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Mercer LK, Harding EF, Sridhar T, White PA. Novel viruses discovered in metatranscriptomic analysis of farmed barramundi in Asia and Australia. Virology 2024; 599:110208. [PMID: 39154629 DOI: 10.1016/j.virol.2024.110208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/22/2024] [Accepted: 08/12/2024] [Indexed: 08/20/2024]
Abstract
Barramundi aquaculture is at risk of severe disease outbreaks and massive production losses. Here we used bioinformatics to screen 84 farmed barramundi transcriptomes to identify novel viruses that could threaten barramundi aquaculture and to establish a barramundi aquaculture virome. We discovered five novel viruses: latid herpesvirus 1 (LatHV-1) from the Alloherpesviridae family, barramundi parvovirus 1 (BParV1) from the Parvoviridae family, barramundi calicivirus 1 (BCaV1) from the Caliciviridae family, and barramundi associated picorna-like virus 1 and 2 (BPicV1 and BPicV2) from the Picornaviridae family. LatHV-1, BCaV1, and BParV1 are closely related to pathogenic viruses found in other fish species that can cause mass mortality in farms. To aid in future viral surveillance, we also designed and successfully tested an RT-PCR assay for the detection of BCaV1. Overall, we discovered a range of pathogenic viruses in barramundi aquaculture, paving the way for developing effective detection methods to assist early outbreak management.
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Affiliation(s)
- Lewis K Mercer
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Emma F Harding
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Tanu Sridhar
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia.
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Simmelink B, Coolen JPM, Vogels W, Deijs M, van der Last-Kempkes JLM, Ng KS, Chang SF, Gevers K, Harkema L, van der Hoek L, de Groof A. Discovery, Pathogenesis, and Complete Genome Characterization of Lates calcarifer Herpesvirus. Genes (Basel) 2024; 15:264. [PMID: 38540323 PMCID: PMC10970581 DOI: 10.3390/genes15030264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/03/2024] [Accepted: 02/16/2024] [Indexed: 06/15/2024] Open
Abstract
In 2015 and 2016, two Barramundi (Lates calcarifer) farms in Singapore reported a disease outbreak characterized by lethargic behavior, pronounced inappetence, generalized skin lesions, erosions of the fins and tail, and ultimately high mortality in their fish. Next-generation sequencing and PCR confirmed presence of a novel virus belonging to the Alloherpesviridae family, Lates calcarifer herpesvirus (LCHV), which was subsequently isolated and cultured. We characterize, for the first time, the complete genome of two cultured LCHV isolates. The genome contains a long unique region of approximately 105,000 bp flanked by terminal repeats of approximately 24,800 bp, of which the first 8.2 kb do not show any similarity to described genomes in the Alloherpesviridae family. The two cultured isolates share 89% nucleotide identity, and their closest relatives are the viruses belonging to the genus Ictalurivirus. Experimental infections using one of the cultured LCHV isolates resulted in identical clinical signs as originally described in the index farm, both in intraperitoneal-injection infected fish and cohabitant fish, with mortality in both groups. Histopathological analysis showed pronounced abnormalities in the gills. Virus culture and PCR analysis confirmed the replication of LCHV in the infected fish, and thus Koch's postulates were fulfilled.
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Affiliation(s)
- Bartjan Simmelink
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (B.S.); (W.V.); (J.L.M.v.d.L.-K.); (K.G.)
| | - Jordy P. M. Coolen
- Department R&D-IT, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands;
| | - Wannes Vogels
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (B.S.); (W.V.); (J.L.M.v.d.L.-K.); (K.G.)
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
- Amsterdam Institute for Infection and Immunity, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Jessica L. M. van der Last-Kempkes
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (B.S.); (W.V.); (J.L.M.v.d.L.-K.); (K.G.)
| | - Kah Sing Ng
- MSD Animal Health Innovation Pte Ltd., 1 Perahu Road, Singapore 718847, Singapore; (K.S.N.); (S.F.C.)
| | - Siow Foong Chang
- MSD Animal Health Innovation Pte Ltd., 1 Perahu Road, Singapore 718847, Singapore; (K.S.N.); (S.F.C.)
| | - Koen Gevers
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (B.S.); (W.V.); (J.L.M.v.d.L.-K.); (K.G.)
| | - Liesbeth Harkema
- Department Animal Research & Pathology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands;
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
- Amsterdam Institute for Infection and Immunity, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Ad de Groof
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (B.S.); (W.V.); (J.L.M.v.d.L.-K.); (K.G.)
