Presently, most bacterial diseases of eel (Anguilla japonica) are controlled by antibiotics. However, antibiotics not only kill the bacterial pathogens but also kill those bacteria which might be beneficial to eels. In the meantime, application of antibiotics may result in spreading and accumulation of the resistance genes which may in turn lower the efficacy the antibiotics in the future and may threat public health. The recent trend to such problems is to screen non-pathogenic bacteria which are competitive to the pathogenic bacteria in the same environments. The eel pathogen, Edwardsiella tarda, was chosen as the target in this study. Bacterial strains were isolated from different eel ponds and tested for the ability to inhibit the growth of E. tarda. Of 2,412 strains tested, eight of them showed the inhibition capability. The molecular weights of the bioactive ingredients are all smaller than 12,000 daltons indicating they are not protein in nature. One of the strains is Bacillus cereus, four of the strains are Bacillus sphaericus, two of the strains are Bacillus laterosporus, and one of the strains of identified as Pseudomonas areuginosa competed extremely well with E. tarda. These antagonistic bacteria may have the potential of becoming as bio-control agents.Tiger shrimp (Penaeus monodon) is an important agricultural product in Taiwan. The over all production peaked in 1988, since then the outbreak of viral infection has caused the shrimp aquaculture a heavy damage. The current production is merely 1/10 of the peak. Many solutions were proposed to solve the problem, such as: increase the immunity of the shrimp, study pumping of the underground water has caused serious land subsidence in the coastal areas. Therefore, conservation of water is the trend of current aquaculture. In this study, culturable bacteria were isolated from a closed tiger shrimp pond. The taxonomy of the bacteria was based on 16S rDNA sequence phylogeny. Roughly 8 groups (genera) of bacteria were identified, including: Vibrio, Pseudoalteromonas, Porphyrobacter, Flavobacterium, Rhodthermus and three uncertain genera.

Three experiments were conducted to evaluate the effects of dietary chitin and chitosan on growth, immune responses and resistance of grass prawn Penaeus monodon against white spot syndrome virus (WSSV) and Vibrio infections. In the first experiment, two levels (0.5¡B1 g/100g diet) of chitin and three levels (0.5¡B1¡B5 g/100g diet) of chitosan were evaluated. The results show that weight gain of the shrimp fed on diet containing no chitosan or the lowest level of chitosan (0.5 %) was higher than other groups. In the second experiment, four levels of chitosan (0¡B0.5¡B1¡B5 g/100g diet) were tested. Weight gains of the control (0 %) and 0.5 % chitosan groups were significantly (P<0.05) higher than the 0.1 and 1 % chitosan groups. Shrimp survival rate was not influenced by chitosan inclusion. The test shrimp of the first experiment were evaluated for their immune responses after dietary exposures. The results show that phenoloxidase activity and superoxide dismutase were not significantly different (P>0.05) among treatments. The production of superoxide anion in the 0.5 % chitin group was significantly (P<0.05) lower than the other groups at day 3 and 12. The last experiment evaluated the effectiveness of dietary chitosan against infection of WSSV and Vibrio damsela. Shrimp were fed for 20 days on test diets containing four levels of chitosan (0¡B0.5¡B1¡B5 g/100g diet) and then challenged by injection of WSSV or Vibrio solution. In the WSSV challenge, except at day 7, shrimp survivals were not different among treatments. At day 7, however, the survival rates of the shrimp fed the diet containing 0.1 or 1 % chitosan were significantly (P<0.05) higher than those of the other groups. When challenged with Vibrio damsela, there was no difference in shrimp survival among dietary treatments. The present study shows that dietary chitin and chitosan do not significantly enhance immune responses and disease resistance of juvenile P. monodon. Dietary incorporation of chitin or chitosan negatively affects shrimp growth.

