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)

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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 languageEnglish
Article number16307
JournalScientific Reports
Volume8
DOIs
Publication statusPublished - 5 Nov 2018

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Nanopores
RNA Viruses
Alphavirus
Genome
Isavirus
Fishes
Polymerase Chain Reaction
Aquaculture
Virus Diseases
Disease Management
Disease Outbreaks
Viruses
Technology

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Gallagher, M. D., Matejusova, I., Nguyen, L., Ruane, N. M., Falk, K., & MacQueen, D. (2018). Nanopore sequencing for rapid diagnostics of salmonid RNA viruses. Scientific Reports, 8, [16307 ]. https://doi.org/10.1038/s41598-018-34464-x

Nanopore sequencing for rapid diagnostics of salmonid RNA viruses. / Gallagher, Michael D; Matejusova, Iveta; Nguyen, Lien; Ruane, Neil M; Falk, Knut; MacQueen, Daniel (Corresponding Author).

In: Scientific Reports, Vol. 8, 16307 , 05.11.2018.

Research output: Contribution to journalArticle

Gallagher, MD, Matejusova, I, Nguyen, L, Ruane, NM, Falk, K & MacQueen, D 2018, 'Nanopore sequencing for rapid diagnostics of salmonid RNA viruses', Scientific Reports, vol. 8, 16307 . https://doi.org/10.1038/s41598-018-34464-x
Gallagher MD, Matejusova I, Nguyen L, Ruane NM, Falk K, MacQueen D. Nanopore sequencing for rapid diagnostics of salmonid RNA viruses. Scientific Reports. 2018 Nov 5;8. 16307 . https://doi.org/10.1038/s41598-018-34464-x
Gallagher, Michael D ; Matejusova, Iveta ; Nguyen, Lien ; Ruane, Neil M ; Falk, Knut ; MacQueen, Daniel. / Nanopore sequencing for rapid diagnostics of salmonid RNA viruses. In: Scientific Reports. 2018 ; Vol. 8.
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