New approaches to characterize viral diseases affecting Atlantic salmon
Lead Research Organisation:
University of Aberdeen
Department Name: Inst of Biological and Environmental Sci
Abstract
The Atlantic salmon aquaculture industry is worth >£1 billion to the UK economy per annum and represents an important provider of employment and food security. However the expansion of this industry is threatened by a range of infectious diseases, including several different viruses, which can cause fish mortality, slow growth and reduce the quality of the final flesh product, in addition to the substantial costs of treating fish stock with expensive vaccines and preventative measures. Thus the overall goal of this project is to build research capacity in UK (and global) aquaculture by developing tools to characterise genomic diversity in disease-causing salmonid viruses and use this genomic information to characterise the dispersal, adaptation and pathogenicity of these viruses. One untapped framework to support the expansion of the salmon aquaculture industry is the use of 'evolutionary epidemiology'. This field attempts to characterise the epidemiology of pathogens using quantitative phylogenetic methods which can lead to data on the origins, transmission and adaptation of viruses. Such approaches have already been used to provide insight into the human diseases caused by Ebola, HIV and influenza-A. However one of the current limitations of using this approach to benefit aquaculture is a lack of tools to effectively and efficiently sequence and analyse genome-scale variation between and within viral strains. Moreover, there is a current lack of detailed insights into how variation in salmonid viruses is ultimately linked to pathogenicity and prospects for disease severity, which might be resolved with a genome-wide investigation. To achieve this goal, our project will develop molecular and computational tools for research of diseases affecting salmonid aquaculture, focussing on the widely present salmonid alphavirus (SAV) and infectious salmon anaemia virus (ISAV). The specific objectives are: 1) To develop tools for viral genome sequencing, rapid diagnostics and analysis of viral diversity using current generation sequencing and bioinformatics tools for assembly and annotation. This approach will generate data by second and third generation sequencing platforms. This work will generate protocols that will be broadly used in the future for applied and fundamental fish virus research. 2) To develop phylogenetic approaches to model viral population dynamics - inferring viral origins, dispersal, transmission routes and population growth. This objective will use newly generated (i.e. under objective 1) and archived sequence data sampled from salmonid farms and the natural environment, including hundreds of salmonid individuals and wild species acting as potential disease reservoirs. This approach will generate new epidemiological insights about salmonid viruses affecting aquaculture. 3) To characterize viral adaptation in the natural environment and under in vitro conditions of cell culture through serial passaging. This approach will identify adaptive sequence variation associated with distinct disease outbreaks and host species, as well as that allowing adaptation to cell culture, which may alter a virus's scope to cause cytopathic effects in vitro and modify pathogenicity in vivo. This will therefore inform a better understanding of the functional-evolutionary basis of salmonid virus pathogenicity.
People |
ORCID iD |
Daniel Macqueen (Primary Supervisor) |
Publications
Gallagher M
(2018)
Nanopore sequencing for rapid diagnostics of salmonid RNA viruses
in Scientific Reports
Gallagher MD
(2020)
Genome-wide target enriched viral sequencing reveals extensive 'hidden' salmonid alphavirus diversity in farmed and wild fish populations
in Aquaculture
Gallagher MD
(2020)
Genome Sequencing of SAV3 Reveals Repeated Seeding Events of Viral Strains in Norwegian Aquaculture.
in Frontiers in microbiology
Gallagher Michael D.
