Genotyping of white spot syndrome virus prevalent in shrimp farms of India

DNA extracts from white spot syndrome virus (WSSV) that had infected post-larvae and juveniles of cultured shrimp, wild shrimp and crabs, which had been collected from different hatcheries and farms located along both the east and west coasts of India, revealed considerable variation in several previously identified WSSV DNA repeat regions. These include the 54 bp repeat in ORF 94, the 69 bp repeat in ORF 125 and the compound 45 and 57 bp repeat region in ORF 75. In ORF 94, 13 genotypes were observed with the number of repeats ranging from 2 to 16 units. While 7 repeat units were commonly observed (11.3%), no samples with 11 or 15 repeat units were found. In ORF 125, 11 types were found, with repeats ranging from 2 to 14 units. The most prevalent genotype displayed 4 repeat units (47.1%); no samples with 6 or 13 repeats were observed. The compound repeat region of ORF 75 displayed 6 different patterns of repeats. Samples with the same repeat pattern in one ORF did not always show identical repeat patterns in one or both of the other repeat regions. These data suggest that combined analysis of all 3 variable loci could be used to differentiate and characterize specific WSSV strains. For general epidemiological studies, the best marker with maximum variation is ORF 94, followed by ORF 125 and ORF 75. The 3 repeat regions above were used to compare WSSV genotypes from disease outbreaks on 3 sets of farms from different locations in the state of Andhra Pradesh. The genotypes within each farm set were almost identical, but differed between farm sets, suggesting that WSSV transmission occurred directly through virus carriers or water exchange between adjacent farms at each location. These findings show that genotyping can be a useful epidemiological tool for tracing the movement of WSSV within infected populations.     

Increasing production in Korean shrimp farms with white-spot syndrome virus PCR-negative brood stock

White-spot syndrome virus (WSSV) is a devastating, infectious virus affecting shrimp. Although sensitive techniques involving PCR have been developed to assist farmers in screening shrimp (brood stock) for WSSV prior to stocking ponds, such practices have not yet been applied in Korea. Despite the rationality of implementing screening, there has been some doubt as to whether the stocking of WSSV-PCR-negative fry epidemiologically decreases white-spot disease outbreaks. Here, we report a retrospective analysis of data from shrimp farms in the western coast of Korea where WSSV-PCR-negative brood stocks were used to stock rearing ponds. A total of 366 shrimp from Heuksan Island were sampled for WSSV with PCR. Of the tested shrimp, 7.2% (28 brood stocks) were identified as WSSV positive; only WSSV-PCR-negative shrimp were used for brood stocks. Total unit production (final shrimp production/ the area of the ponds) was higher, at 1.96, in ponds where WSSV-PCR-negative shrimp were used, as compared with 1.02 in other ponds in Korea in 2004. This retrospective analysis of WSSV in Korea may be useful to the shrimp aquaculture industry, suggesting a testable hypothesis that may contribute to the eventual control of WSSV outbreaks.     

Genotyping of White Spot Syndrome Virus in Chinese Cultured Shrimp during 1998-1999

Recent studies showed that white spot syndrome virus(WSSV)isolates from different geographic locations share a high genetic similarity except the variable regions in ORF23/24 and ORF14/15,and variable number of tandem repeats(VNTR)within ORF94.In this study,genotyping was performed according to these three variable regions among WSSV isolates collected during 1998/1999 from Southern China.These WSSV isolates contain a deletion of 1168,5657,5898,9316 and 11093 bp,respectively in the variable region ORF23/24compared with WSSV-TW,and a deletion of 4749 or 5622 bp in the variable region ORF14/15 relative to TH-96-II.Four types of repeat units(RUs)(6,8,9 and 13 RUs)in ORF94 were detected in these isolates,with the shortest 6 RUs as the most prevalent type.Our results provide important information for a better understanding of the spatio-temporal transmission mode and the WSSV genetic evolution lineage.     