Sex-specific nutritional requirements for crude protein and fat were demonstrated in cultured (F1) Penaeus stylirostris brood stock. Female shrimp required diets which had higher protein (32 versus 27%), lower fat (2.5 versus 3.9%), higher protein/calorie ratios (8.5 versus 6.8% protein/kcal/g), and much higher protein/fat ratios (15.4 versus 7.8% protein/% fat) than males. These studies have also demonstrated a nutritional demand corresponding to the onset of ovarian maturation, a phenomenon which was explained as a reduction in growth rates at the attainment of 30 to 35 g in shrimp fed deficient diets. Both the quality and the quantity of dietary fat were shown to affect the growth of P. stylirostris brood stock. Male growth was positively correlated with the quantity of eicosapentaenoic acid (20:5 ω3) in the diets. The females were not affected by the types of fatty acids in the fat; they were influenced more by the quantity of fat, i.e., as the fat level of the diet increased, the growth decreased. Cold extrusion feed (CEF) diets supplemented with squid, and diets which included squid as one of the ingredients in the formulation, were found to stimulate better growth in both male and female brood stock as compared to CEF diets of equal protein and fat content without squid. The protein/fat ratio, as well as the content of polyunsaturated fatty acids (PUFA), were suggested to be responsible for the improved growth. Comparisons were made between the quality of spawns from wild P. stylirostris matured in captivity (P1) and F1 shrimp. Protein levels of the eggs did not correlate with either the number of eggs spawned or the eclosion rate. The number of the eggs spawned was correlated positively with the levels of eicosaenoic acid (20:1 ω9) in both P1 and F1 eggs, and correlated negatively with linoleic acid (18:2 ω6) in P1 eggs only. Spawning times were reported to occur later in the evening as summer approached. A significant, negative correlation was observed between the elapsed time from copulation, i.e., collection of fertilized shrimp, to spawning and eclosion rate. Also, a significant positive correlation was observed between the number of spawns which contained eggs which did not hatch, and the elapsed time from copulation to spawning. The number of eggs spawned and the eclosion rate were found to be higher in P1 shrimp as compared to F1 shrimp. Also, first breeding season spawners (FBS) had better quality spawns than second breeding season (SBS) spawners, i.e., more eggs with higher eclosion rates. A general reduction in the quality of the spawns was therefore implicated as a result of the culture conditions. Multiple spawning behavior was observed and there appeared to be no qualitative or quantitative difference between spawns. Tank size and shape were demonstrated to affect the onset of ovarian development and the transfer of the spermatophore. A minimum of three meters was thought to be required for the development of the ovaries and the successful transfer of the spermatophore.

Clinical signs and lesions of Taura syndrome virus (TSV) infection in Penaeus monodon were investigated by histological and in situ hybridization (ISH) analyses. Mortality among P. monodon inoculated with 2 genotypic variants of TSV (Th04Pm and Th04Lv) appeared on Day 3, with 2 out of 10 shrimp dying. Severe necrosis of cuticular epithelial cells and lymphoid organ spheroids, indicative of acute and chronic phase lesions of TSV infection, respectively, were detected in the samples. Both Th04Pm and Th04Lv belonged to a phylogenetic family of Asian TSV isolates. The results demonstrate that both mortality and histological lesions are associated with TSV infection in P. monodon.Infection with 4 genotypic variants of TSV (Bz01, Th04, UsHi94, and Ve05) in TSV-resistant (TSR) and TSV-susceptible (Kona) Litopenaeus vannamei was investigated. Survival probabilities of TSR shrimp were higher than those for Kona shrimp with all 4 variants. Th04, UsHi94, and Ve05 gave no Taura syndrome lesions with TSR shrimp. In contrast, TSR shrimp challenged with Bz01 and Kona shrimp with all 4 TSV variants exhibited severe necrosis of cuticular epithelial cells and lymphoid organ spheroids. Real-time reverse transcription polymerase chain reaction (RT-PCR) revealed that mean TSV copy numbers in TSR shrimp infected with Bz01, Th04, and UsHi94 were significantly (p &lt; 0.0005) lower than those in Kona shrimp. In contrast, mean TSV copy numbers in TSR and Kona shrimp infected with Ve05 were not significantly different (p &gt; 0.4). The results show that TSR L. vannamei are susceptible to infection but give high survival rates following challenge by all 4 variants of TSV.To identify the viral replication site within shrimp infected cells, the viral RNA was located in association with virus-induced membrane rearrangement by electron microscopic ISH. Ultrastructure in the infected cells, analyzed by transmission electron microscopy, included the induction and proliferation of intracellular vesicle-like membranes, while the intracytoplasmic inclusion bodies and pyknotic nuclei were frequently seen. TSV RNA and TSV particles were found to be associated with the membranous structures. The results suggest that the proliferating membranes carry the RNA replication complex and that they are the site of nascent viral RNA synthesis.

