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Filipa-Silva A, Parreira R, Martínez-Puchol S, Bofill-Mas S, Barreto Crespo MT, Nunes M. The Unexplored Virome of Two Atlantic Coast Fish: Contribution of Next-Generation Sequencing to Fish Virology. Foods 2020; 9:E1634. [PMID: 33182306 PMCID: PMC7695296 DOI: 10.3390/foods9111634] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 12/24/2022] Open
Abstract
Much of the knowledge on viruses is focused on those that can be propagated using cell-cultures or that can cause disease in humans or in economically important animals and plants. However, this only reflects a small portion of the virosphere. Therefore, in this study, we explore by targeted next-generation sequencing, how the virome varies between Atlantic horse mackerels and gilthead seabreams from fisheries and aquaculture from the center and south regions of Portugal. Viral genomes potentially pathogenic to fish and crustaceans, as well as to humans, were identified namelyese included Astroviridae, Nodaviridae, Hepadnaviridae, Birnaviridae, Caliciviridae, and Picornaviridae families. Also bacteriophages sequences were identified corresponding to the majority of sequencese detected, with Myoviridae, Podoviridae, and Siphoviridae, the most widespread families in both fish species. However, these findings can also be due to the presence of bacteria in fish tissues, or even to contamination. Overall, seabreams harbored viruses from a smaller number of families in comparison with mackerels. Therefore, the obtained data show that fish sold for consumption can harbor a high diversity of viruses, many of which are unknown, reflecting the overall uncharacterized virome of fish. While cross-species transmission of bonafide fish viruses to humans is unlikely, the finding of human pathogenic viruses in fish suggest that fish virome can be a potential threat regarding food safety.
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Affiliation(s)
- Andreia Filipa-Silva
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (A.F.-S.); (M.T.B.C.)
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
| | - Ricardo Parreira
- Global Health and Tropical Medicine (GHTM) Research Center, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical (IHTM), Universidade Nova de Lisboa (NOVA), 1349-008 Lisboa, Portugal;
| | - Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Department, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain; (S.M.-P.); (S.B.-M.)
- The Water Research Institute (idRA), Universitat de Barcelona, 08001 Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Department, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain; (S.M.-P.); (S.B.-M.)
- The Water Research Institute (idRA), Universitat de Barcelona, 08001 Barcelona, Catalonia, Spain
| | - Maria Teresa Barreto Crespo
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (A.F.-S.); (M.T.B.C.)
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
| | - Mónica Nunes
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (A.F.-S.); (M.T.B.C.)
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
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The Infectious Pancreatic Necrosis Virus (IPNV) and its Virulence Determinants: What is Known and What Should be Known. Pathogens 2020; 9:pathogens9020094. [PMID: 32033004 PMCID: PMC7168660 DOI: 10.3390/pathogens9020094] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/25/2020] [Accepted: 01/31/2020] [Indexed: 12/30/2022] Open
Abstract
Infectious pancreatic necrosis (IPN) is a disease of great concern in aquaculture, mainly among salmonid farmers, since losses in salmonid fish—mostly very young rainbow trout (Salmo gairdnery) fry and Atlantic salmon (Salmo salar) post-smolt—frequently reach 80–90% of stocks. The virus causing the typical signs of the IPN disease in salmonids, named infectious pancreatic necrosis virus (IPNV), has also been isolated from other fish species either suffering related diseases (then named IPNV-like virus) or asymptomatic; the general term aquabirnavirus is used to encompass all these viruses. Aquabirnaviruses are non-enveloped, icosahedral bisegmented dsRNA viruses, whose genome codifies five viral proteins, three of which are structural, and one of them is an RNA-dependent RNA polymerase. Due to the great importance of the disease, there have been great efforts to find a way to predict the level of virulence of IPNV isolates. The viral genome and proteins have been the main focus of research. However, to date such a reliable magic marker has not been discovered. This review describes the processes followed for decades in the attempts to discover the viral determinants of virulence, and to help the reader understand how viral components can be involved in virulence modulation in vitro and in vivo. There is also a brief description of the disease, of host defenses, and of the molecular structure and function of the virus and its viral components.
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Tapia D, Barría A, Kuznar J, Yáñez JM. Comparison of mortality and viral load in rainbow trout (Oncorhynchus mykiss) infected with infectious pancreatic necrosis virus (IPNV) genogroups 1 and 5. JOURNAL OF FISH DISEASES 2020; 43:139-146. [PMID: 31724200 DOI: 10.1111/jfd.13113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Infectious pancreatic necrosis virus (IPNV) is the aetiological agent of a highly contagious disease that affects farmed salmonids. IPNV isolates have been phylogenetically classified into eight genogroups, of which two are present in Chile, genogroups 1 and 5. Here, we compare the mortality rate caused by isolates from both genogroups in rainbow trout (Oncorhynchus mykiss) fry to determine if there is an association between host susceptibility and phylogenetic characterization of IPNV. Fish were challenged by immersion with one of four isolates (two for each genogroup), and mortality curves were assessed after 30 days. Viral load was measured in all mortalities and in live fish sampled at 1, 7 and 20 days post-infection. Although mortality was low throughout the challenge, differences were found between fish infected with different isolates. Both isolates from genogroup 1 caused greater cumulative mortalities than either of the isolates from genogroup 5. When combined, the overall mortality rate of fish challenged with genogroup 1 isolates was significantly higher than those infected with genogroup 5. However, viral load was lower on trout infected with genogroup 1 isolates. These results suggest that rainbow trout are more susceptible to IPNV isolates from genogroup 1 than genogroup 5.