Genotyping of white spot syndrome virus in Chinese cultured shrimp during 1998–1999

Recent studies showed that white spot syndrome virus (WSSV) isolates from different geographic locations share a high genetic similarity except the variable regions in ORF23/24 and ORF14/15, and variable number of tandem repeats (VNTR) within ORF94. In this study, genotyping was performed according to these three variable regions among WSSV isolates collected during 1998/1999 from Southern China. These WSSV isolates contain a deletion of 1168, 5657, 5898, 9316 and 11093 bp, respectively in the variable region ORF23/24 compared with WSSV-TW, and a deletion of 4749 or 5622 bp in the variable region ORF14/15 relative to TH-96-II. Four types of repeat units (RUs) (6, 8, 9 and 13 RUs) in ORF94 were detected in these isolates, with the shortest 6 RUs as the most prevalent type. Our results provide important information for a better understanding of the spatio-temporal transmission mode and the WSSV genetic evolution lineage.     

Usefulness of dead shrimp specimens in studying the epidemiology of white spot syndrome virus (WSSV) and chronic bacterial infection

This paper describes the utility of dead shrimp samples in epidemiological investigations of the white spot syndrome virus (WSSV) and chronic bacterial infections. A longitudinal observational study was undertaken in shrimp farms in Kundapur, Karnataka, India, from September 1999 to April 2000 to identify risk factors associated with outbreaks of white spot disease (WSD) in cultured Penaeus monodon. As a part of the larger study, farmers were trained to collect and preserve dead and moribund shrimp (when observed) during the production cycle. At the end of the production cycle, 73 samples from 50 ponds had been collected for histopathology and 55 samples from 44 ponds for PCR. Intranuclear viral inclusion bodies diagnostic of WSSV infection were detected in dead samples from 32 ponds (64 %). Samples of dead shrimp from 18 ponds (36%) showed no histopathological evidence of WSSV infection. However, of these, samples from 13 ponds (26%) showed clear evidence of shell, oral, enteric and systemic chronic inflammatory lesions (CIL) in the form of haemocytic nodules, typical of bacterial infection. Samples from 5 ponds (10%) were negative for both WSSV and CIL. Samples from 8 ponds had dual WSSV and CIL, although both WSSV and CIL were only observed in the same shrimp from 1 pond. Useful information was obtained from these shrimp despite the presence of post-mortem changes. Samples from 19 ponds (43%) tested positive for WSSV by 1-step PCR and samples from an additional 10 ponds (22.7%) were positive by 2-step nested PCR. Samples from 15 ponds (34.1%) were negative for WSSV by 2-step nested PCR. There was moderate to substantial agreement between PCR and histopathology in the diagnosis of WSSV infection in dead shrimp. WSSV infection in dead shrimp was significantly associated with crop failures as defined by a shorter length of the production cycle (<90 d) and lower average weight at harvest (<22 g). WSSV infection was also associated with lower survival (<50%), but this was not significant. Ponds with CIL did not experience any crop failures, and the presence of CIL was significantly associated with successful crops. The study demonstrates that samples of dead shrimp can provide useful information for disease surveillance and epidemiological investigations of WSSV and chronic bacterial infections.     

Analysis of variable genomic loci in white spot syndrome virus to predict its origins in Procambarus clarkii crayfish farmed in China

Variable genomic loci were examined in 4 white spot syndrome virus (WSSV) isolates (08HB, 09HB, 08JS and 09JS) from Procambarus clarkii crayfish collected from Jiangsu and Hubei Provinces in China in 2008 and 2009. In ORF75, sequence variation detected in the 4 isolates, as well as in isolates sequenced previously, suggested that WSSV might have segregated into 2 lineages since first emerging as a serious pathogen of farmed shrimp in East Asia in the early-mid 1990s, with one lineage remaining in East Asia and the other separating to South Asia. In ORF23/24, deletions of 9.31, 10.97, or 11.09 kb were evident compared to a reference isolate from Taiwan (WSSV-TW), and, in ORF14/15, deletions of 5.14 or 5.95 kb were evident compared to a reference isolate from Thailand with the largest genome size (TH-96-II). With respect to these genome characteristics, the crayfish isolates 08HB, 09HB and 08JS were similar to WSSV-TW and the isolate 09JS was similar to a reference isolate from China (WSSV-CN). In addition to these loci, sequence variation was evident in ORF94 and ORF125 that might be useful for differentiating isolates and in epidemiological tracing of WSSV spread in crayfish farmed in China. However, as all 4 crayfish isolates possessed a Homologous Region 9 sequence identical to isolate WSSV-TW and another Thailand isolate (WSSV-TH), and as their transposase sequence was identical to isolates WSSV-CN and WSSV-TH, these 2 loci were not useful in predicting their origins.     