Tesis para optar al grado de Magíster en Ciencias Agropecuarias mención Producción Agroindustrial / En Chile, el consumo de camarones aumentó las importaciones del año 2001 al 2011. Dada esta intensificación, es relevante generar información sobre la preferencia de consumidores chilenos, hacia atributos de camarón blanco importado. El objetivo fue analizar el comportamiento del consumidor de camarón en el mercado chileno: segmentos y preferencias. El diseño fue observacional y de tipo transversal exploratorio. Se utilizó una muestra no probabilística por conveniencia de 400 consumidores pertenecientes a la comuna de Santiago Centro, Región Metropolitana. La principal fuente de información: fue una encuesta, con preguntas 100% cerradas. Se analizaron las respuestas utilizando métodos multivariables y estadística descriptiva. Estableciendo la mayor tendencia del consumo; siendo la ocasional con 66,2%, seguida de mensual 25,2% y semanal 8,5%. La cantidad frecuentemente consumida es ½ a 1 kg, seguida de menos ½ kg; de tamaño mediano (36/50), seguido de grande (21/35) y pequeño (51/70). Para la segmentación se usó el análisis de conglomerados jerárquico, utilizando pruebas Tukey, Dunnett, y Chi-cuadrado (P< 0,05). Se determinó la existencia de cuatro segmentos basado en actitudes hacia el consumo: segmento 1(36,5%), segmento 2 (23,8%), segmento 3 (14,5%) y segmento 4 (25,3%). Se utilizaron los factores obtenidos en el análisis factorial (KMO 0.71) y estableciéndose que en dos segmentos se tienen actitudes positivas para el país de origen y otros dos segmentos consideran muy importante el precio. En tres segmentos existe una valoración positiva hacia el camarón pelado y desvenado y otros los sellos de garantía de calidad. Estableciendo que existe una relación de dependencia entre ingresos familiares y frecuencia de compra. Finalmente la determinación de preferencias, se estableció a través del análisis conjunto, utilizando representaciones visuales en 11 tarjetas, evaluando los atributos: país de origen (Ecuador, Guatemala, China), valor agregado (camarón entero y colas) proceso (cocido y crudo), con tres precios hipotéticos del camarón. El producto ideal fue la combinación de: colas de camarón, cocidas, de origen ecuatoriano y una leve valoración positiva en precios. En virtud de lo expuesto se establecieron orientaciones de desarrollo comercial, basados en las actitudes en función a la segmentación. / In Chile, the consumption of shrimp increased the imports from 2001 to 2011. Given this intensification, it is relevant to generate information regarding the preference of Chilean consumers. The objective was to analyze the behavior of shrimp consumers in the Chilean market. A non-probabilistic sample by coexistence of 400 consumers that belong to the community of the center of Santiago, Metropolitan region was used. The main information source was a survey with 100% closed-ended questions. The answers were analyzed using multi-variable methods. Establishing the highest consumption trend, where 66.2% occasional, followed by 25.2% monthly, and 8.5% weekly. The amount frequently consumed is from ½ to 1 kg, followed by less than ½ kg of middle size (36/50), followed by big (21/35) and small (51/70). For the segmentation, the analysis of hierarchical conglomerates, using Tukey’s, Dunnett and Chi-square tests (P< 0,05) was carried out. The existence of four segments based on attitudes towards the consumption was determined: segment 1 (36.5%), segment 2 (23.8%), segment 3 (14.5%) and segment 4 (25.3%). The factors obtained in the factorial analysis (KMO 0.71) were used and it was established that there are positive attitudes in two segments towards the country of origin, and two other segments consider the price as very important. There is a positive valuation towards peeled and deveined shrimp in three segments, and other quality guarantee seals, establishing that there is a positive correlation between the family incomes and purchase frequency. Finally, the preference determination was established through the conjoint analysis using visual representations in 11 cards, evaluating the attributes: country of origin (Ecuador, Guatemala, and China), added value (whole shrimp and tails) process (cooked and uncooked), with three hypothetical prices of shrimp. The ideal product was the combination of: tails and cooked, Ecuadorian shrimp and positive price valuation. Consequently, commercial development orientations were established.

