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Min JG, Jeong HD, Kim KI. Identification of Various InDel-II Variants of the White Spot Syndrome Virus Isolated from Frozen Shrimp and Bivalves Obtained in the Korean Commercial Market. Animals (Basel) 2023; 13:3348. [PMID: 37958102 PMCID: PMC10650675 DOI: 10.3390/ani13213348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
White spot syndrome virus (WSSV) poses a significant threat to the global shrimp industry. We investigated the presence of WSSV in frozen shrimp (n = 86) and shellfish (n = 185) from the Korean market (2010-2018). The detection rate of first-step polymerase chain reaction (PCR) in domestic shrimp was 36.8% (7/19), whereas that in imported shrimp was 0.01% (1/67). Furthermore, the WSSV genome was amplified from domestic bivalve mollusks by first- and second-step PCR with accuracies of 3.4% (5/147) and 15.6% (23/147), respectively. The genetic relatedness of InDel-II regions among WSSVs detected in domestic shrimp groups revealed four variants (777, 5649, 11,070 and 13,046 bp insertion or deletion), and imported shrimp groups had four variants (10,778, 11,086, 11,500 and 13,210 bp) compared with the putative ancestor WSSV strain. The 5649 bp variant was the dominant type among the WSSV variants detected in domestic shrimp (54.5%, 6/11). Notably, bivalve mollusks exhibited six variants (777, 5649, 5783, 5876, 11,070 and 13,046 bp), including four variants detected in shrimp, indicating that bivalve mollusks could facilitate WSSV tracking. In a challenge test, whiteleg shrimp (Litopenaeus vannamei) exhibited varying mortality rates, indicating a link between InDel-II deletion and viral replication. These findings highlight the complexity of WSSV transmission.
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Affiliation(s)
| | | | - Kwang-Il Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan 48513, Republic of Korea; (J.-G.M.)
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Genotype Diversity and Spread of White Spot Syndrome Virus (WSSV) in Madagascar (2012-2016). Viruses 2021; 13:v13091713. [PMID: 34578294 PMCID: PMC8472404 DOI: 10.3390/v13091713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/20/2021] [Accepted: 08/26/2021] [Indexed: 11/29/2022] Open
Abstract
White Spot Disease (WSD) caused by the White Spot Syndrome Virus (WSSV) is the most devastating viral disease threatening the shrimp culture industry worldwide, including Madagascar. WDS was first reported on the island in 2012; however, little is known about the circulation of the virus and its genetic diversity. Our study aimed at describing the molecular diversity and the spread of WSSV in the populations of Madagascan crustaceans. Farmed and wild shrimps were collected from various locations in Madagascar from 2012 to 2016 and were tested for WSSV. Amplicons from positive specimens targeting five molecular markers (ORF75, ORF94, ORF125, VR14/15 and VR23/24) were sequenced for genotyping characterizations. Four genotypes were found in Madagascar. The type-I genotype was observed in the south-west of Madagascar in April 2012, causing a disastrous epidemic, then spread to the North-West coast. Type-II strains were detected in October 2012 causing an outbreak in another Penaeus monodon farm. In 2014 and 2015, types II and III were observed in shrimp farms. Finally, in 2016, types II and IV were found in wild species including Fenneropenaeus indicus, Metapenaeus monoceros, Marsupenaeus japonicus and Macrobrachium rosenbergii. Considering the economic importance of the shrimp industry for Madagascar, our study highlights the need to maintain WSSV surveillance to quickly take appropriate countermeasures in case of outbreak and to sustain this industry.