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Shahrajabian MH, Sun W. The Significance and Importance of dPCR, qPCR, and SYBR Green PCR Kit in the Detection of Numerous Diseases. Curr Pharm Des 2024; 30:169-179. [PMID: 38243947 DOI: 10.2174/0113816128276560231218090436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 01/22/2024]
Abstract
Digital PCR (dPCR) is the latest technique that has become commercially accessible for various types of research. This method uses Taq polymerase in a standard polymerase chain reaction (PCR) to amplify a target DNA fragment from a complex sample, like quantitative PCR (qPCR) and droplet digital PCR (dd- PCR). ddPCR may facilitate microRNA (miRNA) measurement, particularly in liquid biopsy, because it has been proven to be more effective and sensitive, and in this method, ddPCR can provide an unprecedented chance for deoxyribonucleic acid (DNA) methylation research because of its capability to increase sensitivity and precision over conventional PCR-based methods. qPCR has also been found to be a valuable standard technique to measure both copy DNA (cDNA) and genomic DNA (gDNA) levels, although the finding data can be significantly variable and non-reproducible without relevant validation and verification of both primers and samples. The SYBR green quantitative real-time PCR (qPCR) method has been reported as an appropriate technique for quantitative detection and species discrimination, and has been applied profitably in different experiments to determine, quantify, and discriminate species. Although both TaqMan qRT-PCR and SYBR green qRT-PCR are sensitive and rapid, the SYBR green qRT-PCR assay is easy and the TaqMan qRT-PCR assay is specific but expensive due to the probe required. This review aimed to introduce dPCR, qPCR, SYBR green PCR kit, and digital PCR, compare them, and also introduce their advantages in the detection of different diseases.
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Affiliation(s)
- Mohamad Hesam Shahrajabian
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100086, China
| | - Wenli Sun
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100086, China
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Phasunon R, Taengphu S, Panphut W, Chatchaiphan S, Dong HT, Senapin S. Improving the diagnosis of Streptococcus iniae using a novel probe-based qPCR assay combined with an enrichment step. JOURNAL OF FISH DISEASES 2023; 46:1391-1401. [PMID: 37723600 DOI: 10.1111/jfd.13857] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/07/2023] [Accepted: 08/28/2023] [Indexed: 09/20/2023]
Abstract
Streptococcus iniae is a bacterial pathogen that causes streptococcosis, leading to significant losses in fish aquaculture globally. This study reported a newly developed probe-based quantitative polymerase chain reaction (qPCR) method for the detection of S. iniae. The primers and probes were designed to target the lactate oxidase gene. The optimized method demonstrated a detection limit of 20 copies per reaction and was specific to S. iniae, as evidenced by no cross-reactivity when assayed against genetic materials extracted from 23 known aquatic animal pathogens, and fish samples infected with Streptococcus agalactiae or Streptococcus dysgalactiae. To validate the newly developed qPCR protocol with field samples, fish specimens were systematically investigated following the Food and Agriculture Organization of the United Nations & Network of Aquaculture Centres in Asia-Pacific three diagnostic levels approach, which integrated basic and advanced techniques for disease diagnosis, including observation of gross signs (level I), bacterial isolation (level II), qPCR and 16S rDNA sequencing (level III). The result showed that 7/7 affected farms (three Asian seabass farms and four tilapia farms) experiencing clinical signs of streptococcosis were diagnosed positive for S. iniae. qPCR assays using DNA extracted directly from fish tissue detected S. iniae in 11 out of 36 fish samples (30.6%), while 24 out of 36 samples (66.7%) tested positive after an enrichment step, including apparently healthy fish from affected farms. Bacterial isolation of S. iniae was only successful in a proportion of clinically diseased fish but not in healthy-looking fish from the same farm. Overall, the newly developed qPCR protocol combined with enrichment would be a useful tool for the diagnosis and surveillance of S. iniae infections in fish populations, thereby aiding in the disease control and prevention.