The immunostimulatory property of glucan isolates from three marine yeasts (Debaryomyces hansenii S8, Debaryomyces hansenii S169 and Candida tropicalis S186) and one Baker's yeast (Saccharomyces cerevisiae S36) as examined for potential application as immunostimulants in Penaeus monodon postlarvae against White Spot Syndrome Virus (WSSV) infection. Structural characterization of the glucan component in the isolates by proton nuclear magnetic resonance (NMR) indicated similar structures containing (1-3)-linked anhydroglucose repeat units (AGRUs) in the backbone with (1-6)-linked AGRUs in side chains that are (1-6)-linked to the backbone AGRUs. Glucan from C. tropicalis (S186) with the highest molecular weight and the lowest level of branching supported maximum survival (69%) followed by the other two marine yeast (S169 and S8) glucans of 27% and 23% respectively while glucan from Baker's yeast, S. cerevisiae S36 with the lowest molecular weight and the highest level of branching exhibited poor survival (4%) in P. monodon post challenge WSSV. The present study showed that the glucan isolate from marine yeast with a higher molecular weight and a lower degree of branching acts as better immunostimulants in P. monodon postlarvae than did the glucan isolate from S. cerevisiae.

Le bruissement enzymatiques, appelé mélanose post mortem chez les crustacés est un phénomène enzymatique catalysé par des protéines à activités phénoloxydases (tyronase, catécholase, laccase et hémocyanine). L'utilisation de conservateurs de type sulfites (E220 à E228 et E539) reste à l'heure actuelle la solution la plus répandue pour éviter le développement de cette coloration peu attrayante pour le consommateur. Mais une partie de la population développe des réactions d'hypersensibilité en consommant des aliments sulfités. Dans l'onbjectif de rechercher une alternative à ces conservateurs, deux axes de recherche ont été développés durant ces travaux de thèse : la caractérisation biochimique des protéines responsables de la mélanose post mortem chez la crevette P. monodon, puis la recherche de molécules inhibitrices. Un fractionnement sur résine Phenyl Sepahrose™ CL-4B (HIC) suivie d'une séparation par électrophorèse SDS-PAGE ont montré la présence de trois protéines de 46, 82 et 89 kDa à activité principalement laccase. Une identification par RP-HPLC-Q/TOF a mis en évidence la présence d'hémocyanine uniquement. Un pH de 7,0 et une température comprise entre 37 et 50 °C ont mis en évidence les activités les plus importantes, en utilisant le dosage enzymatique dit "test au MBTH". Par ailleurs, un criblage à haut débit de 45 molécules potentiellement inhibitrices a été réalisé dans des conditions d'analyses standardisées grâce à l'outil de robotique de la plateforme Realcat. Une inhibition a été mise en évidence pour 23 composés, certains étant suffisamment efficaces pour être utilisés seuls. D'autres pourraient être introduits dans un cocktail de molécules inhibitrices aux fonctionnalités complémentaires. Les résultats des tests de trempage réalisés sur des crevettes entières ont montré qu'il était indispensable de compléter les études in vitro avec des essais à l'échelle de la matrice alimentaire dans son intégralité. / Enzymatic browning, called post mortem melanosis in crustaceans, is an enzymatic phenomenon catalyzed by proteins with phenoloxidase activities (tyronase, catecholase, laccase and hemocyanin). The use of sulfite preservatives (E220 to E228 and E539) remains at present the most widespread solution to avoid the development of this unattractive color towards consumers. But, a part of the population develops hypersensitivity reactions by consuming sulfited foods. With the objective to find an alternative to these conversators, two research axes have been planned : the biochemical characterization of the proteins responsible for post mortem melanosis in the P. monodon shrimp, then the search for inhibitory molecules. Fractionation on Phenyl Sepahrose™ CL-4B resin (HIC) followed by SDS-PAGE electrophoresis separation showed the presence of three proteins of 46, 82 and 89 kDa with mainly laccase activity. Identification by RP-HPLC-Q / TOF revealed the presence of hemocyanin only. A pH of 7.0 and a temperature between 37 and 50 °C showed the most important activities, using the enzymatic assay called "MBTH test". On the other hand, a high throughput screening of 45 potentially inhibitory molecules could be performed under standardized analysis conditions thanks to the robotic tools of the Realcat platform

Includes glossary of notation and glossary of terms. / Bibliography: p. 297-311. / xvii, 330 p. : ill., maps ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / This thesis reports the development, testing and application of computer programs for simulating dispersion in coastal seas, with particular application to larvae of the western king prawn (Pencieus latisulcatus) in Spencer Gulf, South Australia. / Thesis (Ph.D.)--University of Adelaide, Dept. of Applied Mathematics, 1996?