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Li F, Gao M, Xu L, Yang F. Comparative genomic analysis of three white spot syndrome virus isolates of different virulence. Virus Genes 2016; 53:249-258. [DOI: 10.1007/s11262-016-1421-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 12/08/2016] [Indexed: 10/20/2022]
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Mendoza-Cano F, Enríquez-Espinoza T, Valenzuela-Castillo A, Encinas-García T, Sánchez-Paz A. High Occurrence of the Decapod Penstyldensovirus (PstDV1) Detected in Postlarvae of Penaeus vannamei Produced in Commercial Hatcheries of Mexico. ECOHEALTH 2016; 13:591-596. [PMID: 27342686 DOI: 10.1007/s10393-016-1143-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 06/01/2016] [Accepted: 06/03/2016] [Indexed: 06/06/2023]
Abstract
The decapod penstyldensovirus (PstDV1) is a widely spread shrimp pathogen that causes high mortalities in the shrimp Penaeus stylirostris, while in P. vannamei, it has been associated with induction of the runt deformity syndrome. Using shrimp post-larvae (PL, stages PL13-PL21) collected from 16 commercial hatcheries from Mexico, and a sensitive PCR protocol for its detection, a survey of the PstDV1 prevalence in larvae was undertaken. A high overall prevalence of PstDV1 (49.5 %) in shrimp PL from the studied hatcheries was found. This study reveals that PstDV1 occurs persistently in PL populations, which may have significant implications for its dispersal.
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Affiliation(s)
- Fernando Mendoza-Cano
- Laboratorio de Referencia, Análisis y Diagnóstico en Sanidad Acuícola, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Calle Hermosa 101, Col. Los Ángeles, CP 83106, Hermosillo, Sonora, Mexico
| | - Tania Enríquez-Espinoza
- Laboratorio de Referencia, Análisis y Diagnóstico en Sanidad Acuícola, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Calle Hermosa 101, Col. Los Ángeles, CP 83106, Hermosillo, Sonora, Mexico
| | - Adán Valenzuela-Castillo
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Av. Colosio s/n, entre Sahuaripa y Reforma, 83000, Hermosillo, Sonora, Mexico
| | - Trinidad Encinas-García
- Laboratorio de Referencia, Análisis y Diagnóstico en Sanidad Acuícola, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Calle Hermosa 101, Col. Los Ángeles, CP 83106, Hermosillo, Sonora, Mexico
| | - Arturo Sánchez-Paz
- Laboratorio de Referencia, Análisis y Diagnóstico en Sanidad Acuícola, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Calle Hermosa 101, Col. Los Ángeles, CP 83106, Hermosillo, Sonora, Mexico.
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Piamsomboon P, Inchaisri C, Wongtavatchai J. White spot disease risk factors associated with shrimp farming practices and geographical location in Chanthaburi province, Thailand. DISEASES OF AQUATIC ORGANISMS 2015; 117:145-153. [PMID: 26648106 DOI: 10.3354/dao02929] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Over the past 2 decades, shrimp aquaculture in Thailand has been impacted by white spot disease (WSD) caused by white spot syndrome virus (WSSV). Described here are results of a survey of 157 intensive shrimp farms in Chanthaburi province, Thailand, to identify potential farm management and location risk factors associated with the occurrence of WSD outbreaks. Logistic regression analysis of the survey responses identified WSD risks to be associated with farms sharing inlet water and culturing shrimp year round and with a single owner operating more than 1 farm. The analysis also showed WSD risks to be reduced at farms that used probiotics and applied lime to pond bottoms when fallow to neutralize acidity and kill microorganisms. Regression modeling identified no association of geographical location with WSD. The data should assist shrimp farms in mitigating the effects of WSD in Thailand.
