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Krishnan K, Katneni VK, Prabhudas SK, Kaikkolante N, Jangam AK, Katneni UK, Hauton C, Peruzza L, Mudagandur SS, Koyadan VK, Poochirian JK, Jena J. MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus. Virol J 2023; 20:72. [PMID: 37072853 PMCID: PMC10111743 DOI: 10.1186/s12985-023-02035-w] [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: 11/29/2022] [Accepted: 04/09/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND The genome of the largest known animal virus, the white spot syndrome virus (WSSV) responsible for huge economic losses and loss of employment in aquaculture, suffers from inconsistent annotation nomenclature. Novel genome sequence, circular genome and variable genome length led to nomenclature inconsistencies. Since vast knowledge has already accumulated in the past two decades with inconsistent nomenclature, the insights gained on a genome could not be easily extendable to other genomes. Therefore, the present study aims to perform comparative genomics studies in WSSV on uniform nomenclature. METHODS We have combined the standard mummer tool with custom scripts to develop missing regions finder (MRF) that documents the missing genome regions and coding sequences in virus genomes in comparison to a reference genome and in its annotation nomenclature. The procedure was implemented as web tool and in command-line interface. Using MRF, we have documented the missing coding sequences in WSSV and explored their role in virulence through application of phylogenomics, machine learning models and homologous genes. RESULTS We have tabulated and depicted the missing genome regions, missing coding sequences and deletion hotspots in WSSV on a common annotation nomenclature and attempted to link them to virus virulence. It was observed that the ubiquitination, transcription regulation and nucleotide metabolism might be essentially required for WSSV pathogenesis; and the structural proteins, VP19, VP26 and VP28 are essential for virus assembly. Few minor structural proteins in WSSV would act as envelope glycoproteins. We have also demonstrated the advantage of MRF in providing detailed graphic/tabular output in less time and also in handling of low-complexity, repeat-rich and highly similar regions of the genomes using other virus cases. CONCLUSIONS Pathogenic virus research benefits from tools that could directly indicate the missing genomic regions and coding sequences between isolates/strains. In virus research, the analyses performed in this study provides an advancement to find the differences between genomes and to quickly identify the important coding sequences/genomes that require early attention from researchers. To conclude, the approach implemented in MRF complements similarity-based tools in comparative genomics involving large, highly-similar, length-varying and/or inconsistently annotated viral genomes.
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Affiliation(s)
- Karthic Krishnan
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Vinaya Kumar Katneni
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India.
| | - Sudheesh K Prabhudas
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Nimisha Kaikkolante
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Ashok Kumar Jangam
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Upendra Kumar Katneni
- The Center for Blood Oxygen Transport and Hemostasis, Department of Pediatrics, University of Maryland School of Medicine, Maryland, USA
| | - Chris Hauton
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton Waterfront Campus, Southampton, UK
| | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padua, Italy
| | - Shashi Shekhar Mudagandur
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Vijayan K Koyadan
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Jithendran Karingalakkandy Poochirian
- Aquatic Animal Health and Environment Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
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Saravanan K, Praveenraj J, Kiruba-Sankar R, Devi V, Biswas U, Kumar TS, Sudhagar A, El-Matbouli M, Kumar G. Co-Infection of Infectious Hypodermal and Hematopoietic Necrosis Virus (IHHNV) and White Spot Syndrome Virus (WSSV) in the Wild Crustaceans of Andaman and Nicobar Archipelago, India. Viruses 2021; 13:v13071378. [PMID: 34372583 PMCID: PMC8310313 DOI: 10.3390/v13071378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022] Open
Abstract
The present study was intended to screen the wild crustaceans for co-infection with Infectious Hypodermal and Hematopoietic Necrosis Virus (IHHNV) and White Spot Syndrome Virus (WSSV) in Andaman and Nicobar Archipelago, India. We screened a total of 607 shrimp and 110 crab samples using a specific polymerase chain reaction, and out of them, 82 shrimps (13.5%) and 5 (4.5%) crabs were found positive for co-infection of IHHNV and WSSV. A higher rate of co-infection was observed in Penaeus monodon and Scylla serrata than other shrimp and crab species. The nucleotide sequences of IHHNV and WSSV obtained from crab in this present study exhibited very high sequence identity with their counterparts retrieved from various countries. Histopathological analysis of the infected shrimp gill sections further confirmed the eosinophilic intra-nuclear cowdry type A inclusion bodies and basophilic intra-nuclear inclusion bodies characteristics of IHHNV and WSSV infections, respectively. The present study serves as the first report on co-infection of WSSV and IHHNV in Andaman and Nicobar Archipelago, India and accentuates the critical need for continuous monitoring of wild crustaceans and appropriate biosecurity measures for brackishwater aquaculture.
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Affiliation(s)
- Kandasamy Saravanan
- Division of Fisheries Science, Indian Council of Agricultural Research-Central Island Agricultural Research Institute, Port Blair 744105, Andaman and Nicobar Islands, India; (J.P.); (R.K.-S.); (V.D.); (U.B.)