Yellow head virus (YHV) is highly pathogenic and was identified as the cause of mass mortalities associated with yellow head disease (YHD) that first appeared in Penaeus monodon farmed in Thailand in 1990. By 1992-1993, YHD was widespread throughout the Thai shrimp farming industry, causing losses estimated at ~US$70 million per annum. By the mid 1990s, gross signs consistent with YHD were also being reported in P. monodon farmed in many regions of the Indo-Pacific. Due to its high pathogenicity and economic impact, YHV has been listed as a notifiable pathogen by the OIE and the control of YHD remains a significant concern. At the outset of this study, two genotypic variants of YHV (genotype 1) had been detected in P. monodon in Australia (gill-associated virus, GAV, genotype 2) and Vietnam (genotype 3), suggesting that more variants might exist in other regions. The aim of this study was, therefore, to test the hypothesis that genotypic variants existed in P. monodon from other locations, and if so, to determine their genetic relationships to the three known genotypes. The study also aimed to improve existing PCR diagnostic protocols to accommodate the detection of all genotypes in the YHV complex. Fifty-seven field isolates of YH-complex viruses were detected by RT-PCR in tissues of P. monodon sampled from nine Indo-Pacific countries. Phylogenetic relationships determined for these isolates using a 671 nucleotide (nt) C-terminal region of the ORF1b gene identified 46 isolates that clustered with the three know genotypes and 11 isolates that clustered in at least three distinct new genotypes. All isolates other than genotype 1 (YHV) were detected in tissues of healthy shrimp. Genotype 4 isolates were detected only in shrimp from India and were slightly less distantly related at the nucleotide level to genotype 5 (85.2% identify) than the other genotypes (80.3%-82.3%). Genotype 6 isolates were only detected in shrimp from Mozambique and were least divergent (3.5%) from genotype 2. One each of three genotype 5 isolates was detected in shrimp from Malaysia, Thailand and the Philippines. The genotype 5 isolate from the Philippines was, however, 6.7% and 7% divergent from the other two isolates, respectively. This level of divergence was greater than found between genotypes 2 and 6 and was similar to that found between isolates of genotype 2 and genotype 3 (~6.7%). This suggests that the Philippine genotype 5 isolate might ultimately be considered as the founding member of a seventh genotype. Genotype 5 isolates were slightly more closely related to genotype 4 (~85.2% identity) than the other genotypes (83.4%-84.8% identity). Genotype 1 (YHV) isolates were only detected in Thai shrimp affected by YHD. Genotype 2 isolates were detected in Australian shrimp as well as shrimp from Vietnam and Thailand. Genotype 3 had the broadest geographic range, being detected in four countries in Southeast Asia. The finding of single genotypes in Australia (genotype 2), India (genotype 4) and Mozambique (genotype 6) supports the hypothesis that they have evolved independently in geographically-isolated populations of P. monodon. The detection of multiple genotypes in Vietnam (genotypes 2 and 3), Malaysia (genotypes 2, 3 and 5) and Thailand (genotypes 1, 2, 3 and 5) suggests that these genotypes have been disseminated by movements of infected P. monodon and the trade in live broodstock used for aquaculture. A ~1.3 kb amplicon at the 5’-terminal region of the ORF3 gene was sequenced for 28 field isolates to examine phylogenetic relationships to assess whether there is evidence of recombination between genotypes. The region, corresponding to N-terminus of gp116 envelope glycoprotein, displayed more sequence variation than the ORF1b amplicon. All isolates of the virulent genotype 1 (YHV) possessed a unique sequence (TILAGIPEKE/D) at the N terminus of gp116 adjacent to the site of endo-proteolysis that cleaves gp116 from the ORF3 polyprotein. In some genotype 1 isolates this unique sequence was followed by a 54 aa deletion that was also not present in other genotypes. The potential role of this unique sequence as a virulence determinant for YHV requires further investigation. Phylogenetic relationships deduced using the ORF3 amplicon sequences were similar to those deduced using the ORF1b amplicon sequence except that genotype 4 was more closely related to genotype 2 than was genotype 3. However, only 18 of the 28 isolates included in the analysis of both ORF1b and ORF3 amplicons clustered in consistent lineages and were assigned as the same genotypes. Inconsistent phylogenies were observed for ten isolates of which six clustered as genotype 3 in ORF1b and as genotype 2 in ORF3, two