Performance of WSSV-infected and WSSV-negative Penaeus monodon postlarvae in culture ponds.

In a survey of 27 Penaeus monodon culture ponds stocked with postlarvae (approximately PL10) at medium density (approximately 40 shrimp m(-2)), single-step nested white spot syndrome virus (WSSV) PCR was used to measure the WSSV infection rates in the shrimp populations within 1 mo after stocking. Seven ponds were initially WSSV-free, and the shrimp in 5 of these were harvested successfully. In the ponds (n = 6) where detection rates were higher than 50%, mass mortality occurred during the growth period, and none of these ponds was harvested successfully. In a subsequent study, P. monodon brooders were classified into 3 groups according to their WSSV infection status before and after spawning: brooders that were WSSV-positive before spawning were assigned to group A; spawners that became WSSV-positive only after spawning were assigned to group B; and group C consisted of brooders that were still WSSV-negative after spawning. WSSV screening showed that 75, 44 and 14%, respectively, of group A, B and C brooders produced nauplii that were WSSV-positive. Most (57%; 16/28) of the brooders in group A produced nauplii in which the WSSV prevalence was high (>50%).When a pond was stocked with high-prevalence nauplii from 1 of these group A brooders, an outbreak of white spot syndrome occurred within 3 wk and only approximately 20% of the initial population survived through to harvest (after 174 d). By contrast, 2 other ponds stocked with low-prevalence and WSSV-negative nauplii (derived respectively from 2 brooders in group B), both had much higher survival rates (70 to 80%) and yielded much larger (approximately 3x by weight) total harvests. We conclude that testing the nauplii is an effective and practical screening strategy for commercially cultured P. monodon.     

Risk factors associated with white spot syndrome virus infection in a Vietnamese rice-shrimp farming system

White spot disease (WSD) is a pandemic disease caused by a virus commonly known as white spot syndrome virus (WSSV). Several risk factors for WSD outbreaks have been suggested. However, there have been very few studies to identify risk factors for WSD outbreaks in culture systems. This paper presents and discusses the risk factors for WSSV infection identified during a longitudinal observational study conducted in a Vietnamese rice-shrimp farming system. A total of 158 variables were measured comprising location, features of the pond, management practices, pond bottom quality, shrimp health and other animals in the pond. At the end of the study period WSSV was detected in 15 of the 24 ponds followed through the production cycle (62.5%). One hundred and thirty-nine variables were used in univariate analyses. All the variables with a p-value < or = 0.10 were used in unconditional logistic regression in a forward stepwise model. An effect of location was identified in both univariate and multivariate analyses showing that ponds located in the eastern portion of the study site, closer to the sea, were more likely to test positive for WSSV by 1-step PCR at harvest. Ponds with shrimp of a smaller average size 1 mo after stocking tended to be positive for WSSV at the end of the production cycle. Average weight at 1 mo was also highlighted in multivariate analyses when considered as either a risk factor or an outcome. Other risk factors identified in univariate analyses were earlier date of stocking and use of commercial feed. A number of variables also appeared to be associated with a reduced risk of WSSV at harvest including the presence of dead post larvae in the batch sampled at stocking, presence of Hemigrapsus spp. crabs during the first month of production, feeding vitamin premix or legumes, presence of high numbers of shrimp with bacterial infection and the presence of larger mud crabs or gobies at harvest. No associations were detected with WSSV at harvest and stocking density, presence, or number or weight of wild shrimp in the pond. The multivariate model to identify outcomes associated with WSSV infection highlighted the presence of high mortality as the main variable explaining the data. The results obtained from this study are discussed in the context of WSD control and areas requiring further investigation are suggested.     

