66 results
Industry
Adoption
PROJECT NUMBER • 2018-127
PROJECT STATUS:
COMPLETED

Validation and implementation of rapid test kits for detection of OsHV-1

Following the outbreak of Pacific Oyster Mortality Syndrome (POMS) in the Port River, South Australia in summer 2017-18, a need was identified for rapid diagnostic technology for OsHV-1, the causative agent of POMS. During the February 2016 OsHV-1 outbreak in Tasmania, tracing activities in...
ORGANISATION:
SARDI Food Safety and Innovation

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.
Industry
PROJECT NUMBER • 2016-801
PROJECT STATUS:
COMPLETED

Future oysters CRC-P: Enhancing Pacific Oyster breeding to optimise national benefits

The research was conducted as a direct consequence of the 2016 Pacific Oyster Mortality Syndrome (POMS) outbreak TAS which decimated parts of this State’s Pacific Oyster (Crassostrea gigas) industry and caused numerous flow on effects throughout the entire Australian industry. The project was...
ORGANISATION:
Australian Seafood Industries Pty Ltd (ASI)
Industry
PROJECT NUMBER • 2019-147
PROJECT STATUS:
COMPLETED

Risk factors and management strategies associated with summer mortality in Australian abalone

In this project, we reviewed the scientific literature and collaborated with Australian abalone growers to develop a case definition for summer mortality. The case definition developed for summer mortality is as follows: i. Chronic mortality of unknown cause (if in doubt take this to mean...
ORGANISATION:
University of Adelaide
Communities
PROJECT NUMBER • 2017-098
PROJECT STATUS:
COMPLETED

Southern Bluefin Tuna: Changing The Trajectory

Life on the Line is the true story of the Southern Bluefin Tuna, its biological traits and its history of exploitation and most recently its recovery. This documentary covers how research, managers and the fishing industry - commercial and recreational have contributed to the recovering status of...
ORGANISATION:
Australian Fisheries Management Authority (AFMA)
Industry
PROJECT NUMBER • 2018-102
PROJECT STATUS:
COMPLETED

Understanding Ostreid herpesvirus type 1 risk: alternative hosts and in situ hybridisation

South Australia (SA) has a large edible oyster industry primarily growing Pacific oysters (Crassostrea gigas). The industry is regionally-based, an important employer and a substantial contributor to regional economies. Pacific oyster mortality syndrome (POMS) is a serious infectious disease of C....
ORGANISATION:
Flinders University
Environment
PROJECT NUMBER • 2017-127
PROJECT STATUS:
COMPLETED

NCCP: defining best practice for viral susceptibility testing of non-target species to Cyprinid herpesvirus 3 -a discussion paper based on systematic quantitative literature reviews

This report based on systematic quantitative literature reviews aims to identify best practice for testing to determine the viral susceptibility of non-target species to CyHV-3. 
ORGANISATION:
University of Adelaide Roseworthy Campus
Adoption
PROJECT NUMBER • 2017-233
PROJECT STATUS:
COMPLETED

Future Oysters CRC-P Communication and Adoption

The Future Oysters CRC-P project (CRC-P 2016-553805; Future Oysters) was funded by the Australian Government’s Business Cooperative Research Centres (CRC) Program, which is managed by the Department of Industry, Innovation and Science (DIIS). The Future Oysters CRC-P project was developed to...
ORGANISATION:
Australian Seafood Industries Pty Ltd (ASI)
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