(2020)
New approaches to characterise viral pathogens in aquaculture
Tighe AJ
(2020)
Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7).
in Diseases of aquatic organisms
Studentship Projects
Project Reference | Relationship | Related To | Start | End | Student Name |
---|---|---|---|---|---|
BB/M010996/1 | 30/09/2015 | 31/03/2024 | |||
1804933 | Studentship | BB/M010996/1 | 30/09/2016 | 29/09/2020 |
Description | - An original objective of the project was to develop methods to routinely sequence the whole genomes of viruses affecting salmonids in aquaculture. This has been achieved using multiple methods (e.g. MinION sequencing, Illumina sequence capture). - Viral strain diversity is far higher than previously thought in salmonid alphavirus infections - Human-mediated transmission of virus dominates the spread of SAV between geographically distant farms - Genome sequencing provides much better resolution of the evolution of SAV compared to current standards of sequencing an individual gene for genotyping |
Exploitation Route | Further research is required to determine if there is a link between viral diversity and disease phenotype. Additionally, with the knowledge of much greater genetic diversity, tracking viral transmissions will become more nuanced and will require much denser sampling of infected fish. |
Sectors | Agriculture Food and Drink Environment |
Description | Data from my project has encouraged a non-academic vaccine company in Norway (PHARMAQ) to adopt genomic surveillance techniques of viral epidemics in Norwegian aquaculture. While widespread adoption of such methods has not yet been fully realised in the European aquaculture industry, the ongoing collection of genomic data to understand the changing landscape of viral epidemics (particularly that of SAV) in Norway points to a broader appreciation of infectious disease genomic surveillance efforts. |
First Year Of Impact | 2016 |
Sector | Agriculture, Food and Drink |
Impact Types | Economic |
Description | Funding from Vaxxinova (Vaccine Company). Sequencing of salmonid alphavirus genomes |
Amount | £3,750 (GBP) |
Organisation | Vaxxinova Italia |
Sector | Private |
Country | Italy |
Start | 07/2018 |
End | 08/2018 |
Description | MASTS Small Grants |
Amount | £3,000 (GBP) |
Funding ID | SG406 |
Organisation | Marine Alliance for Science and Technology for Scotland |
Sector | Academic/University |
Country | United Kingdom |
Start | 05/2017 |
End | 07/2017 |
Description | Microbiology Society Conference Grant 2018 |
Amount | £233 (GBP) |
Funding ID | GA000307 |
Organisation | Microbiology Society |
Sector | Learned Society |
Country | United Kingdom |
Start | 02/2018 |
End | 04/2018 |
Description | Novel sequencing approaches to characterize viral diseases in salmon aquaculture: an undergraduate research experience |
Amount | £1,500 (GBP) |
Organisation | Marine Alliance for Science and Technology for Scotland |
Sector | Academic/University |
Country | United Kingdom |
Start | 06/2017 |
End | 07/2017 |
Description | Salmonid alphavirus genomic surveillance in Norwegian Aquaculture |
Amount | £5,714 (GBP) |
Organisation | Pharmaq |
Sector | Private |
Country | Norway |
Start | 07/2020 |
End | 03/2021 |
Title | Nanopore sequencing of aquaculture viruses |
Description | Methods for targeted whole genome sequencing were developed for several economically important aquaculture RNA viruses for use on nanopore MinION sequencing platform. No whole genome sequencing of these viruses had previously been performed using nanopore sequencing. This work also established this method for use in other experimental scenarios and is currently being used for other projects. |
Type Of Material | Technology assay or reagent |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | NA |
URL | https://www.nature.com/articles/s41598-018-34464-x |
Title | Targeted sequence capture of viruses in aquacultured fish |
Description | Using a wide-ranging panel of probes, tiled across the genomes of several important aquaculture-related RNA viruses, a whole genome sequencing approach was established to efficiently enrich for viral nucleic acids. This was validated using a number of viral isolates to detect and characterise multi-viral infections which can produce important industry-regulator information. This approach has allowed us to study viral genetic diversity using an unbiased method unlike any other previously attempted. |
Type Of Material | Technology assay or reagent |
Year Produced | 2018 |
Provided To Others? | No |
Impact | Not applicable yet - the paper is currently in preparation |
Title | Viral genome sequencing |