isolates clustered as genotype 3 in ORF1b and as genotype 5 in ORF3, one isolate clustered as genotype 5 in ORF1b and as genotype 2 in ORF3, and one isolate clustered as genotype 5 in ORF1b and as genotype 3 in ORF3. Discrepancies in genotype assignments were only observed to involve permutations of genotypes 2, 3 and 5 and involved isolates from healthy shrimp originating from Southeast Asia. Sequence analysis of the ~3.2 kb region spanned by the ORF1b and ORF3 amplicons of three putative recombinant viruses VNM-02-H258 (genotype 3/5), IDN-04-H10 (genotype 3/2) and PHL-03-H8 (genotype 5/3) indicated that recombination had occurred at a position just upstream of the ORF1b gene 3’-terminus. These data provide the first evidence of genetic recombination for any shrimp virus. The high prevalence of recombinants amongst isolates from Southeast Asia has significant implications for diversification, disease emergence and assignment of genotypes for YH-complex viruses. The region of the genome from the poly[A] tail to the 3’-end of the ORF1b gene (containing all structural protein genes) was sequenced for representative isolates of genotypes 3 and 4. The analysis was conducted to determine whether the evolutionary divergence in the structural protein genes differed significantly from the replicase (ORF1b) gene and to identify conserved motifs likely to be important for protein function and the regulation of RNA transcription and replication. The sequence of the near 3’-terminal genome region of a genotype 5 isolate was also determined to examine whether it possessed an ORF4 gene like genotype 2 or whether it was truncated as in genotypes 1, 3 and 4. Comparisons of the intergenic regions (IGR) upstream of ORF2 and ORF3 identified a conserved sequence 5’-GUCAAUUACACxxAxxUU-3’ surrounding the central adenosine residue corresponding to the 5’-terminus of the sub-genomic (sg)mRNAs that is likely to represent the consensus motif used as a transcription regulatory sequence (TRS). A sequence upstream of ORF4 possessed limited homology to the predicted consensus TRS but A>G/U substitutions (genotypes 2, 3, 4 and 5) or a point deletion (genotype 1) occurred at the central critical adenosine residue. It is possible that these mutations explain why a sgmRNA is not transcribed in abundance to allow translation of an ORF4 protein, and why the apparently redundant ORF4 gene has accumulated nucleotide deletions or insertions interrupting its reading in all genotypes except genotype 2. The 3’-terminal genome sequence of genotypes 1, 2, 3 and 4 downstream of the putative ORF4 gene region was extremely highly conserved and was predicted to form a stable hairpin-loop RNA secondary structure with four bulges. Where nucleotide variations occurred in a genotype, other compensatory changes maintained base-pairing and stability of the structure, suggesting that this region is likely to be important for polymerase recognition of the (+) genomic RNA for transcription of (-) genomic RNA. Conventional and real-time PCR tests for the detection of all genotypes in the YH complex were developed by identifying highly conserved sequences amongst the 57 virus isolates at which primers could be targeted. In the consensus RT-nested PCR, PCR (358 bp) and nested PCR (147 bp) amplicon lengths were kept short to accommodate degraded RNA and pools of two primers were used rather than a single degenerate primer to accommodate all genotypes whist minimizing levels of degeneracy. The consensus real-time PCR used SYBR-Green chemistry and amplified a 147 bp product using single degenerate primers targeted to the same sites as the nested PCR primer pools. Each PCR method detected the RNA of representatives of all six genotypes. The RT-nested PCR was extremely sensitive, detecting down to a single copy of a GAV synthetic RNA. Phylogenetic analysis using the 95 nt sequence bounded by the nested PCR primers generated genotype associations similar to those generated using the 671 nt sequence, allowing the assignment of genotypes from the amplified products. The consensus RT-nested PCR test has been included in the 5th Edition of the OIE Manual of Diagnostic Tests for Aquatic Animals (2006). The consensus real-time PCR was slightly less sensitive than the RT-nested PCR, detecting down to ~125 copies of the GAV synthetic RNA. However, the test generated products with the expected Tm (77.5ºC) with isolates of the six genotypes and showed a linear relationship between input RNA and Ct value up to 109 RNA copies. Thus, due to its ability to accurately quantify and compare viral RNA loads in clinical samples, the test could be used to define the infection status of shrimp in relation to threshold levels associated with disease.