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Affiliation(s)
- Ramida Phasunon
- Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, Thailand
| | - Suwimon Taengphu
- Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, Thailand
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani, Thailand
| | - Wattana Panphut
- Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, Thailand
| | - Satid Chatchaiphan
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Ha Thanh Dong
- Department of Food, Agriculture and Bioresources, Aquaculture and Aquatic Resources Management Program, Asian Institute of Technology (AIT), School of Environment, Resources and Development, Klong Luang, Pathum Thani, Thailand
| | - Saengchan Senapin
- Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, Thailand
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Klong Luang, Pathum Thani, Thailand
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Linh NV, Khongcharoen N, Nguyen DH, Dien LT, Rungrueng N, Jhunkeaw C, Sangpo P, Senapin S, Uttarotai T, Panphut W, St-Hilaire S, Van Doan H, Dong HT. Effects of hyperoxia during oxygen nanobubble treatment on innate immunity, growth performance, gill histology, and gut microbiome in Nile tilapia, Oreochromis niloticus. FISH & SHELLFISH IMMUNOLOGY 2023; 143:109191. [PMID: 37890736 DOI: 10.1016/j.fsi.2023.109191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
Oxygen nanobubble (NB-O2) technology has been introduced to the aquaculture industry in recent years. This treatment usually results in a tremendously high level of dissolved oxygen (DO) in the water. However, little is known about the possible negative effects of hyperoxia due to NB-O2 treatment (hyper-NB-O2) on farmed fish. Here, we investigated i) the effect of short-term hyper-NB-O2 exposure (single treatment) on the innate immunity in Nile tilapia, Oreochromis niloticus, and ii) the effect of long-term hyper-NB-O2 exposure (26-day treatments) on survival, growth performance, gill histology, and gut microbiome in Nile tilapia. A single treatment with NB-O2 for 10 min in 50 L of water resulted in 24.2 ± 0.04 mg/L DO (approximately 2-3 × 107 nanoscale oxygen bubbles/mL). This treatment did not result in differences in expression of several immune-related genes (e.g., TNF-α, LYZ and HPS70) in various tissues (e.g., gill, head kidney, and spleen) compared to the non-treated control. Over a 26-day period of exposure, no significant differences were observed in survival and growth performance of the fish, but minor histological changes were occasionally noted on the gills. Analysis of the gut microbiome revealed a significant increase in the genera Bosea, Exiguobacterium, Hyphomicrobium, and Singulisphaera in the group receiving NB-O2. Moreover, no signs of "gas bubble disease" were observed in the fish throughout the duration of the experiment. Overall, these results suggest that both short- and long-term hyper-NB-O2 exposure appears to be benign and has no obvious adverse effects on fish.
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Affiliation(s)
- Nguyen Vu Linh
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand; Functional Feed Innovation Center (FuncFeed), Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Nareerat Khongcharoen
- Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand
| | - Dinh-Hung Nguyen
- Center of Excellence in Fish Infectious Diseases (CE FID), Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Le Thanh Dien
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam
| | - Naruporn Rungrueng
- Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand
| | - Chayuda Jhunkeaw
- Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand
| | - Pattiya Sangpo
- Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand
| | - Saengchan Senapin
- Fish Health Platform, Centex of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Toungporn Uttarotai
- Department of Highland Agriculture and Natural Resources, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Wattana Panphut
- Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand
| | - Sophie St-Hilaire
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Hien Van Doan
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand; Functional Feed Innovation Center (FuncFeed), Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Ha Thanh Dong
- Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand; Aquaculture and Aquatic Resources Management Program, Department of Food, Agriculture and Biore-sources (AARM/FAB), School of Environment, Resources and Development, Asian Institute of Technology, Pathum Thani, Thailand.
