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Costa VA, Holmes EC. Diversity, evolution, and emergence of fish viruses. J Virol 2024; 98:e0011824. [PMID: 38785422 PMCID: PMC11237817 DOI: 10.1128/jvi.00118-24] [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] [Indexed: 05/25/2024] Open
Abstract
The production of aquatic animals has more than doubled over the last 50 years and is anticipated to continually increase. While fish are recognized as a valuable and sustainable source of nutrition, particularly in the context of human population growth and climate change, the rapid expansion of aquaculture coincides with the emergence of highly pathogenic viruses that often spread globally through aquacultural practices. Here, we provide an overview of the fish virome and its relevance for disease emergence, with a focus on the insights gained through metagenomic sequencing, noting potential areas for future study. In particular, we describe the diversity and evolution of fish viruses, for which the majority have no known disease associations, and demonstrate how viruses emerge in fish populations, most notably at an expanding domestic-wild interface. We also show how wild fish are a powerful and tractable model system to study virus ecology and evolution more broadly and can be used to identify the major factors that shape vertebrate viromes. Central to this is a process of virus-host co-divergence that proceeds over many millions of years, combined with ongoing cross-species virus transmission.
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Affiliation(s)
- Vincenzo A. Costa
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
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2
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Bondavalli F, Schleicherová D, Pastorino P, Mugetti D, Pedron C, Prearo M. Detection of Acipenser European Iridovirus (AcIV-E) in Sturgeon Farms in Northern Italy between 2021-2023. Viruses 2024; 16:465. [PMID: 38543830 PMCID: PMC10975281 DOI: 10.3390/v16030465] [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: 01/12/2024] [Revised: 03/10/2024] [Accepted: 03/16/2024] [Indexed: 05/23/2024] Open
Abstract
Sturgeon farming is rapidly expanding in Europe, where Italy ranks first in farmed caviar production. A major threat to sturgeon health in captivity is infection with Acipenser European Iridovirus (AcIV-E), a viral disease definitively identified in 2016. Here we present data on the occurrence of AcIV-E in 482 sturgeons (age ≤ 12 months, species of the genus Acipenser and the species Huso huso) collected from sturgeon farms in northern Italy between January 2021 and December 2023. The health status of each specimen was determined by necroscopy and virological assay. Virological analysis was performed on gill samples and real-time PCR specific to the MCP gene of the iridovirus viral capsid. Molecular analysis revealed positivity to the virus in 204 samples (42.68% of the total), while anatomopathological examination of nearly all fish with positive real-time PCR disclosed swollen abdomen, hepatic steatosis, splenomegaly, and increased gill volume. Two challenges to timely diagnosis are the absence of pathognomonic symptoms and the inability to isolate the virus on cell monolayers. Continuous and widespread health monitoring is therefore crucial for disease management and to effectively control spread of the virus.
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Affiliation(s)
- Fabio Bondavalli
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle D’Aosta, 10154 Torino, Italy; (F.B.); (D.S.); (M.P.); (D.M.)
| | - Dáša Schleicherová
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle D’Aosta, 10154 Torino, Italy; (F.B.); (D.S.); (M.P.); (D.M.)
- Department of Life Sciences and Systems Biology (DBIOS), University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy
| | - Paolo Pastorino
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle D’Aosta, 10154 Torino, Italy; (F.B.); (D.S.); (M.P.); (D.M.)
| | - Davide Mugetti
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle D’Aosta, 10154 Torino, Italy; (F.B.); (D.S.); (M.P.); (D.M.)
- ASL VCO, Department of Public Health, Omegna Health District, Via G. Mazzini, 96, 28887 Omegna, Italy
| | | | - Marino Prearo
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle D’Aosta, 10154 Torino, Italy; (F.B.); (D.S.); (M.P.); (D.M.)