- Correspondence: (K.S.); (G.K.)
| | - Jayasimhan Praveenraj
- Division of Fisheries Science, Indian Council of Agricultural Research-Central Island Agricultural Research Institute, Port Blair 744105, Andaman and Nicobar Islands, India; (J.P.); (R.K.-S.); (V.D.); (U.B.)
| | - Rajendran Kiruba-Sankar
- Division of Fisheries Science, Indian Council of Agricultural Research-Central Island Agricultural Research Institute, Port Blair 744105, Andaman and Nicobar Islands, India; (J.P.); (R.K.-S.); (V.D.); (U.B.)
| | - Varsha Devi
- Division of Fisheries Science, Indian Council of Agricultural Research-Central Island Agricultural Research Institute, Port Blair 744105, Andaman and Nicobar Islands, India; (J.P.); (R.K.-S.); (V.D.); (U.B.)
| | - Utpal Biswas
- Division of Fisheries Science, Indian Council of Agricultural Research-Central Island Agricultural Research Institute, Port Blair 744105, Andaman and Nicobar Islands, India; (J.P.); (R.K.-S.); (V.D.); (U.B.)
| | - Thangaraj Sathish Kumar
- Aquatic Animal Health and Environment Division, Indian Council of Agricultural Research-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, Chennai 600028, Tamil Nadu, India;
| | - Arun Sudhagar
- Peninsular and Marine Fish Genetic Resources Centre, Indian Council of Agricultural Research-National Bureau of Fish Genetic Resources, Ernakulam North P.O., Kochi 682018, Kerala, India;
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine Vienna, Veterinarplatz 1, 1210 Vienna, Austria;
| | - Gokhlesh Kumar
- Clinical Division of Fish Medicine, University of Veterinary Medicine Vienna, Veterinarplatz 1, 1210 Vienna, Austria;
- Correspondence: (K.S.); (G.K.)
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Jain A, Sharma PC. Occurrence and distribution of compound microsatellites in the genomes of three economically important virus families. INFECTION GENETICS AND EVOLUTION 2021; 92:104853. [PMID: 33839312 DOI: 10.1016/j.meegid.2021.104853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/01/2021] [Accepted: 04/04/2021] [Indexed: 11/15/2022]
Abstract
Microsatellites are nonrandom hypervariable iterations of one to six nucleotides, existing across the coding as well as noncoding regions of virtually all known genomes, arising primarily due to polymerase slippage and unequal crossing over during replication events. Two or more perfect microsatellites located in close proximity form compound microsatellites. We studied the distribution of compound microsatellites in 118 ssDNA virus genomes belonging to three economically important virus families, namely Anelloviridae, Circoviridae, and Parvoviridae, known to predominantly infect livestock and humans. Among these virus families, 0-58.49% of perfect microsatellites were involved in the formation of compound microsatellites, the majority being located in the coding regions. No clear relationship existed between the genomic features (genome size and GC%) and compound microsatellite characteristics (relative abundance and relative density). The majority of the compound microsatellites resulted from di-SSR couples. A strong positive relationship was observed between the maximum distance value and length of compound microsatellite, percentage of microsatellites involved in the compound microsatellite formation, and relative microsatellite density. The degree of variability among microsatellite characteristics studied was largely a species-specific phenomenon. A major proportion of compound microsatellites was represented by similar motif combinations. The findings of the present study will help in better understanding of the structural, functional, and evolutionary role of compound microsatellites prevailing in the smaller genomes.
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Affiliation(s)
- Ankit Jain
- Merck Life Science Pvt. Ltd, Sector-17, Chandigarh, India
| | - Prakash C Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka Sector-16 C, New Delhi 11078, India.
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Comparative analysis, distribution, and characterization of microsatellites in Orf virus genome. Sci Rep 2020; 10:13852. [PMID: 32807836 PMCID: PMC7431841 DOI: 10.1038/s41598-020-70634-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/01/2020] [Indexed: 11/09/2022] Open
Abstract
Genome-wide in-silico identification of microsatellites or simple sequence repeats (SSRs) in the Orf virus (ORFV), the causative agent of contagious ecthyma has been carried out to investigate the type, distribution and its potential role in the genome evolution. We have investigated eleven ORFV strains, which resulted in the presence of 1,036-1,181 microsatellites per strain. The further screening revealed the presence of 83-107 compound SSRs (cSSRs) per genome. Our analysis indicates the dinucleotide (76.9%) repeats to be the most abundant, followed by trinucleotide (17.7%), mononucleotide (4.9%), tetranucleotide (0.4%) and hexanucleotide (0.2%) repeats. The Relative Abundance (RA) and Relative Density (RD) of these SSRs varied between 7.6-8.4 and 53.0-59.5 bp/kb, respectively. While in the case of cSSRs, the RA and RD ranged from 0.6-0.8 and 12.1-17.0 bp/kb, respectively. Regression analysis of all parameters like the incident of SSRs, RA, and RD significantly correlated with the GC content. But in a case of genome size, except incident SSRs, all other parameters were non-significantly correlated. Nearly all cSSRs were composed of two microsatellites, which showed no biasedness to a particular motif. Motif duplication pattern, such as, (C)-x-(C), (TG)-x-(TG), (AT)-x-(AT), (TC)- x-(TC) and self-complementary motifs, such as (GC)-x-(CG), (TC)-x-(AG), (GT)-x-(CA) and (TC)-x-(AG) were observed in the cSSRs. Finally, in-silico polymorphism was assessed, followed by in-vitro validation using PCR analysis and sequencing. The thirteen polymorphic SSR markers developed in this study were further characterized by mapping with the sequence present in the database. The results of the present study indicate that these SSRs could be a useful tool for identification, analysis of genetic diversity, and understanding the evolutionary status of the virus.