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Affiliation(s)
- Patharapol Piamsomboon
- Department of Veterinary Medicine, Faculty of Veterinary Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
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de Jesús Durán-Avelar M, Pérez-Enríquez R, Zambrano-Zaragoza JF, Montoya-Rodríguez L, Vázquez-Juárez R, Vibanco-Pérez N. Genotyping WSSV isolates from northwestern Mexican shrimp farms affected by white spot disease outbreaks in 2010-2012. DISEASES OF AQUATIC ORGANISMS 2015; 114:11-20. [PMID: 25958803 DOI: 10.3354/dao02844] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
White spot disease (WSD) causes high mortality in cultured shrimp throughout the world. Its etiologic agent is the white spot syndrome virus (WSSV). The genomic repeat regions ORF 75, ORF 94, and ORF 125 have been used to classify WSSV isolates in epidemiological studies using PCR with specific primers and sequencing. The present study investigated the variation in nucleotide sequences from 107, 150, and 143 isolates of WSSV collected from Litopenaeus vannamei shrimp ponds with WSD outbreaks in northwestern Mexico during the period 2010-2012, in the genomic repeat regions ORFs 75, 94, and 125, respectively. The haplotypic nomenclature for each isolate was based on the number of repeat units and the position of single nucleotide polymorphisms on each ORF. We report finding 17, 43, and 66 haplotypes of ORFs 75, 94, and 125, respectively. The study found high haplotypic diversity in WSSV using the complete sequences of ORFs 94 and 125 as independent variables, but low haplotypic diversity for ORF 75. Different haplotypes of WSSV were found from region-to-region and year-to-year, though some individual haplotypes were found in different places and in more than one growing cycle. While these results suggest a high rate of mutation of the viral genome at these loci, or perhaps the introduction of new viral strains into the area, they are useful as a tool for epidemiological surveys. Two haplotypes from some of the ORFs in the same shrimp were encountered, suggesting the possibility of multiple infections.
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Affiliation(s)
- Ma de Jesús Durán-Avelar
- Universidad Autónoma de Nayarit, Unidad Académica de Ciencias Químico Biológicas y Farmacéuticas, Tepic 63000, Nayarit, Mexico
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Tang KFJ, Le Groumellec M, Lightner DV. Novel, closely related, white spot syndrome virus (WSSV) genotypes from Madagascar, Mozambique and the Kingdom of Saudi Arabia. DISEASES OF AQUATIC ORGANISMS 2013; 106:1-6. [PMID: 24062547 DOI: 10.3354/dao02645] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
White spot syndrome virus (WSSV) is highly pathogenic to penaeid shrimp and has caused significant economic losses in the aquaculture industry around the world. During 2010 to 2012, WSSV caused severe mortalities in cultured penaeid shrimp in Saudi Arabia, Mozambique and Madagascar. To investigate the origins of these WSSV, we performed genotyping analyses at 5 loci: the 3 open reading frames (ORFs) 125, 94 and 75, each containing a variable number of tandem repeats (VNTR), and deletions in the 2 variable regions, VR14/15 and VR23/24. We categorized the WSSV genotype as {N125, N94, N75, ΔX14/15, ΔX23/24} where N is the number of repeat units in a specific ORF and ΔX is the length (base pair) of deletion within the variable region. We detected 4 WSSV genotypes, which were characterized by a full-length deletion in ORF94/95, a relatively small ORF75 and one specific deletion length in each variable region. There are 2 closely related genotypes in these 3 countries: {6125, del94, 375, Δ595014/15, Δ1097123/24} and {7125, del94, 375, Δ595014/15, Δ1097123/24}, where del is the full-length ORF deletion. In Saudi Arabia, 2 other related types of WSSV were also found: {6125, 794, 375, Δ595014/15, Δ1097123/24} and {8125, 1394, 375, Δ595014/15, Δ1097123/24}. The identical patterns of 3 loci in these 4 types indicate that they have a common lineage, and this suggests that the WSSV epidemics in these 3 countries were from a common source, possibly the environment.