Yellow head virus (YHV) is highly pathogenic and was identified as the cause of mass mortalities associated with yellow head disease (YHD) that first appeared in Penaeus monodon farmed in Thailand in 1990. By 1992-1993, YHD was widespread throughout the Thai shrimp farming industry, causing losses estimated at ~US$70 million per annum. By the mid 1990s, gross signs consistent with YHD were also being reported in P. monodon farmed in many regions of the Indo-Pacific. Due to its high pathogenicity and economic impact, YHV has been listed as a notifiable pathogen by the OIE and the control of YHD remains a significant concern. At the outset of this study, two genotypic variants of YHV (genotype 1) had been detected in P. monodon in Australia (gill-associated virus, GAV, genotype 2) and Vietnam (genotype 3), suggesting that more variants might exist in other regions. The aim of this study was, therefore, to test the hypothesis that genotypic variants existed in P. monodon from other locations, and if so, to determine their genetic relationships to the three known genotypes. The study also aimed to improve existing PCR diagnostic protocols to accommodate the detection of all genotypes in the YHV complex. Fifty-seven field isolates of YH-complex viruses were detected by RT-PCR in tissues of P. monodon sampled from nine Indo-Pacific countries. Phylogenetic relationships determined for these isolates using a 671 nucleotide (nt) C-terminal region of the ORF1b gene identified 46 isolates that clustered with the three know genotypes and 11 isolates that clustered in at least three distinct new genotypes. All isolates other than genotype 1 (YHV) were detected in tissues of healthy shrimp. Genotype 4 isolates were detected only in shrimp from India and were slightly less distantly related at the nucleotide level to genotype 5 (85.2% identify) than the other genotypes (80.3%-82.3%). Genotype 6 isolates were only detected in shrimp from Mozambique and were least divergent (3.5%) from genotype 2. One each of three genotype 5 isolates was detected in shrimp from Malaysia, Thailand and the Philippines. The genotype 5 isolate from the Philippines was, however, 6.7% and 7% divergent from the other two isolates, respectively. This level of divergence was greater than found between genotypes 2 and 6 and was similar to that found between isolates of genotype 2 and genotype 3 (~6.7%). This suggests that the Philippine genotype 5 isolate might ultimately be considered as the founding member of a seventh genotype. Genotype 5 isolates were slightly more closely related to genotype 4 (~85.2% identity) than the other genotypes (83.4%-84.8% identity). Genotype 1 (YHV) isolates were only detected in Thai shrimp affected by YHD. Genotype 2 isolates were detected in Australian shrimp as well as shrimp from Vietnam and Thailand. Genotype 3 had the broadest geographic range, being detected in four countries in Southeast Asia. The finding of single genotypes in Australia (genotype 2), India (genotype 4) and Mozambique (genotype 6) supports the hypothesis that they have evolved independently in geographically-isolated populations of P. monodon. The detection of multiple genotypes in Vietnam (genotypes 2 and 3), Malaysia (genotypes 2, 3 and 5) and Thailand (genotypes 1, 2, 3 and 5) suggests that these genotypes have been disseminated by movements of infected P. monodon and the trade in live broodstock used for aquaculture. A ~1.3 kb amplicon at the 5’-terminal region of the ORF3 gene was sequenced for 28 field isolates to examine phylogenetic relationships to assess whether there is evidence of recombination between genotypes. The region, corresponding to N-terminus of gp116 envelope glycoprotein, displayed more sequence variation than the ORF1b amplicon. All isolates of the virulent genotype 1 (YHV) possessed a unique sequence (TILAGIPEKE/D) at the N terminus of gp116 adjacent to the site of endo-proteolysis that cleaves gp116 from the ORF3 polyprotein. In some genotype 1 isolates this unique sequence was followed by a 54 aa deletion that was also not present in other genotypes. The potential role of this unique sequence as a virulence determinant for YHV requires further investigation. Phylogenetic relationships deduced using the ORF3 amplicon sequences were similar to those deduced using the ORF1b amplicon sequence except that genotype 4 was more closely related to genotype 2 than was genotype 3. However, only 18 of the 28 isolates included in the analysis of both ORF1b and ORF3 amplicons clustered in consistent lineages and were assigned as the same genotypes. Inconsistent phylogenies were observed for ten isolates of which six clustered as genotype 3 in ORF1b and as genotype 2 in ORF3, two