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3
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Hopper LR, Glenn JA, MacConnell E, Winton JR, Emmenegger EJ. Susceptibility of Pallid Sturgeon to viral hemorrhagic septicemia virus genotype IVb. JOURNAL OF AQUATIC ANIMAL HEALTH 2023. [PMID: 37243311 DOI: 10.1002/aah.10181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/12/2022] [Accepted: 02/21/2023] [Indexed: 05/28/2023]
Abstract
OBJECTIVE Viral hemorrhagic septicemia virus (VHSV) is an aquatic rhabdovirus causing severe disease in freshwater and saltwater fish species. The susceptibility of endangered Pallid Sturgeon Scaphirhynchus albus to VHSV genotype IVb (VHSV-IVb) infection was investigated. METHODS An in vitro assessment using two Pallid Sturgeon cell lines derived from skin and spleen tissue and in vivo evaluation of juvenile Pallid Sturgeon after exposure to VHSV-IVb were performed. RESULT Plaque assay and RT-PCR results confirmed VHSV-IVb replication in Pallid Sturgeon cell lines. Sturgeon were also susceptible to VHSV-IVb infection after immersion and injection exposures during laboratory experiments. However, after widespread mortality occurred in all treatment groups, including negative control fish, it was determined that the Pallid Sturgeon stock fish were infected with Missouri River sturgeon iridovirus (MRSIV) prior to experimental challenge. Nevertheless, mortalities were equal or higher among VHSV-exposed fish than among negative controls (MRSIV infected), and histopathological assessments indicated reduced hematopoietic cells in spleen and kidney tissues and hemorrhage in the gastrointestinal organs only in fish from the VHSV treatment. CONCLUSION These results indicate that Pallid Sturgeon is a susceptible host for VHSV-IVb, but the degree of pathogenicity was confounded by the underlying MRSIV infection. Research comparing susceptibility of specific pathogen-free and MRSIV-infected fish to VHSV-IVb is needed to accurately assess the vulnerability of Pallid Sturgeon to VHSV-IVb.
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Affiliation(s)
- Lacey R Hopper
- U.S. Fish and Wildlife Service, Bozeman Fish Health Center, Bozeman, Montana, USA
| | - Jolene A Glenn
- U.S. Geological Survey, Western Fisheries Research Center, Seattle, Washington, USA
- Austin, Texas, USA
| | | | - James R Winton
- U.S. Geological Survey, Western Fisheries Research Center, Seattle, Washington, USA
| | - Eveline J Emmenegger
- U.S. Geological Survey, Western Fisheries Research Center, Seattle, Washington, USA
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Volpe E, Errani F, Mandrioli L, Ciulli S. Advances in Viral Aquatic Animal Disease Knowledge: The Molecular Methods' Contribution. BIOLOGY 2023; 12:biology12030466. [PMID: 36979158 PMCID: PMC10045235 DOI: 10.3390/biology12030466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Aquaculture is the fastest-growing food-producing sector, with a global production of 122.6 million tonnes in 2020. Nonetheless, aquatic animal production can be hampered by the occurrence of viral diseases. Furthermore, intensive farming conditions and an increasing number of reared fish species have boosted the number of aquatic animals' pathogens that researchers have to deal with, requiring the quick development of new detection and study methods for novel unknown pathogens. In this respect, the molecular tools have significantly contributed to investigating thoroughly the structural constituents of fish viruses and providing efficient detection methods. For instance, next-generation sequencing has been crucial in reassignment to the correct taxonomic family, the sturgeon nucleo-cytoplasmic large DNA viruses, a group of viruses historically known, but mistakenly considered as iridoviruses. Further methods such as in situ hybridisation allowed objectifying the role played by the pathogen in the determinism of disease, as the cyprinid herpesvirus 2, ostreid herpesvirus 1 and betanodaviruses. Often, a combination of molecular techniques is crucial to understanding the viral role, especially when the virus is detected in a new aquatic animal species. With this paper, the authors would critically revise the scientific literature, dealing with the molecular techniques employed hitherto to study the most relevant finfish and shellfish viral pathogens.