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Affiliation(s)
- Kathy F J Tang
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, Arizona 85721, USA
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Chai CY, Yoon J, Lee YS, Kim YB, Choi TJ. Analysis of the complete nucleotide sequence of a white spot syndrome virus isolated from pacific white shrimp. J Microbiol 2013; 51:695-9. [DOI: 10.1007/s12275-013-3171-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 04/26/2013] [Indexed: 11/24/2022]
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Mendoza-Cano F, Sánchez-Paz A. Development and validation of a quantitative real-time polymerase chain assay for universal detection of the White Spot Syndrome Virus in marine crustaceans. Virol J 2013; 10:186. [PMID: 23758658 PMCID: PMC3685563 DOI: 10.1186/1743-422x-10-186] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/28/2013] [Indexed: 11/23/2022] Open
Abstract
Background The White Spot Syndrome Virus (WSSV), the sole member of the family Whispoviridae, is the etiological agent that causes severe mortality events in wild and farmed shrimp globally. Given its adverse effects, the WSSV has been included in the list of notifiable diseases of the Office of International Epizootic (OIE) since 1997. To date there are no known therapeutic treatments available against this lethal virus, and a surveillance program in brood-stock and larvae, based on appropriate diagnostic tests, has been strongly recommended. However, some currently used procedures intended for diagnosis of WSSV may be particularly susceptible to generate spurious results harmfully impacting the shrimp farming industry. Methods In this study, a sensitive one-step SYBR green-based real-time PCR (qPCR) for the detection and quantitation of WSSV was developed. The method was tested against several WSSV infected crustacean species and on samples that were previously diagnosed as being positive for WSSV from different geographical locations. Results A universal primer set for targeting the WSSV VP28 gene was designed. This method demonstrated its specificity and sensitivity for detection of WSSV, with detection limits of 12 copies per sample, comparable with the results obtained by other protocols. Furthermore, the primers designed in the present study were shown to exclusively amplify the targeted WSSV VP28 fragment, and successfully detected the virus in different samples regardless of their geographical origin. In addition, the presence of WSSV in several species of crustaceans, including both naturally and experimentally infected, were successfully detected by this method. Conclusion The designed qPCR assay here is highly specific and displayed high sensitivity. Furthermore, this assay is universal as it allows the detection of WSSV from different geographic locations and in several crustacean species that may serve as potential vectors. Clearly, in many low-income import-dependent nations, where the growth of shrimp farming industries has been impressive, there is a demand for cost-effective diagnostic tools. This study may become an alternative molecular tool for a less expensive, rapid and efficient detection of WSSV.
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Affiliation(s)
- Fernando Mendoza-Cano
- Laboratorio de Referencia, Análisis y Diagnóstico en Sanidad Acuícola, Centro de Investigaciones Biológicas del Noroeste S. C.-CIBNOR, Calle Hermosa 101, Col. Los Ángeles, Hermosillo Son C.P. 83106, México
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Hoa TTT, Zwart MP, Phuong NT, de Jong MCM, Vlak JM. Low numbers of repeat units in variable number of tandem repeats (VNTR) regions of white spot syndrome virus are correlated with disease outbreaks. JOURNAL OF FISH DISEASES 2012; 35:817-826. [PMID: 22913744 DOI: 10.1111/j.1365-2761.2012.01406.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 12/12/2011] [Accepted: 12/12/2011] [Indexed: 06/01/2023]
Abstract
White spot syndrome virus (WSSV) is the most important pathogen in shrimp farming systems worldwide including the Mekong Delta, Vietnam. The genome of WSSV is characterized by the presence of two major 'indel regions' found at ORF14/15 and ORF23/24 (WSSV-Thailand) and three regions with variable number tandem repeats (VNTR) located in ORF75, ORF94 and ORF125. In the current study, we investigated whether or not the number of repeat units in the VNTRs correlates with virus outbreak status and/or shrimp farming practice. We analysed 662 WSSV samples from individual WSSV-infected Penaeus monodon shrimp from 104 ponds collected from two important shrimp farming regions of the Mekong Delta: Ca Mau and Bac Lieu. Using this large data set and statistical analysis, we found that for ORF94 and ORF125, the mean number of repeat units (RUs) in VNTRs was significantly lower in disease outbreak ponds than in non-outbreak ponds. Although a higher mean RU number was observed in the improved-extensive system than in the rice-shrimp or semi-intensive systems, these differences were not significant. VNTR sequences are thus not only useful markers for studying WSSV genotypes and populations, but specific VNTR variants also correlate with disease outbreaks in shrimp farming systems.