Model of white spot syndrome virus (WSSV) epidemics in Litopenaeus vannamei

White spot syndrome virus (WSSV) is devastating shrimp aquaculture throughout the world, but despite its economic importance no work has been done on modeling epidemics of this pathogen. Therefore we developed a Reed-Frost epidemic model for WSSV in Litopenaeus vannamei. The model includes uninfected susceptible, latently infected, acutely infected, and dead infected shrimp. The source of new infections during an outbreak is considered to be dead infected shrimp. The transmission coefficient, patency coefficient, virulence coefficient, and removal coefficient (disappearance of dead infected shrimp) control the dynamics of the model. In addition, an explicit area parameter is included to help to clarify the distinction between density and absolute shrimp population size. An analysis of the model finds that as number of shrimp, initial dose, transmission coefficient, patency coefficient, virulence coefficient, or removal coefficient changes, the speed of the epidemic changes. The model predicts that a threshold density of susceptible shrimp exists below which an outbreak of WSSV will not occur. Only initial dose, transmission coefficient, removal coefficient, and area coefficient affect the predicted threshold density. Increases in the transmission coefficient reduce the threshold value, whereas increases in the other factors cause the threshold value to increase. Epidemic models may prove useful to the shrimp aquaculture industry by suggesting testable hypotheses, some of which may contribute to the eventual control of WSSV outbreaks.     

White spot syndrome virus (WSSV) detected by PCR in rotifers and rotifer resting eggs from shrimp pond sediments

White spot syndrome virus (WSSV) was detected by PCR-dot blot hybridization in rotifer resting eggs from shrimp Penaeus chinensis culture-pond sediments. It was also detected in rotifers hatched from those eggs. Surface disinfection before analysis indicated that WSSV was probably present within the resting eggs. Results suggested that rotifer resting eggs may be an overwintering reservoir for WSSV in shrimp ponds.     

Results from black tiger shrimp penaeus monodon culture ponds stocked with postlarvae PCR-positive or -negative for white-spot syndrome virus (WSSV).

Commercial, intensive, earthen shrimp ponds (188) in southern Thailand were stocked with postlarvae (PL) of Penaeus monodon that had tested positive or negative for white-spot syndrome virus (WSSV) infection by polymerase chain reaction (PCR) assay. All the PL were grossly healthy. At 2 wk intervals after stocking, shrimp from each pond were examined for gross WSSV lesions and tested for WSSV by PCR. Shrimp from all the ponds stocked with WSSV-PCR-positive PL (Group 0, n = 43) eventually showed gross signs of white-spot disease (WSD) at an average of 40 d after stocking. Of the remaining ponds stocked with WSSV-PCR-negative PL (n = 145), some remained WSSV-PCR-negative throughout the study (Group 5, n = 52), while others (93) became WSSV-PCR-positive after stocking, during the first month (Group 1, n = 23), second month (Group 2, n = 40), third month (Group 3, n = 24), or fourth month (Group 4, n = 6). Crop failure was defined as a pond drain or forced harvest before 14 wk or 98 d of cultivation. For Group 0 the proportion of ponds failing was 0.953, while it was only 0.019 for Group 5. Thus, the relative risk of failure for Group 0 was approximately 50 times that of Group 5. The relative risk of failure for Group 0 was also 3 times that for ponds stocked with WSSV-PCR-negative PL. Obviously, not all WSSV outbreaks resulted in crop failure. Of the 93 ponds stocked with PCR-negative PL that later yielded WSSV-PCR-positive shrimp, 53% reached successful harvest. The study showed that PCR screening of PL and rejection of WSSV-positive batches before stocking could greatly improve the chances of a successful harvest.     

White spot syndrome virus (WSSV) in Litopenaeus vannamei captured from the Gulf of California near an area of extensive aquaculture activity

For the shrimp farming industry of Mexico, disease outbreaks caused by white spot syndrome virus (WSSV) are relatively recent. Efforts to control the virus are assisted by monitoring for its prevalence in aquaculture systems, but few attempts have been made to search for it in carriers from coastal waters. To search for WSSV carriers in the Gulf of California, we made surveys off the coast of Sinaloa, Mexico, in March 2001, November 2001, and September 2003 using polymerase chain reaction (PCR) assays and histopathology. WSSV-positive shrimp were detected only in November 2001, after hurricane Julliete. This suggested possible dispersal of WSSV to the marine environment from infected shrimp farms.     

Detection of white spot syndrome virus (WSSV) in the Pacific oyster Crassostrea gigas

Oysters Crassostrea gigas were placed at water supply canals of three shrimp farms in Guasave, Mexico where WSSV outbreaks occur. Animals were sampled through April-August and September-December to detect WSSV DNA.By using three different PCR protocols, only oysters from a farm undergoing a WSSV outbreak were found WSSV-positive in gills and digestive gland. Two WSSV amplicons were sequenced and they corresponded over 99% to WSSV genome segments. Results showed that oysters can capture WSSV particles suspended in water. Susceptibility of oysters to WSSV infection and their role as a carrier remain to be determined.     