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Parrilla-Taylor DP, Vibanco-Pérez N, Durán-Avelar MDJ, Gomez-Gil B, Llera-Herrera R, Vázquez-Juárez R. Molecular variability and genetic structure of white spot syndrome virus strains from northwest Mexico based on the analysis of genomes. FEMS Microbiol Lett 2019; 365:5090402. [PMID: 30184198 DOI: 10.1093/femsle/fny216] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/02/2018] [Indexed: 12/14/2022] Open
Abstract
White spot syndrome virus (WSSV) has a ∼300 kb double-stranded DNA genome. It originated in China, spread rapidly through shrimp farms in Asia, and subsequently to America. This study determined complete genome sequences for nine historic WSSV strains isolated from Pacific white shrimp (Litopenaeus vannamei) captured in farm ponds in northwest Mexico (Sinaloa and Nayarit). Genomic DNA was captured by an amplification method using overlapping long-range PCR and sequencing by Ion Torrent-PGM. Complete genome sequences were assembled (length range 255-290 kb) and comparative genome analysis with WSSV strains revealed substantial deletions (3 and 10 kb in two regions) in seven strains, with two strains differing from the rest. Phylogenetic analysis identified that the WSSV strains from the northern area of the state of Sinaloa clustered with strains from China (LC1, LC10, DVI) and Korea (ACF2, ACF4), while those from the southern region of the state of Nayarit (AC1 and JP) differed from both of those and from strains found in Taiwan and Thailand. Our data offer insights into the diversity of the WSSV genome in one country and their divergent origin, suggest that it entered Mexico via multiple routes and that specific genome regions can accommodate substantial deletions without compromising viability.
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Affiliation(s)
- Delia Patricia Parrilla-Taylor
- Centro de Investigaciones Biológicas del Noroeste, Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, La Paz, B.C.S. 23096. México
| | - Norberto Vibanco-Pérez
- Universidad Autónoma de Nayarit. Unidad Académica de Ciencias Químico Biológicas y Farmacéuticas, Tepic, Nayarit. 63000. México
| | - Maria de Jesús Durán-Avelar
- Universidad Autónoma de Nayarit. Unidad Académica de Ciencias Químico Biológicas y Farmacéuticas, Tepic, Nayarit. 63000. México
| | - Bruno Gomez-Gil
- CIAD, A.C. Mazatlán Unit for Aquaculture, Sinaloa. 82000. México
| | - Raúl Llera-Herrera
- Instituto de Ciencias del Mar y Limnología - Unidad Académica Mazatlán, Universidad Nacional Autónoma de México. Joel Montes Camarena s/n, P.O.Box 811. Mazatlán, Sinaloa, Mexico. 82000
| | - Ricardo Vázquez-Juárez
- Centro de Investigaciones Biológicas del Noroeste, Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita Sur, La Paz, B.C.S. 23096. México
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Mani T, Subramaniya BR, Chidambaram Iyer S, Sivasithamparam ND, Devaraj H. Modulation of complex coordinated molecular signaling by 5HT and a cocktail of inhibitors leads to ovarian maturation of Penaeus monodon in captivity. Mol Reprod Dev 2019; 86:576-591. [PMID: 30825396 DOI: 10.1002/mrd.23135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/11/2018] [Accepted: 01/23/2019] [Indexed: 11/07/2022]
Abstract
In aquaculture practices, prawn cultivation holds the major share and Penaeus monodon is the main species cultured. The decline in production of P. monodon is mainly due to the limited availability of domesticated broodstock, which is attributed to its reproductive cycle, controlled by complex coordinated signaling mechanisms. Unilateral eyestalk ablation of domesticated females held in captivity is done to induce ovary development, which has certain disadvantages, including a high rate of mortality. Thus, developing alternative techniques for eyestalk ablation in captive broodstock is necessary to induce maturation of ovary. This study exemplifies the role of 5HT along with a cocktail of inhibitors (U0126, Rp-cAMP, and LY294002) in inducing ovarian maturation. In this study, inhibition of pERK by U0126 inhibited vitellogenesis-inhibiting hormone (VIH), which in turn led to the overexpression of vitellogenin. 5HT induces steroidogenesis (estradiol-17β) through induction of the gonadotropin-releasing hormone by activating calcium-calmodulin signaling. Steroidogenesis is also aided by synthesis of StAR protein. Estradiol-17β stimulates the formation of the maturation-promoting factor (MPF) complex by cdc25 activation and Myt1 inactivation. LY294002 aids in keeping cdc25 activated by inhibiting calcium-calmodulin induced phosphorylation of Akt which is a negative regulator of mitogen-activated protein kinases. VIH induced activation of Myt1, through protein kinase A (PKA), was inhibited by Rp-cAMP which inhibits adenylate cyclase, thus stabilizing the activated MPF complex. To conclude, the coordinated effect of inhibitors and 5HT accelerates the development of ovary from previtellogenic to matured oocytes, yielding high quality and quantity larvae compared with eyestalk-ablated P. monodon.