Description | Whole genomes of salmonid alphavirus sequenced using second and third generation methods |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Ongoing collaborations with industry partners and Marine Scotland Science |
URL | https://www.sciencedirect.com/science/article/pii/S0044848619321970 |
Description | Collaboration on salmonid virus genomics |
Organisation | Marine Scotland Science (MSS) |
Country | United Kingdom |
Sector | Public |
PI Contribution | Analysis of salmonid virus genomes to understand disease transmission and for strain/subtype diagnostics |
Collaborator Contribution | Marine Scotland - co-supervision of PhD, sample and data provision, intellectual input PHARMAQ AS - sample provision, intellectual input |
Impact | In process |
Start Year | 2017 |
Description | Collaboration on salmonid virus genomics |
Organisation | Zoetis |
Department | PHARMAQ AS |
Country | Norway |
Sector | Private |
PI Contribution | Analysis of salmonid virus genomes to understand disease transmission and for strain/subtype diagnostics |
Collaborator Contribution | Marine Scotland - co-supervision of PhD, sample and data provision, intellectual input PHARMAQ AS - sample provision, intellectual input |
Impact | In process |
Start Year | 2017 |
Description | Nanopore whole genome sequencing of a novel SAV subtype |
Organisation | Marine Institute |
Country | Ireland |
Sector | Academic/University |
PI Contribution | Whole genome sequencing of a salmonid alphavirus isolate representing a novel subtype was performed along with bioinformatic and phylogenetic analyses of the resulting genome sequence |
Collaborator Contribution | Provision of the viral isolate, PCR amplicons and downstream analyses of the sequence made by Dr Neil Ruane (sample provision) and Andy Tighe (lab work and data analysis) |
Impact | Research article manuscript in prep currently |
Start Year | 2018 |
Description | Whole genome sequencing of SAV natural and cultured samples |
Organisation | Vaxxinova |
Country | Netherlands |
Sector | Private |
PI Contribution | Whole genome sequencing of SAV isolates before and after cell culture, as well as downstream bioinformatic analyses |
Collaborator Contribution | Provision of viral RNA samples |
Impact | Potential manuscript |
Start Year | 2018 |
Description | Whole genome sequencing of SAV2 and SAV3 isolates on the MinION |
Organisation | Zoetis |
Country | United States |
Sector | Private |
PI Contribution | MinION whole genome sequencing, bioinformatic analysis and phylogenetic analysis of several salmonid alphavirus isolates |
Collaborator Contribution | Viral RNA was provided by PHARMAQ-Analytiq (part of Zoetis), as well as intellectual contributions to the analyses |
Impact | Ongoing project but potential to inform governmental policy surrounding the spread of SAV within Norway |
Start Year | 2018 |
Description | Coordinated meeting of the international 'Functional Annotation of All Salmonid Genomes' initiative |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | This meeting was attended by 30 salmonid biologists linked to the international FAASG initiative (https://www.faasg.org/). Key discussions were held on the future of the initiative, its links to UK infrastructure (EMBL-EBI) and future funding priorities, influencing funders in attendence (Norwegian Research Council and Genome Canada) |
Year(s) Of Engagement Activity | 2019 |
URL | https://icisb.org/faasg-meeting/ |
Description | GCFR Zoonoses Workshop - Talk on rapid Nanopore sequencing of viral pathogens |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | I was an invited speaker at a GCRF Zoonoses workshop held at the University of Aberdeen and hosted by Dr Sandra Telfer. I spoke about my work on using Nanopore sequencing as a rapid and accurate alternative to other sequencing methods in the field. The primary audience were researchers and disease surveillance workers based in Madagascar (who Dr Telfer collaborates with) but also included researchers at the University of Aberdeen and collaborators from research institutes in England |
Year(s) Of Engagement Activity | 2017 |
Description | Lead coordinator of the fourth International Conference on the Integrative Biology of Salmonids (https://icisb.org/). |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | The fourth International Conference on Integrative Salmonid Biology (ICISB 2019), followed on from previous meetings in 2012 (Oslo, Norway), 2014 (Vancouver, Canada) and 2016 (Puerto Varas, Chile). The ICISB meetings have been core funded and organized by the International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG), a trilateral effort between Canada, Chile and Norway. The theme of ICISB 2019 was'Beyond the genome: taking leaps forward in salmonid biology' to reflect the recent staggering progress in genomic resource development and exploitation since the Atlantic salmon reference genome was published in 2016. There was an audience of ~200, which represented a mixture of researchers from Professors leading in the field, to undergraduate students. Many international collaborations and opportunities for further research, funding and meetings were explored with a range of stakeholders, including funders, media and industry. |
