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Aquatic Animal Health and Biosecurity Coordination Program: strategic planning, project management and adoption

Project number: 2020-052
Project Status:
Current
Budget expenditure: $605,748.56
Principal Investigator: Nicholas J. Moody
Organisation: CSIRO Australian Animal Health Laboratory
Project start/end date: 23 Jun 2022 - 31 May 2026
Contact:
FRDC

Need

Australia’s aquatic animals are free from many diseases that occur overseas, providing us with a competitive advantage in both production and trade. Australian aquaculture has grown from an industry valued at AU$260 million in 1993 to an industry valued at AU$1.6 billion in 2020 (ABARES, 2021). This dramatic growth has been accompanied by the emergence of new diseases/infectious agents, e.g., NNV since 1989, Bonamia since 1992, OOD since 2006, OsHV since 2010, POMV since 2012, new YHV genotypes since 2013, PMMS since 2015 and WSD since 2016, all of which threaten the sustainability of major aquaculture enterprises. Consequently, the need for health research to support this expanding sector is also growing. The wild-harvest, recreational, Indigenous and ornamental sectors are also under threat; e.g., crayfish plague, Edwardsiella ictaluri in catfish, Perkinsus in oysters, WSD in crustacea and gourami iridovirus in a range of finfish species pose significant risks.

Thus, identification and prioritisation of aquatic animal health and biosecurity research and capacity building needs to be coordinated across all aquatic sectors to ensure synergy while avoiding duplication. FRDC, through AAHBRCP, plays a major role in addressing research needs and training in aquatic animal health and biosecurity and is able to direct funding priorities to the most pressing areas. AAHBRCP provides a cohesive national approach to FRDC-supported R&D by providing leadership, direction and focus for health R&D and other related non-R&D activities. According to an external review of AAHBRCP undertaken in 2015 the consensus among major stakeholders was that AAHBRCP provides an essential service for the aquatic animal sector. Given the success of the AAHBRCP there is a need to continue it as a means of providing the service with consideration given to adjustments (reflected in this proposal) to enhance the service it provides for the evolving needs of Australia’s seafood industry, public policy and program needs

Objectives

1. In consultation with key stakeholders (industry, government, aquatic animal health providers and industry representatives) identify and prioritise R&D needed to deliver national, jurisdictional and industry sector aquatic animal health and biosecurity related planning objectives
2. Promote and manage aquatic animal health and biosecurity training and capacity building
3. Facilitate the dissemination of outputs (information and results) from R&D projects to key stakeholders
4. Through the biannual AAHBRCP scientific conference, cultivate research community collaboration, engagement, and foster early career researchers.

Diagnostic detection of aquatic pathogens using real-time next generation sequencing

Project number: 2018-147
Project Status:
Current
Budget expenditure: $216,000.00
Principal Investigator: David Cummins
Organisation: CSIRO Australian Animal Health Laboratory
Project start/end date: 30 Jun 2019 - 28 Oct 2021
Contact:
FRDC

Need

Current diagnostic programs generally rely on highly -specific assays for pathogen detection. While these techniques are invaluable, they are one dimensional and do not provide detailed information critical to a disease investigation. These gaps include the inability to detect unknown pathogens and potential variants of know pathogens and provide no additional genomic or transcriptomic data. Moreover, samples must be shipped to trained personnel in a laboratory, further delaying the time to diagnosis. The MinION, on the other hand, can theoretically detect any pathogen and can potentially be deployed to the field. Moreover, the MinION can rapidly generate full-length genomes, allowing for epidemiological tracking of viral or bacterial strains in near real-time. Such rapid data, which cannot be obtained as quickly using existing methods, are vital if the intention is to intervene in an outbreak and reduce impacts on the productivity and profitability of aquaculture facilities. For example, a rapid, early diagnosis may allow mitigating actions to be taken on-farm, such as the diversion of intake water, movement restrictions of stock and the isolation of infected ponds.
These qualities make the MinION an attractive complimentary platform to fill several gaps in the data obtained during disease outbreak investigations, or routine diagnostics, and potentially for use in the field. However, results from the misuse or lack of understanding of the technology could also have adverse regulatory implications for aquaculture industries. For example, without appropriate guidelines, an inexperienced diagnostician may misinterpret a distant DNA match in a pathogen database as a significant result, this may create unwanted attention to industry and potential stock destruction or changes to disease status that are unjustified. Thus, it is critical that the MinION is evaluated at the Australian Animal Health Laboratory, and guidelines and procedures are developed for accurate diagnostic evaluations. The activities detailed in this application will establish the feasibility of using the MinION for diagnostic applications, and ensure that the data is reliably generated and interpreted appropriately.

Objectives

1. Evaluate if MinION data meets or exceeds the data obtained using established laboratory-based NGS platforms. Objectives (1) and (2) align with Methods section (1).The first objective of this project is to demonstrate if the MinION can obtain quality genome assemblies of known pathogens, such as WSSV, AHPND, OsHV-1 and HaHV that have been created using existing NGS technology. Moreover, determine if the MinION is capable of producing a diagnostic result more rapidly and with greater confidence than traditional techniques. STOP/GO POINT: If MinION data does not produce reliable genome assemblies, no improvement in genome quality, or is significantly more laborious to set-up/run or analyse than existing NGS technologies, do not proceed with objective 2.
2. Evaluate the performance of the MinION using existing diagnostic extraction techniques and produce robust methods and protocols for sample preparation, sequencing and data analysis. This objective will optimise MinION protocols for sample pre-processing, optimal sequencing conditions, and data post-processing. We will then evaluate the MinION data produced from a range of aquatic organisms against data produced using traditional techniques from the same samples. STOP/GO POINT: If after these optimisations, the MinION cannot detect pathogens as reliably as traditional techniques, do not proceed with objective 3.
3. Compare the applicability of MinION to standard molecular assays for identification of pathogens in diagnostic samples. Objective (3) is aligned with Methods section (2).In this objective, diagnostic samples will be tested using existing diagnostics tools (qPCR, cPCR) and MinION sequencing. Analysis between the methods will be detailed, including time to result, pathogen identity and genomic information. This objective will not only provide an insight into real-time sequencing for diagnostics, but in addition the feasibility of MinION technology for field application in the future.
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