis of pathogen genome variation is essential for informing disease management and control measures in farmed animals. For farmed fish, the standard approach is to use PCR and Sanger sequencing to study partial regions of pathogen genomes, with second and third-generation sequencing tools yet to be widely applied. Here we demonstrate rapid and accurate sequencing of two disease-causing viruses affecting global salmonid aquaculture, salmonid alphavirus (SAV) and infectious salmon anaemia virus (ISAV), using third-generation nanopore sequencing on the MinION platform (Oxford Nanopore Technologies). Our approach complements PCR from infected material with MinION sequencing to recover genomic information that matches near perfectly to Sanger-verified references. We use this method to present the first SAV subtype-6 genome, which branches as the sister to all other SAV lineages in a genome-wide phylogenetic reconstruction. MinION sequencing offers an effective strategy for fast, genome-wide analysis of fish viruses, with major potential applications for diagnostics and robust investigations into the origins and spread of disease outbreaks.

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Nanopore sequencing for rapid diagnostics of salmonid RNA viruses

Abstract

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