Year(s) Of Engagement Activity | 2019 |
URL | https://icisb.org/ |
Description | Oral Presentation at EAFP 2019, Porto |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Third sector organisations |
Results and Impact | I gave a presentation at the EAFP annual conference in Porto, Portugal regarding the use of genome wide sequencing of SAV3 for use in molecular epidemiological studies. The primary audience were members of aquaculture research institutes from around the world, leaders in the industry and government policy makers |
Year(s) Of Engagement Activity | 2019 |
Description | Oral Presentation at PD Trination conference - Bergen March 2018 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | I gave a presentation at the PD Trination conference in Bergen, Norway regarding rapid whole genome sequencing on the Nanopore platform of salmonid alphavirus - the viral agent of an economically important disease in salmon farming. The primary audience were members of Irish, Scottish and Norwegian aquaculture research institutes, leaders in the industry and Norwegian policy makers. |
Year(s) Of Engagement Activity | 2018 |
Description | Oral Presentation at PD Trination conference - Dublin June 2019 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | I gave a presentation at the PD Trination conference in Dublin, Ireland regarding identifying complex viral infections in both wild and farmed fish in Irish and Scottish waters using a targeted sequence capture approach. The primary audience were members of Irish, Scottish and Norwegian aquaculture research institutes, leaders in the industry and Norwegian policy makers. |
Year(s) Of Engagement Activity | 2019 |
URL | https://www.sciencedirect.com/science/article/pii/S0044848619321970 |
Description | Presentation to industry collaborator - PHARMAQ - 29th May 2018 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | I gave a presentation and Q&A session to industry leaders at PHARMAQ Analytiq (part of animal health company Zoetis). This was in direct relation to my work on Nanopore sequencing of RNA viruses which they wanted to explore as a method for disease surveillance in Norwegian aquaculture. |
Year(s) Of Engagement Activity | 2018 |
Description | Seminar at the Infectious disease diagnosis symposium - 14th Nov 2018, University of Edinburgh. Talk "'Advanced sequencing diagnostics of salmon viral disease reveals unrecognized strain diversity affecting aquaculture" |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Postgraduate students |
Results and Impact | I gave a talk titled "Advanced sequencing diagnostics of salmon viral disease reveals unrecognized strain diversity affecting aquaculture'. The purpose was to outline the progress made in our understanding of fish virus genetic diversity at the whole genome level, gained from the BBSRC award in question (Mike Gallagher's PhD). The audience was diverse, ranging from medical practitioners working in diagnosics, to researchers working on improving animal production. |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.ed.ac.uk/vet/news-events/events/infectious-disease-diagnosis-symposium-programme |
Description | Seminar at the Roslin Institute |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Other audiences |
Results and Impact | I gave a seminar at the Roslin Institute, which was an overview of my PhD research to date. The seminar is weekly and is pitched at other members of the Roslin Institute but not necessarily experts in my field. I presented my work on rapid whole genome sequencing as well as characterising the genetic diversity found in natural viral infections in salmon farming. |
Year(s) Of Engagement Activity | 2019 |
Description | Seminar at the Roslin Institute: "Farmed Fish Integrative Genomics" |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Other audiences |
Results and Impact | I gave a seminar at the Roslin Institute, which was an overarching overview of the major research projects in my lab. The seminar was linked to job vacancy, so pitched towards the relevance of my work to BBSRC/UKRI remit and the interests/remit of the Roslin Institute. I was succesful in getting the position (Reader, University of Edinburgh), so a major impact followed this seminar. |
Year(s) Of Engagement Activity | 2018 |