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Affiliation(s)
- Thiyagu Mani
- Department of Biochemistry, School of Life Sciences, Guindy Campus, University of Madras, Chennai, Tamil Nadu, India.,Department of Zoology, School of Life Sciences, Guindy Campus, University of Madras, Chennai, Tamil Nadu, India
| | - Bharathi Raja Subramaniya
- Department of Biochemistry, School of Life Sciences, Guindy Campus, University of Madras, Chennai, Tamil Nadu, India
| | - Sowmya Chidambaram Iyer
- Department of Zoology, School of Life Sciences, Guindy Campus, University of Madras, Chennai, Tamil Nadu, India
| | | | - Halagowder Devaraj
- Department of Zoology, School of Life Sciences, Guindy Campus, University of Madras, Chennai, Tamil Nadu, India
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Thamizhvanan S, Sivakumar S, Santhosh Kumar S, Vinoth Kumar D, Suryakodi S, Balaji K, Rajkumar T, Vimal S, Abdul Majeed S, Taju G, Sahul Hameed AS. Multiple infections caused by white spot syndrome virus and Enterocytozoon hepatopenaei in pond-reared Penaeus vannamei in India and multiplex PCR for their simultaneous detection. JOURNAL OF FISH DISEASES 2019; 42:447-454. [PMID: 30659620 DOI: 10.1111/jfd.12956] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
White leg shrimp, Penaeus vannamei, were collected on a monthly basis from grow-out ponds located at Tamil Nadu and Andhra Pradesh states along the east coast of India for screening of viral and other pathogens. Totally 240 shrimp samples randomly collected from 92 farms were screened for white spot syndrome virus (WSSV), infectious hypodermal and haematopoietic necrosis virus (IHHNV), infectious myonecrosis virus (IMNV) and Enterocytozoon hepatopenaei (EHP). The number of shrimp collected from shrimp farms ranged from 6 to 20 based on the body weight of the shrimp. All the shrimp collected from one farm were pooled together for screening for pathogens by PCR assay. Among the samples screened, 28 samples were WSSV-positive, one positive for IHHNV and 30 samples positive for EHP. Among the positive samples, four samples were found to be positive for both WSSV and EHP, which indicated that the shrimp had multiple infections with WSSV and EHP. This is the first report on the occurrence of multiple infections caused by WSSV and EHP. Multiplex PCR (m-PCR) protocol was standardized to detect both pathogens simultaneously in single reaction instead of carrying out separate PCR for both pathogens. Using m-PCR assay, naturally infected shrimp samples collected from field showed two prominent bands of 615 and 510 bp for WSSV and EHP, respectively.
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Affiliation(s)
- S Thamizhvanan
- Aquatic Animal Health Laboratory, C. Abdul Hakeem College, Melvisharam, Vellore, Tamil Nadu, India
| | - S Sivakumar
- Aquatic Animal Health Laboratory, C. Abdul Hakeem College, Melvisharam, Vellore, Tamil Nadu, India
| | - S Santhosh Kumar
- Aquatic Animal Health Laboratory, C. Abdul Hakeem College, Melvisharam, Vellore, Tamil Nadu, India
| | - D Vinoth Kumar
- Aquatic Animal Health Laboratory, C. Abdul Hakeem College, Melvisharam, Vellore, Tamil Nadu, India
| | - S Suryakodi
- Aquatic Animal Health Laboratory, C. Abdul Hakeem College, Melvisharam, Vellore, Tamil Nadu, India
| | - K Balaji
- Aquatic Animal Health Laboratory, C. Abdul Hakeem College, Melvisharam, Vellore, Tamil Nadu, India
| | - T Rajkumar
- Aquatic Animal Health Laboratory, C. Abdul Hakeem College, Melvisharam, Vellore, Tamil Nadu, India
| | - S Vimal
- Aquatic Animal Health Laboratory, C. Abdul Hakeem College, Melvisharam, Vellore, Tamil Nadu, India
| | - S Abdul Majeed
- Aquatic Animal Health Laboratory, C. Abdul Hakeem College, Melvisharam, Vellore, Tamil Nadu, India
| | - G Taju
- Aquatic Animal Health Laboratory, C. Abdul Hakeem College, Melvisharam, Vellore, Tamil Nadu, India
| | - A S Sahul Hameed
- Aquatic Animal Health Laboratory, C. Abdul Hakeem College, Melvisharam, Vellore, Tamil Nadu, India
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Sivakumar S, Vimal S, Abdul Majeed S, Santhosh Kumar S, Taju G, Madan N, Rajkumar T, Thamizhvanan S, Shamsudheen KV, Scaria V, Sivasubbu S, Sahul Hameed AS. A new strain of white spot syndrome virus affecting Litopenaeus vannamei in Indian shrimp farms. JOURNAL OF FISH DISEASES 2018; 41:1129-1146. [PMID: 29745450 DOI: 10.1111/jfd.12811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/01/2018] [Indexed: 06/08/2023]
Abstract
White spot syndrome virus (WSSV)-infected shrimp samples collected from grow-out ponds located at Nellore, Andhra Pradesh, India, showed WSSV negative and positive by PCR using primer sets specific to ORF119 and VP28 gene of WSSV, respectively. This indicated the deletion of genetic fragments in the genome of WSSV. The WSSV isolate along with lab strain of WSSV was subjected to next-generation sequencing. The sequence analysis revealed a deletion of 13,170 bp at five positions in the genome of WSSV-NS (new strain) relative to WSSV-TH and WSSV-LS (lab strain). The PCR analysis using the ORF's specific primer sets revealed the complete deletion of 10 ORFs in the genome of WSSV-NS strain. The primer set was designed based on sequence covering ORF161/162/163 to amplify a product of 2,748 bp for WSSV-LS and 402 bp for WSSV-NS. Our surveillance programme carried out since 2002 revealed the replacement of WSSV-LS by WSSV-NS in Indian shrimp culture system.