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Dong HT, Sangpo P, Dien LT, Mai TT, Linh NV, Del-Pozo J, Salin KR, Senapin S. Usefulness of the pancreas as a prime target for histopathological diagnosis of Tilapia parvovirus (TiPV) infection in Nile tilapia, Oreochromis niloticus. JOURNAL OF FISH DISEASES 2022; 45:1323-1331. [PMID: 35638102 DOI: 10.1111/jfd.13663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/12/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Tilapia parvovirus (TiPV) is an emerging virus reportedly associated with disease and mortality in farmed tilapia. Although previous descriptions of histopathological changes are available, the lesions reported in these are not pathognomonic. Here, we report Cowdry type A inclusion bodies (CAIB) in the pancreas as a diagnostic histopathological feature found in adult Nile tilapia naturally infected with TiPV. This type of inclusion body has been well-known as a histopathological landmark for the diagnosis of other parvoviral infections in shrimp and terrestrial species. Interestingly, this lesion could be exclusively observed in pancreatic acinar cells, both in the hepatopancreas and pancreatic tissue along the intestine. In situ hybridization (ISH) using a TiPV-specific probe revealed the intranuclear presence of TiPV DNA in multiple tissues, including the liver, pancreas, kidney, spleen, gills and the membrane of oocytes in the ovary. These findings suggest that although TiPV can replicate in several tissue types, CAIB manifest exclusively in pancreatic tissues. In addition to TiPV, most diseased fish were co-infected with Streptococcus agalactiae, and presented with multifocal granulomas secondary to this bacterial infection. Partial genome amplification of TiPV was successful and revealed high nucleotide identity (>99%) to previously reported isolates. In summary, this study highlights the usefulness of pancreatic tissue as a prime target for histopathological diagnosis of TiPV in diseased Nile tilapia. This pattern may be critical when determining the presence of TiPV infection in new geographic areas, where ancillary testing may not be available. TiPV pathogenesis in this landmark organ warrants further investigation.
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Affiliation(s)
- Ha Thanh Dong
- AARM/FAB, School of Environment, Resources and Development, Asian Institute of Technology, Pathum Thani, Thailand
| | - Pattiya Sangpo
- Fish Heath Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Le Thanh Dien
- Faculty of Applied Technology, School of Engineering and Technology, Van Lang University, Ho Chi Minh City, Vietnam
| | - Thao Thu Mai
- Division of Aquacultural Biotechnology, Biotechnology Center of Ho Chi Minh City, Ho Chi Minh, Vietnam
| | - Nguyen Vu Linh
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
| | - Jorge Del-Pozo
- Easter Bush Pathology, Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | - Krishna R Salin
- AARM/FAB, School of Environment, Resources and Development, Asian Institute of Technology, Pathum Thani, Thailand
| | - Saengchan Senapin
- Fish Heath Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, Thailand
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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Linh NV, Dien LT, Sangpo P, Senapin S, Thapinta A, Panphut W, St-Hilaire S, Rodkhum C, Dong HT. Pre-treatment of Nile tilapia (Oreochromis niloticus) with ozone nanobubbles improve efficacy of heat-killed Streptococcus agalactiae immersion vaccine. FISH & SHELLFISH IMMUNOLOGY 2022; 123:229-237. [PMID: 35288305 DOI: 10.1016/j.fsi.2022.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/13/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Nanobubble technology has shown appealing technical benefits and potential applications in aquaculture. We recently found that treatment with ozone nanobubbles (NB-O3) activated expression of several immune-related genes leading to effective response to subsequent exposure to fish pathogens. In this study, we investigated whether pre-treatment of Nile tilapia (Oreochromis niloticus) with NB-O3 can enhance specific immune responses and improve efficacy of immersion vaccination against Streptococcus agalactiae. Spleen and head kidney of fish in the vaccinated groups showed a substantial upregulation in expression levels of pro-inflammatory cytokine genes (IL-1β, TNF-α, IL-6) and immunoglobulin classes (IgM, IgD, IgT) compared with the unvaccinated control groups. The mRNA transcript of pro-inflammatory cytokine genes was greatest (approx. 2.8-3.3 folds) on day 7 post-vaccination, whereas the relative expression of immunoglobulin genes was greatest (approx. 3.2-4.1 folds) on day 21 post-immunization. Both systemic and mucosal IgM antibodies were elicited in vaccinated groups. As the result, the cumulative survival rate of the vaccinated groups was found to be higher than that of the unvaccinated groups, with a relative percent survival (RPS) ranging from 52.9 to 70.5%. However, fish in the vaccinated groups that received pre-treatment with NB-O3, bacterial antigen uptakes, expression levels of IL-1β, TNF-α, IL-6,IgM, IgD, and IgT, as well as the specific-IgM antibody levels and percent survival, were all slightly or significantly higher than that of the vaccinated group without pre-treatment with NB-O3. Taken together, our findings suggest that utilizing pre-treatment with NB-O3 may improve the immune response and efficacy of immersion vaccination in Nile tilapia.
