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Michael Gallagher

PhD Project: New approaches to characterise viral diseases in Atlantic salmon (Oct 2016 to June 2020)



Dr Iveta Matejusova. Marine Scotland Science. Expert in virology and fish viral diseases.

Postgraduate research

My PhD was a BBSRC funded EASTBIO studentship and partnered with Marine Science Scotland. My work was focused on RNA viruses that infect finfish in aquaculture – particularly pathogens of salmonids (e.g. ISAV and SAV). I used second-generation (Illumina) and third-generation (Nanopore) sequencing to generate whole genome sequences for these viruses, with the goal to develop faster and more efficient approaches to characterise viral diseases in fish. I used these genomes in phylogenetic and molecular evolutionary studies to model the population dynamics of target viruses and characterize viral evolution linked to different outbreaks and transmission routes. In addition, a goal of my project was to improve our ability to rapidly and effectively diagnose viral infections in fish farms.  

Biography and previous work

​I was awarded a 1st class MSci in Biological Sciences here at the University of Aberdeen. During this time, I did Honours and Masters research projects within the Macqueen group, where I also undertook a 10-week research placement funded by the BBSRC EASTBIO scheme. These projects are where my interest in genomics and molecular biology first developed. In my undergraduate research, I investigated the non-blood globin genes of fish using phylogenetic, comparative genomic and gene expression analyses. Globin genes encode oxygen-binding haemproteins that are functionally central to oxygen transport systems in many animals. My work on globins was recently published in the journal Genome Biology and Evolution.


Gallagher MD, Karlsen M, Petterson E, Haugland O, Matejusova I, Macqueen DJ. 2020. Whole Genome Sequencing of SAV reveals repeated seeding events of viral strains in Norwegian aquaculture. Front. Microbiol. 11: 740.

Gallagher MD, Ruane NM, Matejusova I, Macqueen DJ. 2020. Genome-wide target enriched viral sequencing reveals extensive ‘hidden’ salmonid alphavirus diversity in farmed and wild fish populations. Aquaculture. 522: 735117


Gallagher MD, Matejusova I, Nguyen L, Ruane NM, Falk K, Macqueen DJ. 2018. Nanopore sequencing for rapid diagnostics of salmonid RNA viruses. Sci. Rep. 8, Article number: 16307. DOI: 10.1038/s41598-018-34464-x

Gallagher MD, Macqueen DJ. 2017. Evolution and Expression of Tissue Globins in Ray-Finned Fishes. Genome Biol Evol. 9:32-47. DOI: 10.1093/gbe/evw266

From: Gallagher MD, Macqueen DJ. 2017. Evolution and Expression of Tissue Globins in Ray-Finned Fishes. Genome Biol Evol. 9:32-47. 
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