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Affiliation(s)
- S Sivakumar
- OIE Reference Laboratory for WTD, C. Abdul Hakeem College, Melvisharam, India
| | - S Vimal
- OIE Reference Laboratory for WTD, C. Abdul Hakeem College, Melvisharam, India
| | - S Abdul Majeed
- OIE Reference Laboratory for WTD, C. Abdul Hakeem College, Melvisharam, India
| | - S Santhosh Kumar
- OIE Reference Laboratory for WTD, C. Abdul Hakeem College, Melvisharam, India
| | - G Taju
- OIE Reference Laboratory for WTD, C. Abdul Hakeem College, Melvisharam, India
| | - N Madan
- OIE Reference Laboratory for WTD, C. Abdul Hakeem College, Melvisharam, India
| | - T Rajkumar
- OIE Reference Laboratory for WTD, C. Abdul Hakeem College, Melvisharam, India
| | - S Thamizhvanan
- OIE Reference Laboratory for WTD, C. Abdul Hakeem College, Melvisharam, India
| | - K V Shamsudheen
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research, Delhi, India
| | - V Scaria
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research, Delhi, India
| | - S Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research, Delhi, India
| | - A S Sahul Hameed
- OIE Reference Laboratory for WTD, C. Abdul Hakeem College, Melvisharam, India
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Orosco FL, Lluisma AO. Prevalence, diversity and co-occurrence of the white spot syndrome virus, monodon baculovirus and Penaeus stylirostris densovirus in wild populations of Penaeus monodon in the Philippines. DISEASES OF AQUATIC ORGANISMS 2017; 125:199-206. [PMID: 28792418 DOI: 10.3354/dao03150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The farming of the black tiger shrimp Penaeus monodon in the Philippines relies on wild broodstock. PCR was thus used to determine the prevalence of white spot syndrome virus (WSSV), monodon baculovirus (MBV) and Penaeus stylirostris densovirus (PstDV) in a total of 178 shrimp from 6 geographically disparate locations where broodstock are captured for use in hatcheries. PCR amplicons were also sequenced to identify phylogenetic relationships of the virus haplotypes detected. Shrimp from southeastern Luzon (Camarines Norte) had the highest prevalence of each of the 3 viruses and were frequently co-infected with 2 or more viruses. No viruses were detected in shrimp from northwestern Luzon (Pangasinan). MBV was most prevalent and PstDV strains displayed the most genetic diversity. WSSV was detected at 3 sites, and a VP28 gene sequence examined was invariant and consistent with strains found in many countries, including Thailand, China, Japan, Korea, Indonesia, Iran, Brazil and Mexico. WSSV open reading frame 94 gene sequence analysis identified location-specific repeat types. MBV sequences were dissimilar to haplotypes detected in India. PstDV sequences were diverse and included 2 lineages detected either in Australia or in the United States, Ecuador, Taiwan, China and Vietnam. The PCR data confirmed that WSSV, MBV and PstDV are endemic in P. monodon in the Philippines but that populations at some locations might remain free of infection.
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Affiliation(s)
- Fredmoore L Orosco
- Marine Genomics and Molecular Genetics Laboratory, Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Phillippines
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Orosco FL, Lluisma AO. Variation in virome diversity in wild populations of Penaeus monodon (Fabricius 1798) with emphasis on pathogenic viruses. Virusdisease 2017; 28:262-271. [PMID: 29291212 DOI: 10.1007/s13337-017-0389-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/20/2017] [Indexed: 11/28/2022] Open
Abstract
Marine animals typically harbor a community of viruses, a number of which are known to cause diseases. In shrimp aquaculture, viral pathogens are the principal causes of major economic losses. However, the composition of the viral load of shrimps in wild population is poorly known. In this study, we explored the viral diversity in the microbiome of wild Penaeus monodon collected from six sites in the Philippines, with a view to detecting pathogenic forms. We employed a metagenomic approach via particle-associated nucleic acid isolation, sequence-independent single primer amplification, and pyrosequencing. Virome analysis of shrimp samples from different sites revealed distinct virome profiles, and hence significant differences in diversity, among the various sites based on number of OTUs, Shannon-Weaver Index, and Inverse Simpson Index. Sequences of key shrimp pathogens were detected such as the white spot syndrome virus (WSSV), and Penaeus stylirostris densovirus (PstDV). However, the patterns of distribution of the pathogenic viruses varied; whereas WSSV was found only in three out of six sites and PstDV were found in all but one site. The results also revealed shrimp-associated viruses that have not yet been observed in P. monodon such as avian virus-like, insect virus-like, plankton virus-like and bacteriophage-like sequences. Despite the diverse array of viruses detected in the study, a large proportion remains unidentified (i.e., similarity to sequences in the database was lower than the threshold required for definitive identification), and therefore could represent unexplored virus sequences and viral genomes in the environment.