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Affiliation(s)
- Nguyen Vu Linh
- Center of Excellence in Fish Infectious Diseases (CE FID), Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Le Thanh Dien
- Faculty of Applied Technology, School of Engineering and Technology, Van Lang University, Ho Chi Minh City, 71415, Viet Nam
| | - Pattiya Sangpo
- Fish Health Platform, Centex of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Saengchan Senapin
- Fish Health Platform, Centex of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Anat Thapinta
- Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand
| | - Wattana Panphut
- Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand
| | - Sophie St-Hilaire
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Channarong Rodkhum
- Center of Excellence in Fish Infectious Diseases (CE FID), Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Ha Thanh Dong
- Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand; Department of Food, Agriculture and Bioresources, School of Environment, Resources and Development, Asian Institute of Technology, Pathum Thani, 12120, Thailand.
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Sahu R, Vishnuraj MR, Srinivas C, Dadimi B, Megha GK, Pollumahanti N, Malik SS, Vaithiyanathan S, Rawool DB, Barbuddhe SB. Development and comparative evaluation of droplet digital PCR and quantitative PCR for the detection and quantification of Chlamydia psittaci. J Microbiol Methods 2021; 190:106318. [PMID: 34592374 DOI: 10.1016/j.mimet.2021.106318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
Chlamydia psittaci is a zoonotic pathogen mainly transmitted by psittacine birds and poultry. The low shedding rate of the pathogen in the apparently healthy birds and human clinical cases may result in false-negative results. In the present study, a droplet digital PCR (ddPCR) assay was developed and compared with optimized quantitative PCR (qPCR) for the detection of C. psittaci from the clinical samples. The ddPCR assay was found to be comparatively more sensitive than the qPCR, wherein the limit of detection (LOD) of ddPCR was upto 2.4 copies of the DNA template, whereas, the qPCR could detect upto 38 copies of the DNA template in the reaction mixture. Overall, the developed ddPCR assay was found to be robust, specific, and could reliably quantify up to 17.8 copies of the DNA template. Finally, the applicability of the developed ddPCR assay was tested by screening the field samples (n = 124), comprising lung tissues from dead poultry and feral birds; pooled faecal samples from the free-living birds, commercial and backyard poultry farms; pharyngeal and cloacal swabs collected from the duck farms. Of these, a total of seven samples were found to be positive by the ddPCR, whereas, three samples could be detected as positive using the qPCR. The developed ddPCR could serve as a reliable screening tool, particularly in those clinical samples wherein the shedding of C. psittaci is substantially very low.