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Affiliation(s)
- Enrico Volpe
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, 47042 Cesenatico, FC, Italy
| | - Francesca Errani
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, 47042 Cesenatico, FC, Italy
| | - Luciana Mandrioli
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, 47042 Cesenatico, FC, Italy
| | - Sara Ciulli
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, 47042 Cesenatico, FC, Italy
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5
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Deng D, Mu Z, Lv X, Jiang X, Zhou J, Guo H, Zhang W, Wang B, Lu Y, Wu J, Du H, Zhang S, Xu Q, Wei Q. Pathogenicity of Plesiomonas shigelloides and Citrobacter freundii isolated from the endangered Chinese sturgeon (Acipenser sinensis). Microb Pathog 2022; 173:105818. [DOI: 10.1016/j.micpath.2022.105818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/17/2022] [Accepted: 10/04/2022] [Indexed: 11/30/2022]
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6
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Brocca G, Zamparo S, Pretto T, Calore A, Marsella A, Xiccato RL, Cornaggia M, Cortinovis L, Bano L, Toffan A, Quaglio F, Verin R. Severe gastroenteropathy associated with Clostridium perfringens isolation in starving juvenile sturgeons. JOURNAL OF FISH DISEASES 2022; 45:471-477. [PMID: 35007367 DOI: 10.1111/jfd.13579] [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: 10/26/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
In November 2020 a mortality episode (30%) in juvenile Siberian and Russian sturgeons (Acipenser baerii, Brandt, and A. gueldenstaedtii, Brandt & Ratzeburg) and GUBA hybrid sturgeons (A. gueldenstaedtii × A. baerii) occurred in a hatchery in Northern Italy, associated with severe coelomic distension and abnormal reverse surface swimming. The fish were reared in concrete tanks supplied by well water, fed at 0.4% of body weight (b.w.) per day. Thirty sturgeon specimens were collected for necropsy, histological, bacteriological and virological examination. Macroscopic findings included diffuse and severe bloating of gastrointestinal tracts due to foamy contents with thinning and stretching of the gastrointestinal walls. Histological analysis revealed variable degrees of sloughing and necrosis of the intestinal epithelium, and the presence of bacterial aggregates. Anaerobic Gram-positive bacteria were investigated, and Clostridium perfringens was isolated from the gut. Specific PCRs identified the toxinotype A and the β2 toxin gene. The daily feed administration was increased to 1.5% b.w. and after 5 days, the mortality ceased. A new animal cohort from the same groups was examined after 12 weeks, showing neither gut alterations nor isolation of C. perfringens. The imbalance of intestinal microbiota, presumably caused by underfeeding, favoured C. perfringens overgrowth and severe gas formation. The diet increase possibly restored the normal microbiota.
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Affiliation(s)
- Ginevra Brocca
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro (PD), Italy
| | - Samuele Zamparo
- Azienda Agricola Troticoltura Erede Rossi Silvio, Sefro (MC), Italy
| | - Tobia Pretto
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro (PD), Italy
| | - Alessandro Calore
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro (PD), Italy
| | - Andrea Marsella
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro (PD), Italy
| | - Romy Lucon Xiccato
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro (PD), Italy
| | - Matteo Cornaggia
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro (PD), Italy
| | - Luana Cortinovis
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro (PD), Italy
| | - Luca Bano
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro (PD), Italy
| | - Anna Toffan
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro (PD), Italy
| | - Francesco Quaglio
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro (PD), Italy
| | - Ranieri Verin
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro (PD), Italy
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Sorouri M, Chang T, Jesudhasan P, Pinkham C, Elde NC, Hancks DC. Signatures of host-pathogen evolutionary conflict reveal MISTR-A conserved MItochondrial STress Response network. PLoS Biol 2020; 18:e3001045. [PMID: 33370271 PMCID: PMC7793259 DOI: 10.1371/journal.pbio.3001045] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 01/08/2021] [Accepted: 12/09/2020] [Indexed: 11/18/2022] Open
Abstract
Host-pathogen conflicts leave genetic signatures in genes that are critical for host defense functions. Using these "molecular scars" as a guide to discover gene functions, we discovered a vertebrate-specific MItochondrial STress Response (MISTR) circuit. MISTR proteins are associated with electron transport chain (ETC) factors and activated by stress signals such as interferon gamma (IFNγ) and hypoxia. Upon stress, ultraconserved microRNAs (miRNAs) down-regulate MISTR1(NDUFA4) followed by replacement with paralogs MItochondrial STress Response AntiViral (MISTRAV) and/or MItochondrial STress Response Hypoxia (MISTRH). While cells lacking MISTR1(NDUFA4) are more sensitive to chemical and viral apoptotic triggers, cells lacking MISTRAV or expressing the squirrelpox virus-encoded vMISTRAV exhibit resistance to the same insults. Rapid evolution signatures across primate genomes for MISTR1(NDUFA4) and MISTRAV indicate recent and ongoing conflicts with pathogens. MISTR homologs are also found in plants, yeasts, a fish virus, and an algal virus indicating ancient origins and suggesting diverse means of altering mitochondrial function under stress. The discovery of MISTR circuitry highlights the use of evolution-guided studies to reveal fundamental biological processes.