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Affiliation(s)
- Fredmoore L Orosco
- Marine Genomics and Molecular Genetics Laboratory, Marine Science Institute, University of the Philippines - Diliman, 1101 Quezon City, Philippines.,Institute of Biology, University of the Philippines - Diliman, 1101 Quezon City, Philippines
| | - Arturo O Lluisma
- Marine Genomics and Molecular Genetics Laboratory, Marine Science Institute, University of the Philippines - Diliman, 1101 Quezon City, Philippines
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11
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Dhar AK, Robles-Sikisaka R, Saksmerprome V, Lakshman DK. Biology, genome organization, and evolution of parvoviruses in marine shrimp. Adv Virus Res 2014; 89:85-139. [PMID: 24751195 DOI: 10.1016/b978-0-12-800172-1.00003-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
As shrimp aquaculture has evolved from a subsistent farming activity to an economically important global industry, viral diseases have also become a serious threat to the sustainable growth and productivity of this industry. Parvoviruses represent an economically important group of viruses that has greatly affected shrimp aquaculture. In the early 1980s, an outbreak of a shrimp parvovirus, infectious hypodermal and hematopoietic necrosis virus (IHHNV), led to the collapse of penaeid shrimp farming in the Americas. Since then, considerable progress has been made in characterizing the parvoviruses of shrimp and developing diagnostic methods aimed to preventing the spread of diseases caused by these viruses. To date, four parvoviruses are known that infect shrimp; these include IHHNV, hepatopancreatic parvovirus (HPV), spawner-isolated mortality virus (SMV), and lymphoid organ parvo-like virus. Due to the economic repercussions that IHHNV and HPV outbreaks have caused to shrimp farming over the years, studies have been focused mostly on these two pathogens, while information on SMV and LPV remains limited. IHHNV was the first shrimp virus to be sequenced and the first for which highly sensitive diagnostic methods were developed. IHHNV-resistant lines of shrimp were also developed to mitigate the losses caused by this virus. While the losses due to IHHNV have been largely contained in recent years, reports of HPV-induced mortalities in larval stages in hatchery and losses due to reduced growth have increased. This review presents a comprehensive account of the history and current knowledge on the biology, diagnostics methods, genomic features, mechanisms of evolution, and management strategies of shrimp parvoviruses. We also highlighted areas where research efforts should be focused in order to gain further insight on the mechanisms of parvoviral pathogenicity in shrimp that will help to prevent future losses caused by these viruses.
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Affiliation(s)
| | | | - Vanvimon Saksmerprome
- Centex Shrimp, Faculty of Science, Mahidol University, Bangkok, Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Dilip K Lakshman
- USDA-ARS, Floral & Nursery Plants Research Unit, Beltsville, Maryland, USA
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12
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Gandhi S, Felini MJ, Ndetan H, Cardarelli K, Jadhav S, Faramawi M, Johnson ES. A Pilot Case-Cohort Study of Brain Cancer in Poultry and Control Workers. Nutr Cancer 2014; 66:343-50. [DOI: 10.1080/01635581.2013.878734] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Otta SK, Arulraj R, Ezhil Praveena P, Manivel R, Panigrahi A, Bhuvaneswari T, Ravichandran P, Jithendran KP, Ponniah AG. Association of dual viral infection with mortality of Pacific white shrimp (Litopenaeus vannamei) in culture ponds in India. Virusdisease 2013; 25:63-8. [PMID: 24426311 DOI: 10.1007/s13337-013-0180-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 11/11/2013] [Indexed: 11/25/2022] Open
Abstract
Pacific white shrimp, Litopenaeus vannamei has been introduced recently for culture practice in India. Though SPF stocks are imported for larval production and thereafter culture practice, these are prone to infection with the existing viruses in the environment. Here we report mortality of L.vannamei in several farms in India with minimum biosecurity. The shrimp were harvested early within 50-72 days of culture due to the onset of disease and consequent mortality. As per the analysis carried out, the shrimp were infected with two virus, white spot syndrome virus (WSSV) and infectious hypodermal and hematopoietic necrosis virus (IHHNV). About 80 % of the samples collected had either or both of the viruses. A majority of these samples (60 %) had dual infection with WSSV and IHHNV. Infection of shrimp with WSSV and IHHNV could be detected both by PCR and histopathology. Some of the samples had either exclusively WSSV infection or IHHNV infection and were also harvested before the completion of the required culture period. All the samples analyzed were negative for taura syndrome virus, yellow head virus and infectious myonecrosis virus. While it is difficult to point out the exact etiological agent as the cause of mortality, strict biosecurity measures are advisable for the continuity of L. vannamei culture in India.