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Affiliation(s)
- Radhakrishna Sahu
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India; Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | - M R Vishnuraj
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
| | - Ch Srinivas
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
| | - Bhargavi Dadimi
- Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | - G K Megha
- Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | | | - Satyaveer S Malik
- Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | - S Vaithiyanathan
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
| | - Deepak B Rawool
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
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Prasitporn T, Senapin S, Vaniksampanna A, Longyant S, Chaivisuthangkura P. Development of cross-priming amplification (CPA) combined with colorimetric and lateral flow dipstick visualization for scale drop disease virus (SDDV) detection. JOURNAL OF FISH DISEASES 2021; 44:1411-1422. [PMID: 34041757 DOI: 10.1111/jfd.13448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
Scale drop disease virus (SDDV) is one of the most important pathogens that causes scale drop disease (SDD) in Asian sea bass (Lates calcarifer). The outbreaks of this disease are one of the factors causing substantial losses in Asian sea bass aquaculture. In this study, the uracil-DNA glycosylase (UDG)-supplemented cross-priming amplification (UCPA) combined with a colorimetric detection method using the hydroxynaphthol blue (HNB) and lateral flow dipstick (LFD) for detection of SDDV was developed. The UDG was utilized to prevent carryover contamination, and the CPA reactions can be readily observed by HNB and LFD. The CPA primers and probe were designed to target the major capsid protein (MCP) gene of the SDDV. The optimized UCPA conditions were performed at the temperature of 61°C for 60 min. The UCPA assays demonstrated specificity to SDDV without cross-reaction to other tested viruses including red-spotted grouper nervous necrosis virus (RGNNV), infectious spleen and kidney necrosis virus (ISKNV) and Lates calcarifer herpes virus (LCHV), and other bacterial species commonly found in aquatic animals. The sensitivity of the UCPA-HNB and UCPA-LFD was 100 viral copies/µl and 10 pg of extracted total DNA, which was 10-fold more sensitive than that of conventional PCR. The UCPA-HNB and UCPA-LFD assays could be used to detect the SDDV infection in all 25 confirmed SDDV-infected fish samples. Therefore, the UCPA coupled with HNB and LFD was rapid, simple and effective and might be applied for diagnosis of SDDV infection.
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Affiliation(s)
- Terawut Prasitporn
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
- Center of Excellence in Animal, Plant and Parasite Biotechnology, Srinakharinwirot University, Bangkok, Thailand
| | - Saengchan Senapin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | | | - Siwaporn Longyant
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
- Center of Excellence in Animal, Plant and Parasite Biotechnology, Srinakharinwirot University, Bangkok, Thailand
| | - Parin Chaivisuthangkura
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
- Center of Excellence in Animal, Plant and Parasite Biotechnology, Srinakharinwirot University, Bangkok, Thailand
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Kerddee P, Dinh-Hung N, Dong HT, Hirono I, Soontara C, Areechon N, Srisapoome P, Kayansamruaj P. Molecular evidence for homologous strains of infectious spleen and kidney necrosis virus (ISKNV) genotype I infecting inland freshwater cultured Asian sea bass (Lates calcarifer) in Thailand. Arch Virol 2021; 166:3061-3074. [PMID: 34462803 DOI: 10.1007/s00705-021-05207-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/21/2021] [Indexed: 11/30/2022]
Abstract
Infectious spleen and kidney necrosis virus (ISKNV) is a fish-pathogenic virus belonging to the genus Megalocytivirus of the family Iridoviridae. In 2018, disease occurrences (40-50% cumulative mortality) associated with ISKNV infection were reported in grown-out Asian sea bass (Lates calcarifer) cultured in an inland freshwater system in Thailand. Clinical samples were collected from seven distinct farms located in the eastern and central regions of Thailand. The moribund fish showed various abnormal signs, including lethargy, pale gills, darkened body, and skin hemorrhage, while hypertrophied basophilic cells were observed microscopically in gill, liver, and kidney tissue. ISKNV infection was confirmed on six out of seven farms using virus-specific semi-nested PCR. The MCP and ATPase genes showed 100% sequence identity among the virus isolates, and the virus was found to belong to the ISKNV genotype I clade. Koch's postulates were later confirmed by challenge assay, and the mortality of the experimentally infected fish at 21 days post-challenge was 50-90%, depending on the challenge dose. The complete genome of two ISKNV isolates, namely KU1 and KU2, was recovered directly from the infected specimens using a shotgun metagenomics approach. The genome length of ISKNV KU1 and KU2 was 111,487 and 111,610 bp, respectively. In comparison to closely related ISKNV strains, KU1 and KU2 contained nine unique genes, including a caspase-recruitment-domain-containing protein that is potentially involved in inhibition of apoptosis. Collectively, this study indicated that inland cultured Asian sea bass are infected by homologous ISKNV strains. This indicates that ISKNV genotype I should be prioritized for future vaccine research.