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Affiliation(s)
- T T T Hoa
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
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White spot syndrome virus: Genotypes, Epidemiology and Evolutionary Studies. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2012; 23:175-83. [PMID: 23997441 DOI: 10.1007/s13337-012-0078-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 06/26/2012] [Indexed: 10/28/2022]
Abstract
White spot syndrome virus (WSSV) is a pathogen that has emerged globally affecting shrimp populations. Comparison of WSSV genome have shown the virus to share a high genetic similarity except for a few variable genomic loci that has been employed as markers in molecular epidemiology studies for determining the origin, evolution and spread in different geographical regions. Molecular genotyping of WSSV are based on genomic deletions associated with ORF23/24 and ORF14/15 variable regions and the three variable number of tandem repeat regions, ORF75, ORF94 and ORF125. Studies show the prevalence of several genotypes for WSSV with particular genotypes being more prevalent than others in a given geographical area. Deletions associated with ORF23/24 and ORF14/15 variable regions have proven to be of evolutionary significance. Fitness and virulence studies on different genotypes of WSSV suggest that all the strains of WSSV are equally virulent, but the one with smaller genomic size is the fittest. Studies also have shown that mixed genotype infection of WSSV correlates with lower disease outbreaks. This review focuses on the genotyping studies that were undertaken in elucidating WSSV evolution and epidemiology.
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Hoa TTT, Zwart MP, Phuong NT, Oanh DTH, de Jong MCM, Vlak JM. Indel-II region deletion sizes in the white spot syndrome virus genome correlate with shrimp disease outbreaks in southern Vietnam. DISEASES OF AQUATIC ORGANISMS 2012; 99:153-162. [PMID: 22691984 DOI: 10.3354/dao02463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Sequence comparisons of the genomes of white spot syndrome virus (WSSV) strains have identified regions containing variable-length insertions/deletions (i.e. indels). Indel-I and Indel-II, positioned between open reading frames (ORFs) 14/15 and 23/24, respectively, are the largest and the most variable. Here we examined the nature of these 2 indel regions in 313 WSSV-infected Penaeus monodon shrimp collected between 2006 and 2009 from 76 aquaculture ponds in the Mekong Delta region of Vietnam. In the Indel-I region, 2 WSSV genotypes with deletions of either 5950 or 6031 bp in length compared with that of a reference strain from Thailand (WSSV-TH-96-II) were detected. In the Indel-II region, 4 WSSV genotypes with deletions of 8539, 10970, 11049 or 11866 bp in length compared with that of a reference strain from Taiwan (WSSV-TW) were detected, and the 8539 and 10970 bp genotypes predominated. Indel-II variants with longer deletions were found to correlate statistically with WSSV-diseased shrimp originating from more intensive farming systems. Like Indel-I lengths, Indel-II lengths also varied based on the Mekong Delta province from which farmed shrimp were collected.
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Affiliation(s)
- Tran Thi Tuyet Hoa
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, PB Wageningen, The Netherlands
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Zeng W, Zeng Y, Fei RM, Zeng LB, Wei KJ. Analysis of variable genomic loci in white spot syndrome virus to predict its origins in Procambarus clarkii crayfish farmed in China. DISEASES OF AQUATIC ORGANISMS 2011; 96:105-112. [PMID: 22013750 DOI: 10.3354/dao02388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
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.
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Affiliation(s)
- Wei Zeng
- College of Chemistry and Biology, Yantai University, Shandong 264005, PR China
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Hoa TTT, Zwart MP, Phuong NT, Oanh DTH, de Jong MCM, Vlak JM. Mixed-genotype white spot syndrome virus infections of shrimp are inversely correlated with disease outbreaks in ponds. J Gen Virol 2010; 92:675-80. [DOI: 10.1099/vir.0.026351-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Zwart MP, Dieu BTM, Hemerik L, Vlak JM. Evolutionary trajectory of white spot syndrome virus (WSSV) genome shrinkage during spread in Asia. PLoS One 2010; 5:e13400. [PMID: 20976239 PMCID: PMC2954812 DOI: 10.1371/journal.pone.0013400] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 09/19/2010] [Indexed: 01/21/2023] Open
Abstract
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.
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Affiliation(s)
- Mark P Zwart
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands.
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Dieu BTM, Zwart MP, Vlak JM. Can VNTRs be used to study genetic variation within white spot syndrome virus isolates? JOURNAL OF FISH DISEASES 2010; 33:689-693. [PMID: 20487140 DOI: 10.1111/j.1365-2761.2010.01163.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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