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Affiliation(s)
- Mahsa Sorouri
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Institute of Biomedical Studies, Baylor University, Waco, Texas, United States of America
| | - Tyron Chang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Genetics, Development, and Disease PhD Program, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Palmy Jesudhasan
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Chelsea Pinkham
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nels C. Elde
- Eccles Institute of Human Genetics, The University of Utah Medical School, Utah, United States of America
- * E-mail: (NCE); (DCH)
| | - Dustin C. Hancks
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail: (NCE); (DCH)
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8
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Rud Y, Bigarré L, Pallandre L, Briand FX, Buchatsky L. First genetic characterization of sturgeon mimiviruses in Ukraine. JOURNAL OF FISH DISEASES 2020; 43:1391-1400. [PMID: 32882746 DOI: 10.1111/jfd.13239] [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: 03/09/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
A group of pathogenic nucleocytoplasmic large DNA viruses (NCLDVs) related to the Mimiviridae family infect farmed sturgeons across Europe, causing mild-to-severe losses. One of these viruses, Acipenser iridovirus-European (AcIV-E), was identified in six sturgeon species. During the 2018-2019 period, nine sick Siberian (A. baerii) and Russian (A. gueldenstaedtii) sturgeons were sampled in Ukrainian farms and tested for the presence of AcIV-E using real-time PCR. The presence of AcIV-E was confirmed in some samples. High-resolution melting (HRM) assay and Sanger sequencing demonstrated the presence in three farms of two alleles of the major capsid protein (MCP) gene, called var1 and var2. Five samples carried both var1 and var2 at varying ratios, and the sixth sample was infected with only var1. These results constitute the first detection of AcIV-E in Ukraine and the first detection of a sample carrying only var1. The full-length sequences of the MCP genes confirmed the existence of two genetic lineages of AcIV-E, tentatively named V1 and V2, each displaying multiple substitutions in the MCP gene. Some of the MCP sequences showed a genetic relationship to both V1 and V2 lineages, depending on the fragment examined. Most likely, these sequences resulted from recombination events.
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Affiliation(s)
- Yuriy Rud
- Institute of Fisheries, Kyiv, Ukraine
| | - Laurent Bigarré
- ANSES, laboratory Ploufragan-Plouzané-Niort, Plouzané, France
| | | | | | - Leonid Buchatsky
- Taras Shevchenko National University of Kyiv, Institute of Biology and Medicine, Kyiv, Ukraine
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9
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Chelkha N, Levasseur A, La Scola B, Colson P. Host-virus interactions and defense mechanisms for giant viruses. Ann N Y Acad Sci 2020; 1486:39-57. [PMID: 33090482 DOI: 10.1111/nyas.14469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 06/28/2020] [Accepted: 07/26/2020] [Indexed: 12/26/2022]
Abstract
Giant viruses, with virions larger than 200 nm and genomes larger than 340 kilobase pairs, modified the now outdated perception of the virosphere. With virions now reported reaching up to 1.5 μm in size and genomes of up to 2.5 Mb encoding components shared with cellular life forms, giant viruses exhibit a complexity similar to microbes, such as bacteria and archaea. Here, we review interactions of giant viruses with their hosts and defense strategies of giant viruses against their hosts and coinfecting microorganisms or virophages. We also searched by comparative genomics for homologies with proteins described or suspected to be involved in defense mechanisms. Our search reveals that natural immunity and apoptosis seem to be crucial components of the host defense against giant virus infection. Conversely, giant viruses possess methods of hijacking host functions to counteract cellular antiviral responses. In addition, giant viruses may encode other unique and complex pathways to manipulate the host machinery and eliminate other competing microorganisms. Notably, giant viruses have evolved defense mechanisms against their virophages and they might trigger defense systems against other viruses through sequence integration. We anticipate that comparative genomics may help identifying genes involved in defense strategies of both giant viruses and their hosts.