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Affiliation(s)
- Pattarawit Kerddee
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.,Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand
| | - Nguyen Dinh-Hung
- Fish Infectious Diseases Research Unit (FID RU), Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ha Thanh Dong
- Department of Food, Agriculture and Bioresources, School of Environment, Resources and Development, Asian Institute of Technology, Pathum Thani, 12120, Thailand
| | - Ikuo Hirono
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan, Minato, 4-5-7, Tokyo, 108-8477, Japan
| | - Chayanit Soontara
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Nontawith Areechon
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Prapansak Srisapoome
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand.,Center of Excellence in Aquatic Animal Health Management, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Pattanapon Kayansamruaj
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand. .,Center of Excellence in Aquatic Animal Health Management, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand.
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Domingos JA, Shen X, Terence C, Senapin S, Dong HT, Tan MR, Gibson-Kueh S, Jerry DR. Scale Drop Disease Virus (SDDV) and Lates calcarifer Herpes Virus (LCHV) Coinfection Downregulate Immune-Relevant Pathways and Cause Splenic and Kidney Necrosis in Barramundi Under Commercial Farming Conditions. Front Genet 2021; 12:666897. [PMID: 34220943 PMCID: PMC8249934 DOI: 10.3389/fgene.2021.666897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/19/2021] [Indexed: 01/31/2023] Open
Abstract
Marine farming of barramundi (Lates calcarifer) in Southeast Asia is currently severely affected by viral diseases. To better understand the biological implications and gene expression response of barramundi in commercial farming conditions during a disease outbreak, the presence of pathogens, comparative RNAseq, and histopathology targeting multiple organs of clinically “sick” and “healthy” juveniles were investigated. Coinfection of scale drop disease virus (SDDV) and L. calcarifer herpes virus (LCHV) were detected in all sampled fish, with higher SDDV viral loads in sick than in healthy fish. Histopathology showed that livers in sick fish often had moderate to severe abnormal fat accumulation (hepatic lipidosis), whereas the predominant pathology in the kidneys shows moderate to severe inflammation and glomerular necrosis. The spleen was the most severely affected organ, with sick fish presenting severe multifocal and coalescing necrosis. Principal component analysis (PC1 and PC2) explained 70.3% of the observed variance and strongly associated the above histopathological findings with SDDV loads and with the sick phenotypes, supporting a primary diagnosis of the fish being impacted by scale drop disease (SDD). Extracted RNA from kidney and spleen of the sick fish were also severely degraded likely due to severe inflammation and tissue necrosis, indicating failure of these organs in advanced stages of SDD. RNAseq of sick vs. healthy barramundi identified 2,810 and 556 differentially expressed genes (DEGs) in the liver and muscle, respectively. Eleven significantly enriched pathways (e.g., phagosome, cytokine-cytokine-receptor interaction, ECM-receptor interaction, neuroactive ligand-receptor interaction, calcium signaling, MAPK, CAMs, etc.) and gene families (e.g., tool-like receptor, TNF, lectin, complement, interleukin, chemokine, MHC, B and T cells, CD molecules, etc.) relevant to homeostasis and innate and adaptive immunity were mostly downregulated in sick fish. These DEGs and pathways, also previously identified in L. calcarifer as general immune responses to other pathogens and environmental stressors, suggest a failure of the clinically sick fish to cope and overcome the systemic inflammatory responses and tissue degeneration caused by SDD.
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Affiliation(s)
- Jose A Domingos
- Tropical Futures Institute, James Cook University, Singapore, Singapore.,Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Xueyan Shen
- Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Celestine Terence
- Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Saengchan Senapin
- Faculty of Science, Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Bangkok, Thailand.,National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Ha Thanh Dong
- Faculty of Science, Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Bangkok, Thailand.,Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, Thailand
| | - Marie R Tan
- School of Applied Science (SAS), Republic Polytechnic, Singapore, Singapore
| | - Susan Gibson-Kueh
- Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Dean R Jerry
- Tropical Futures Institute, James Cook University, Singapore, Singapore.,Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
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