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Affiliation(s)
- David Tapia
- Doctorado en Acuicultura, Programa Cooperativo Universidad de Chile, Universidad Católica del Norte, Pontificia Universidad Católica de Valparaíso, Santiago, Chile
| | - Agustín Barría
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Juan Kuznar
- Centro de Investigación y Gestión de Recursos Naturales, Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
- Núcleo Milenio INVASAL, Concepción, Chile
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Bello-Pérez M, Falcó A, Galiano V, Coll J, Perez L, Encinar JA. Discovery of nonnucleoside inhibitors of polymerase from infectious pancreatic necrosis virus (IPNV). DRUG DESIGN DEVELOPMENT AND THERAPY 2018; 12:2337-2359. [PMID: 30104863 PMCID: PMC6072831 DOI: 10.2147/dddt.s171087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Introduction Infectious pancreatic necrosis virus (IPNV) causes serious losses in several fish species of commercial interest. IPNV is a non-enveloped double-stranded RNA virus with a genome consisting of two segments A and B. Segment B codes for the VP1 protein, a non-canonical RNA-dependent RNA polymerase that can be found both in its free form and linked to the end of genomic RNA, an essential enzyme for IPNV replication. Materials and methods We take advantage of the knowledge over the allosteric binding site described on the surface of the thumb domain of Hepatitis C virus (HCV) polymerase to design new non-nucleoside inhibitors against the IPNV VP1 polymerase. Results Molecular docking techniques have been used to screen a chemical library of 23,760 compounds over a defined cavity in the surface of the thumb domain. Additional ADMET (absorption, distribution, metabolism, excretion, and toxicity) filter criteria has been applied. Conclusion We select two sets of 9 and 50 inhibitor candidates against the polymerases of HCV and IPNV, respectively. Two non-toxic compounds have been tested in vitro with antiviral capacity against IPNV Sp and LWVRT60 strains in the low µM range with different activity depending on the IPNV strain used.
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Affiliation(s)
- Melissa Bello-Pérez
- Molecular and Cell Biology Institute (IBMC), Miguel Hernández University (UMH), Elche, Spain, ;
| | - Alberto Falcó
- Molecular and Cell Biology Institute (IBMC), Miguel Hernández University (UMH), Elche, Spain, ;
| | - Vicente Galiano
- Department of Physics and Computer Architecture, Miguel Hernández University (UMH), Elche, Spain
| | - Julio Coll
- Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Luis Perez
- Molecular and Cell Biology Institute (IBMC), Miguel Hernández University (UMH), Elche, Spain, ;
| | - José Antonio Encinar
- Molecular and Cell Biology Institute (IBMC), Miguel Hernández University (UMH), Elche, Spain, ;
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Mulei IR, Nyaga PN, Mbuthia PG, Waruiru RM, Njagi LW, Mwihia EW, Gamil AAA, Evensen Ø, Mutoloki S. Infectious pancreatic necrosis virus isolated from farmed rainbow trout and tilapia in Kenya is identical to European isolates. JOURNAL OF FISH DISEASES 2018; 41:1191-1200. [PMID: 29806129 DOI: 10.1111/jfd.12807] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 06/08/2023]
Abstract
Infectious pancreatic necrosis virus (IPNV) is an aquabirnavirus that causes serious diseases in a variety of fish species worldwide. It has been isolated from a large number of healthy fresh and marine water fish. Prior to this study, there was no record of the presence of IPNV infection in Kenya. Here, the presence of IPNV in farmed rainbow trout and tilapia was examined in Nyeri County of central Kenya. Head kidney samples taken from five rainbow trout and three tilapia farms and stored in RNALater® were processed by PCR followed by sequencing of a segment A fragment covering nucleotide positions 2,120-2,343 bp. IPNV was detected in all the farms sampled with infection ratios ranging from 0.3 to 0.78 although the infections were not associated with any specific clinical signs of disease. These findings were supported by immunohistochemistry staining of the virus in the kidney and exocrine pancreas of rainbow trout. Sequence alignment and phylogenetic analysis revealed that the Kenyan isolates were identical to European isolates, suggesting a common origin. These findings highlight the need for better biosecurity procedures with more stringent surveillance programmes and control for fish diseases, especially focusing on imported breeding materials to Kenya.
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Affiliation(s)
- I R Mulei
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
- Department of Veterinary Pathology, Microbiology & Parasitology, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - P N Nyaga
- Department of Veterinary Pathology, Microbiology & Parasitology, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - P G Mbuthia
- Department of Veterinary Pathology, Microbiology & Parasitology, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - R M Waruiru
- Department of Veterinary Pathology, Microbiology & Parasitology, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - L W Njagi
- Department of Veterinary Pathology, Microbiology & Parasitology, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - E W Mwihia
- Department of Veterinary Pathology, Microbiology & Parasitology, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - A A A Gamil
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Ø Evensen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - S Mutoloki
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
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Whole-Genome Sequence of Infectious Pancreatic Necrosis Virus Isolated from Farmed Brook Trout (Salvelinus fontinalis) in Pennsylvania. GENOME ANNOUNCEMENTS 2018; 6:6/17/e00360-18. [PMID: 29700163 PMCID: PMC5920161 DOI: 10.1128/genomea.00360-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Infectious pancreatic necrosis (IPN) is an acute contagious systemic disease affecting several fish species and a critical disease in the salmonid fish farming industry. Here, we report the complete genome sequence of IPN virus (IPNV) RNA segments A and B, isolated from a farmed brook trout in Pennsylvania.
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