Cloning of Hsp21 gene and its expression in Chinese shrimp Fenneropenaeus chinensis in response to WSSV challenge

In the present study, a DNA sequence encoding a small heat shock protein gene (FcHsp21) in the Chinese shrimp, Fenneropenaeus chinensis, was cloned, and its expression was analyzed after white spot syndrome virus (WSSV) infection. The FcHsp21 gene contained an open reading frame (ORF) of 555 bp in length, encoding a 184 amino acid protein with a theoretical size of about 21 kDa and a predicted isoelectric point of 5.38. The mRNA of the Hsp21 had a long Poly(A) tail (748 bp) with six polyadenylation signals (AATAA) downstream from the terminator. In addition, the gene contained a relatively long intron (507 bp), which has not been described in shrimps. The intron contained a long compound type microsatellite repeat sequence. The analysis of the phylogenetics revealed that the Hsp21 was highly conserved among the genomes of animals. Our results show that the expression modes of FcHsp21 can be changed by different WSSV infection methods. The expression of FcHsp21 was inhibited by muscle-injecting WSSV, but induced by feeding WSSV.     

Evolutionary trajectory of white spot syndrome virus (WSSV) genome shrinkage during spread in Asia

Background

White spot syndrome virus (WSSV) is the sole member of the novel Nimaviridae family, and the source of major economic problems in shrimp aquaculture. WSSV appears to have rapidly spread worldwide after the first reported outbreak in the early 1990s. Genomic deletions of various sizes occur at two loci in the WSSV genome, the ORF14/15 and ORF23/24 variable regions, and these have been used as molecular markers to study patterns of viral spread over space and time. We describe the dynamics underlying the process of WSSV genome shrinkage using empirical data and a simple mathematical model.

Methodology/Principal Findings

We genotyped new WSSV isolates from five Asian countries, and analyzed this information together with published data. Genome size appears to stabilize over time, and deletion size in the ORF23/24 variable region was significantly related to the time of the first WSSV outbreak in a particular country. Parameter estimates derived from fitting a simple mathematical model of genome shrinkage to the data support a geometric progression (k<1) of the genomic deletions, with k = 0.371±0.150.

Conclusions/Significance

The data suggest that the rate of genome shrinkage decreases over time before attenuating. Bioassay data provided support for a link between genome size and WSSV fitness in an aquaculture setting. Differences in genomic deletions between geographic WSSV isolates suggest that WSSV spread did not follow a smooth pattern of geographic radiation, suggesting spread of WSSV over long distances by commercial activities. We discuss two hypotheses for genome shrinkage, an adaptive and a neutral one. We argue in favor of the adaptive hypothesis, given that there is support for a link between WSSV genome size and fitness.     

Viruses,biosecurity and specific pathogen-free stocks in shrimp aquaculture

The greatest threat to the future of world shrimp aquaculture is disease, in particular the virulent untreatable viruses, infectious hypodermal and haematopoietic necrosis virus (IHHNV), taura syndrome virus (TSV), yellow head virus (YHV), and white spot syndrome virus (WSSV). To overcome these hazards, the industry of the future must be based on: (i) specific pathogen-free and genetically improved shrimp stocks; (ii) biosecure systems including enclosed, reduced water-exchange/increased water-reuse culture systems; (iii) biosecure management practices; and (iv) co-operative industry-wide disease control strategies. Specific pathogen-free shrimp are those that are known to be free of specified pathogens and such stocks will ensure that seed shrimp are not the conduit for introduction of pathogens and that if pathogens are encountered the stocks will not be severely affected. Commercially acceptable biosecure culture systems that are under cover and use recirculated sea water will need to be developed for shrimp production. Adherence to operating protocols that incorporate strict biosecurity practices, including restricted access and disinfection strategies, will need to become standard. Co-operative efforts will include: early warning surveillance; co-ordination of harvest and water exchange schedules of contaminated ponds; processor co-operation to ensure that processing wastes are not threats; quick response to outbreaks.