In 1995, global production from aquaculture reached 27.8 million tones and was valued at US$ 42,300 million. Developing countries contributed over 87% of total production, of which 90.1% was from Asia. China contributed 63.4% of total world production. Over the past decade, global aquaculture production has grown at an average annual rate of 9.6% compared to 3.1% for livestock meat and 1.6% for capture fisheries. Between 1984 and 1995, growth in aquaculture production in low-income food deficit countries (LIFDCs) was over five times faster than in developed countries (Rana, 1997).
Disease outbreaks are recognized as a significant constraint to aquaculture production and trade, affecting both the economic development and socioeconomic revenue of the sector in many countries in the world. According to Chamberlain (in press), disease is a primary limiting factor for shrimp farming today and the risk of disease losses is likely to increase as the shrimp sector continues to grow. Economic loss attributed to outbreaks of disease in developing countries in the Asian region was estimated to be at least US$ 1,400 million in 1990 (ADB/NACA, 1991). The cost of lost production in China alone was approximately US$ 1,000 million in 1993. In Thailand, the loss in 1996 due to yellow head virus (YHV) and white spot syndrome virus (WSSV) was estimated to be 40% of total production (70,000 tones) valued at over US$ 500 million (Alday-Sanz and Flegel, 1997). Recent estimates, based on farm level surveys in 16 Asian countries, suggest that disease and environment-related problems have caused annual losses of more than US$ 3,000 million to aquaculture production (ADB/NACA, in press). Serious financial losses have also been recorded in other regions of the world. In 1993, Ecuador lost 28,000 tones of shrimp production in due to an epizootic of Taura syndrome virus. Salmon farming in many countries also faced serious disease problems that resulted in significant production losses. Various factors have been related to the apparent increased incidence of disease. Environmental factors and poor water quality, sometimes resulting from increased self-pollution due to effluent discharge and pathogen transfer via movements of aquatic organisms appear to be an important underlying cause of such epizootics.
The effective control and treatment of diseases of aquatic animals requires access to diagnostic tests that are rapid, reliable and highly sensitive. In many cases, post-mortem necropsy and histopathology have been the primary methods for the diagnosis of fish and shellfish diseases. However, these methods often lack specificity and many pathogens are difficult to detect when present in low numbers or when there are no clinical signs of disease (Ambrosia and De Wall, 1990). Direct culture of pathogens is also widely used. However, these methods are time-consuming and costly, and, for shrimp and other crustaceans, cell lines suitable for virus culture have not been available.
Efforts to overcome these problems have led to the development of immunoassay and DNA-based diagnostic methods including fluorescent antibody tests (FAT), enzyme-linked immunosorbent assays (ELISA), radioimmunoassay (RIA), in situ hybridization (ISH), dot blot hybridization DBH) and polymerase chain reaction (PCR) amplification techniques. The use of DNA-based methods derives from the premise that each species of pathogen carries unique DNA or RNA sequences that differentiate it from other organisms. The techniques offer high sensitivity and specificity, and diagnostics kits allowing rapid screening for the presence of pathogen DNA are moving rapidly from development in specialized laboratories to routine application. DNA probes are expected to find increasing use in routine disease monitoring and treatment programs in aquaculture, in field epidemiology and in efforts to prevent the international spread of pathogens (national quarantine and certification programs).
DNA-based methods have been used in diagnosis and for detection of many economically important viral pathogens of cultured finfish and penaeid shrimp. For finfish, tests have been developed for pathogens such as channel catfish virus (CCV), infectious hematopoietic necrosis virus (IHNV), infectious pancreatic necrosis virus (IPNV), viral hemorrhagic septicemia virus (VHSV), viral nervous necrosis virus (VNNV) and Renibacterium salmoninarum (see Muroga, 1997; Plumb, 1997). PCR has been used in Japan to screen striped jack (Pseudocaranx dentex) broodstock for VNNV, permitting selection of PCR-negative spawners as an effective means of preventing vertical transmission of this pathogenic virus to the larval offspring (Muroga, 1997).
DNA-based detection methods for detection of penaeid shrimp viruses are now used routinely in a number of laboratories around the world. These include probes for such diseases as white spot syndrome virus (WSSV), yellow head virus (YHV), infectious hematopoietic and infectious hypodermal and haematopoeitic necrosis virus (IHHNV) and Taura syndrome virus (TSV) which pose the greatest threat to world shrimp culture production (Lotz, 1997). DNA probes have also been developed for an intracellular parasites and bacteria infecting shrimp. DNA-based techniques will have an important role to play in efforts to develop sustainable shrimp culture in Asia and elsewhere. Production facilities in Thailand are currently using PCR techniques to screen shrimp post-larvae for WSSV. Culturing such larvae in closed (biosecure) or semi-closed culture systems can prevent or minimize viral infections, leading to a viable shrimp industry. The development of specific pathogen-free shrimp stocks will also depend on the use of such techniques.
The further development and use of DNA-based diagnostic techniques will also assist international efforts to control the introduction of exotic diseases into new geographic areas. Reliable and rapid techniques are needed by national and regional diagnostic laboratories to screen imported fish and shellfish for important pathogens. The Office International des Epizootics (OIE) or World Animal Health Organization, is a veterinary organization with 147 member countries. The OIE (through its Fish Diseases Commission) is responsible for tracking diseases of fish and shellfish that have a serious economic impact on aquaculture and capture fisheries. There is considerable potential to apply DNA-based methods for OIE testing if they can meet the stringent criteria of a standardized, validated, accurate, reliable and accessible diagnostic technique.
Although offering considerable potential, the routine use of DNA-based diagnostic techniques is hampered by a number of potential problems (Chanratchakool et al., 1998).
The extreme sensitivity of these methods allows the detection of target DNA present at very low levels. However, positive results provide little quantitative assessment of the infection level, and do not indicate whether the pathogen is replicating or causing disease in the species tested. Thus, carrier status and viability of the pathogen are not determined using DNA-probes.
The extremely high specificity of these tests, coupled with the ability of many viruses to rapidly change in genetic structure, can result in failure to detect a virus that has altered its genetic profile.
Large differences in sensitivity are related to the PCR method used (e.g., 1-step PCR or 2-step PCR with nested primers).
PCR methodologies are highly susceptible to contamination. Contamination during processing may result in false positives, particularly in 2-step PCR methods. PCR tests must be conducted in very well managed, clean laboratories.
"False negatives" are easily caused by the selection of inappropriate host tissue sources for detection of the pathogen in question, incorrect choice of DNA extraction method, or low pathogen prevalence in the population sampled.
DNA-based detection and diagnostic methods have the potential for widespread application of in aquaculture. As the technology is already being adopted rapidly in developing countries in Asia, there is an urgent need to address these issues and to develop an action plan for research and training activities that will facilitate more effective utilization.