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Affiliation(s)
- S K Otta
- Aquatic Animal Health and Environment Division, Central Institute of Brackishwater Aquaculture, 75. Santhome High Road, RA Puram, Chennai, 600 028 India
| | - R Arulraj
- Aquatic Animal Health and Environment Division, Central Institute of Brackishwater Aquaculture, 75. Santhome High Road, RA Puram, Chennai, 600 028 India
| | - P Ezhil Praveena
- Aquatic Animal Health and Environment Division, Central Institute of Brackishwater Aquaculture, 75. Santhome High Road, RA Puram, Chennai, 600 028 India
| | - R Manivel
- Aquatic Animal Health and Environment Division, Central Institute of Brackishwater Aquaculture, 75. Santhome High Road, RA Puram, Chennai, 600 028 India
| | - A Panigrahi
- Aquatic Animal Health and Environment Division, Central Institute of Brackishwater Aquaculture, 75. Santhome High Road, RA Puram, Chennai, 600 028 India
| | - T Bhuvaneswari
- Aquatic Animal Health and Environment Division, Central Institute of Brackishwater Aquaculture, 75. Santhome High Road, RA Puram, Chennai, 600 028 India
| | - P Ravichandran
- Aquatic Animal Health and Environment Division, Central Institute of Brackishwater Aquaculture, 75. Santhome High Road, RA Puram, Chennai, 600 028 India
| | - K P Jithendran
- Aquatic Animal Health and Environment Division, Central Institute of Brackishwater Aquaculture, 75. Santhome High Road, RA Puram, Chennai, 600 028 India
| | - A G Ponniah
- Aquatic Animal Health and Environment Division, Central Institute of Brackishwater Aquaculture, 75. Santhome High Road, RA Puram, Chennai, 600 028 India
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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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15
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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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Haq MAB, Vignesh R, Srinivasan M. Deep insight into white spot syndrome virus vaccines: A review. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2012. [DOI: 10.1016/s2222-1808(12)60018-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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18
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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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19
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Multiplex real-time PCR and high-resolution melting analysis for detection of white spot syndrome virus, yellow-head virus, and Penaeus monodon densovirus in penaeid shrimp. J Virol Methods 2011; 178:16-21. [PMID: 21906627 DOI: 10.1016/j.jviromet.2011.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 07/11/2011] [Accepted: 07/20/2011] [Indexed: 12/11/2022]
Abstract
A multiplex real-time PCR and high-resolution melting (HRM) analysis was developed to detect simultaneously three of the major viruses of penaeid shrimp including white spot syndrome virus (WSSV), yellow-head virus (YHV), and Penaeus monodon densovirus (PmDNV). Plasmids containing DNA/cDNA fragments of WSSV and YHV, and genomic DNAs of PmDNV and normal shrimp were used to test sensitivity of the procedure. Without the need of any probe, the products were identified by HRM analysis after real-time PCR amplification using three sets of viral specific primers. The results showed DNA melting curves that were specific for individual virus. No positive result was detected with nucleic acids from shrimp, Penaeus monodon nucleopolyhedrovirus (PemoNPV), Penaeus stylirostris densovirus (PstDNV), or Taura syndrome virus (TSV). The detection limit for PmDNV, YHV and WSSV DNAs were 40fg, 50fg, and 500fg, respectively, which was 10 times more sensitive than multiplex real-time PCR analyzed by agarose gel electrophoresis. In viral nucleic acid mixtures, HRM analysis clearly identified each virus in dual and triple infection. To test the capability to use this method in field, forty-one of field samples were examined by HRM analysis in comparison with agarose gel electrophoresis. For HRM analysis, 11 (26.83%), 9 (21.95%), and 4 (9.76%) were infected with WSSV, PmDNV, and YHV, respectively. Agarose gel electrophoresis detected lesser number of PmDNV infection which may due to the limit of sensitivity. No multiple infection was found in these samples. This method provides a rapid, sensitive, specific, and simultaneous detection of three major viruses making it as a useful tool for diagnosis and epidemiological studies of these viruses in shrimp and carriers.
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20
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Tan YW, Shi ZL. Genotyping of white spot syndrome virus in Chinese cultured shrimp during 1998-1999. Virol Sin 2011; 26:123-30. [PMID: 21468935 DOI: 10.1007/s12250-011-3181-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 02/18/2011] [Indexed: 11/26/2022] Open
Abstract
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.
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Affiliation(s)
- Yan-wei Tan
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
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21
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Prevalence of three shrimp viruses in Zhejiang Province in 2008. Virol Sin 2011; 26:67-71. [PMID: 21331893 DOI: 10.1007/s12250-011-3157-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 10/17/2010] [Indexed: 10/18/2022] Open
Abstract
White spot syndrome virus (WSSV), Taura syndrome virus (TSV) and Infectious hypodermal and haematopoietic necrosis virus (IHHNV) are three shrimp viruses responsible for major pandemics affecting the shrimp farming industry. Shrimps samples were collected from 12 farms in Zhejiang province, China, in 2008 and analyzed by PCR to determine the prevalence of these viruses. From the 12 sampling locations, 8 farms were positive for WSSV, 8 for IHHNV and 6 for both WSSV and IHHNV. An average percentage of 57.4% of shrimp individuals were infected with WSSV, while 49.2% were infected with IHHNV. A high prevalence of co-infection with WSSV and IHHNV among samples was detected from the following samples: Bingjiang (93.3%), liuao (66.7%), Jianshan (46.7%) and Xianxiang (46.7%). No samples exhibited evidence of infection with TSV in collected samples. This study provides comprehensive information of the prevalence of three shrimp viruses in Zhejiang and may be helpful for disease prevention control in this region.