isolates clustered as genotype 3 in ORF1b and as genotype 5 in ORF3, one isolate clustered as genotype 5 in ORF1b and as genotype 2 in ORF3, and one isolate clustered as genotype 5 in ORF1b and as genotype 3 in ORF3. Discrepancies in genotype assignments were only observed to involve permutations of genotypes 2, 3 and 5 and involved isolates from healthy shrimp originating from Southeast Asia. Sequence analysis of the ~3.2 kb region spanned by the ORF1b and ORF3 amplicons of three putative recombinant viruses VNM-02-H258 (genotype 3/5), IDN-04-H10 (genotype 3/2) and PHL-03-H8 (genotype 5/3) indicated that recombination had occurred at a position just upstream of the ORF1b gene 3’-terminus. These data provide the first evidence of genetic recombination for any shrimp virus. The high prevalence of recombinants amongst isolates from Southeast Asia has significant implications for diversification, disease emergence and assignment of genotypes for YH-complex viruses. The region of the genome from the poly[A] tail to the 3’-end of the ORF1b gene (containing all structural protein genes) was sequenced for representative isolates of genotypes 3 and 4. The analysis was conducted to determine whether the evolutionary divergence in the structural protein genes differed significantly from the replicase (ORF1b) gene and to identify conserved motifs likely to be important for protein function and the regulation of RNA transcription and replication. The sequence of the near 3’-terminal genome region of a genotype 5 isolate was also determined to examine whether it possessed an ORF4 gene like genotype 2 or whether it was truncated as in genotypes 1, 3 and 4. Comparisons of the intergenic regions (IGR) upstream of ORF2 and ORF3 identified a conserved sequence 5’-GUCAAUUACACxxAxxUU-3’ surrounding the central adenosine residue corresponding to the 5’-terminus of the sub-genomic (sg)mRNAs that is likely to represent the consensus motif used as a transcription regulatory sequence (TRS). A sequence upstream of ORF4 possessed limited homology to the predicted consensus TRS but A>G/U substitutions (genotypes 2, 3, 4 and 5) or a point deletion (genotype 1) occurred at the central critical adenosine residue. It is possible that these mutations explain why a sgmRNA is not transcribed in abundance to allow translation of an ORF4 protein, and why the apparently redundant ORF4 gene has accumulated nucleotide deletions or insertions interrupting its reading in all genotypes except genotype 2. The 3’-terminal genome sequence of genotypes 1, 2, 3 and 4 downstream of the putative ORF4 gene region was extremely highly conserved and was predicted to form a stable hairpin-loop RNA secondary structure with four bulges. Where nucleotide variations occurred in a genotype, other compensatory changes maintained base-pairing and stability of the structure, suggesting that this region is likely to be important for polymerase recognition of the (+) genomic RNA for transcription of (-) genomic RNA. Conventional and real-time PCR tests for the detection of all genotypes in the YH complex were developed by identifying highly conserved sequences amongst the 57 virus isolates at which primers could be targeted. In the consensus RT-nested PCR, PCR (358 bp) and nested PCR (147 bp) amplicon lengths were kept short to accommodate degraded RNA and pools of two primers were used rather than a single degenerate primer to accommodate all genotypes whist minimizing levels of degeneracy. The consensus real-time PCR used SYBR-Green chemistry and amplified a 147 bp product using single degenerate primers targeted to the same sites as the nested PCR primer pools. Each PCR method detected the RNA of representatives of all six genotypes. The RT-nested PCR was extremely sensitive, detecting down to a single copy of a GAV synthetic RNA. Phylogenetic analysis using the 95 nt sequence bounded by the nested PCR primers generated genotype associations similar to those generated using the 671 nt sequence, allowing the assignment of genotypes from the amplified products. The consensus RT-nested PCR test has been included in the 5th Edition of the OIE Manual of Diagnostic Tests for Aquatic Animals (2006). The consensus real-time PCR was slightly less sensitive than the RT-nested PCR, detecting down to ~125 copies of the GAV synthetic RNA. However, the test generated products with the expected Tm (77.5ºC) with isolates of the six genotypes and showed a linear relationship between input RNA and Ct value up to 109 RNA copies. Thus, due to its ability to accurately quantify and compare viral RNA loads in clinical samples, the test could be used to define the infection status of shrimp in relation to threshold levels associated with disease.