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Abstract
The rise of aquaculture has been one of the most profound changes in global food production of the past 100 years. Driven by population growth, rising demand for seafood and a levelling of production from capture fisheries, the practice of farming aquatic animals has expanded rapidly to become a major global industry. Aquaculture is now integral to the economies of many countries. It has provided employment and been a major driver of socio-economic development in poor rural and coastal communities, particularly in Asia, and has relieved pressure on the sustainability of the natural harvest from our rivers, lakes and oceans. However, the rapid growth of aquaculture has also been the source of anthropogenic change on a massive scale. Aquatic animals have been displaced from their natural environment, cultured in high density, exposed to environmental stress, provided artificial or unnatural feeds, and a prolific global trade has developed in both live aquatic animals and their products. At the same time, over-exploitation of fisheries and anthropogenic stress on aquatic ecosystems has placed pressure on wild fish populations. Not surprisingly, the consequence has been the emergence and spread of an increasing array of new diseases. This review examines the rise and characteristics of aquaculture, the major viral pathogens of fish and shrimp and their impacts, and the particular characteristics of disease emergence in an aquatic, rather than terrestrial, context. It also considers the potential for future disease emergence in aquatic animals as aquaculture continues to expand and faces the challenges presented by climate change.
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Affiliation(s)
- Peter J Walker
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, Victoria, Australia.
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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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24
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Seibert CH, Borsa M, Rosa RD, Cargnin-Ferreira E, Pereira AML, Grisard EC, Zanetti CR, Pinto AR. Detection of major capsid protein of infectious myonecrosis virus in shrimps using monoclonal antibodies. J Virol Methods 2010; 169:169-75. [PMID: 20678523 DOI: 10.1016/j.jviromet.2010.07.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 07/16/2010] [Accepted: 07/22/2010] [Indexed: 12/12/2022]
Abstract
Infectious myonecrosis virus (IMNV) has been causing a progressive disease in farm-reared shrimps in Brazil and Indonesia. Immunodiagnostic methods for IMNV detection, although reliable, are not employed currently because monoclonal antibodies (MAbs) against this virus are not available. In this study, a fragment of the IMNV major capsid protein gene, comprising amino acids 300-527 (IMNV(300-527)), was cloned and expressed in Escherichia coli. The nucleotide sequence of the recombinant IMNV(300-527) fragment displayed a high degree of identity to the major capsid protein of IMNV isolates from Brazil (99%) and Indonesia (98%). Ten MAbs were generated against the expressed fragment, and eight of these, mostly IgG(2a) or IgG(2b), were able to bind to IMNV in tissue extracts from shrimps infected naturally in immunodot-blot assays. Six of these MAbs recognized a approximately 100 kDa protein in a Western-blot, which is the predicted mass of IMNV major capsid protein, and also bound to viral inclusions present in muscle fibroses and in coagulative myonecrosis, as demonstrated by immunohistochemistry. Among all those MAbs created, four did not cross-react with non-infected shrimp tissues; this observation supports their applicability as a sensitive and specific immunodiagnosis of IMNV infection in shrimps.
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Affiliation(s)
- Caroline H Seibert
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, 88040-970, Florianópolis, SC, Brazil
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25
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Dieu BTM, Marks H, Zwart MP, Vlak JM. Evaluation of white spot syndrome virus variable DNA loci as molecular markers of virus spread at intermediate spatiotemporal scales. J Gen Virol 2010; 91:1164-72. [PMID: 20089797 DOI: 10.1099/vir.0.018028-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Variable genomic loci have been employed in a number of molecular epidemiology studies of white spot syndrome virus (WSSV), but it is unknown which loci are suitable molecular markers for determining WSSV spread on different spatiotemporal scales. Although previous work suggests that multiple introductions of WSSV occurred in central Vietnam, it is largely uncertain how WSSV was introduced and subsequently spread. Here, we evaluate five variable WSSV DNA loci as markers of virus spread on an intermediate (i.e. regional) scale, and develop a detailed and statistically supported model for the spread of WSSV. The genotypes of 17 WSSV isolates from along the coast of Vietnam--nine of which were newly characterized in this study--were analysed to obtain sufficient samples on an intermediate scale and to allow statistical analysis. Only the ORF23/24 variable region is an appropriate marker on this scale, as geographically proximate isolates show similar deletion sizes. The ORF14/15 variable region and variable-number tandem repeat (VNTR) loci are not useful as markers on this scale. ORF14/15 may be suitable for studying larger spatiotemporal scales, whereas VNTR loci are probably suitable for smaller scales. For ORF23/24, there is a clear pattern in the spatial distribution of WSSV: the smallest genomic deletions are found in central Vietnam, and larger deletions are found in the south and the north. WSSV genomic deletions tend to increase over time with virus spread in cultured shrimp, and our data are therefore congruent with the hypothesis that WSSV was introduced in central Vietnam and then radiated out.
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Affiliation(s)
- Bui Thi Minh Dieu
- Laboratory of Virology, Wageningen University, Radix building (#107), Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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