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Affiliation(s)
- Nisrine Chelkha
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Philippe Colson
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- IHU Méditerranée Infection, Marseille, France
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10
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Clouthier S, Caskenette A, Van Walleghem E, Schroeder T, Macdonald D, Anderson ED. Molecular phylogeny of sturgeon mimiviruses and Bayesian hierarchical modeling of their effect on wild Lake Sturgeon (Acipenser fulvescens) in Central Canada. INFECTION GENETICS AND EVOLUTION 2020; 84:104491. [PMID: 32763443 DOI: 10.1016/j.meegid.2020.104491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/12/2020] [Accepted: 07/31/2020] [Indexed: 10/23/2022]
Abstract
Sturgeon mimiviruses can cause a lethal disease of the integumentary systems of sturgeon (Acipenseridae). Here we provide phylogeographic evidence that sturgeon mimivirus is endemic in endangered populations of wild Lake Sturgeon within Canada's Hudson Bay drainage basin. Namao virus (NV) variants were diagnosed in 24% of Lake Sturgeon samples (n = 1329) collected between 2010-2015. Lake Sturgeon populations with the highest virus prevalence were from the Nelson River (58%) in 2015, Saskatchewan River (41%) in 2010 and South Saskatchewan River (36%) in 2011. Bayesian phylogenetic reconstructions suggested that four NV variants, designated HBDB I-IV, co-circulate temporally and spatially within and between the genetically and biogeographically distinct Lake Sturgeon populations. Evidence from recapture studies suggested that Lake Sturgeon across the basin are persistently infected with NV at prevalence and titer (103.6 equivalent plasmid copies per μg DNA) levels consistent with the hypothesis that wild Lake Sturgeon populations serve as a maintenance population and reservoir for sturgeon mimiviruses. Bayesian hierarchical modeling of NV in the Landing River population of Lake Sturgeon suggested that host weight and age were the best predictors of sturgeon mimivirus presence and titer, respectively, whereas water flow rate, level and temperature, and number of previous captures did not significantly improve model fit. A negative relationship was estimated between sturgeon mimivirus presence and Lake Sturgeon weight and between virus titer and Lake Sturgeon age.
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Affiliation(s)
- Sharon Clouthier
- Fisheries and Oceans Canada, 501 University Crescent, Winnipeg, Manitoba R3T 2N6, Canada.
| | - Amanda Caskenette
- Fisheries and Oceans Canada, 501 University Crescent, Winnipeg, Manitoba R3T 2N6, Canada.
| | - Elissa Van Walleghem
- Fisheries and Oceans Canada, 501 University Crescent, Winnipeg, Manitoba R3T 2N6, Canada.
| | - Tamara Schroeder
- Fisheries and Oceans Canada, 501 University Crescent, Winnipeg, Manitoba R3T 2N6, Canada.
| | - Don Macdonald
- Department of Sustainable Development, Province of Manitoba, Box 28, 59 Elizabeth Drive, Thompson, Manitoba R8N 1X4, Canada.
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Mugetti D, Pastorino P, Menconi V, Messina M, Masoero L, Ceresa L, Pedron C, Prearo M. Two New Sturgeon Species are Susceptible to Acipenser Iridovirus European (AcIV-E) Infection. Pathogens 2020; 9:pathogens9030156. [PMID: 32106550 PMCID: PMC7157826 DOI: 10.3390/pathogens9030156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 11/28/2022] Open
Abstract
We report the first case of Acipenser iridovirus European (AcIV-E) infection in starry sturgeon (Acipenser stellatus) and in sterlet (A. ruthenus) reared in Northern Italy. During 2018, mortality began in A. stellatus and A. ruthenus specimens reared in co-habitation with Russian sturgeon positive for AcIV-E. Molecular analyses were done on the gills to amplify a fragment of the major capsid protein (MCP) gene using real-time PCR against AcIV-E. DNA of the positive samples was further sequenced and phylogenetic analyses were performed. The MCP gene sequences were highly similar to a virus previously identified in Italy (nucleotide identities between 99.38% and 99.69%). Phylogenetic analysis confirmed our hypothesis of passage of the virus from the infected Russian sturgeon. The detection of AcIV-E in new species of the Acipenseridae family may impact on sturgeon production, with relevant economic losses.
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Affiliation(s)
- Davide Mugetti
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (V.M.); (M.M.); (L.M.); (M.P.)
- Correspondence: (D.M.); (P.P.); Tel.: +39-0112686251 (P.P.)
| | - Paolo Pastorino
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (V.M.); (M.M.); (L.M.); (M.P.)
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, 34127 Trieste, Italy
- Correspondence: (D.M.); (P.P.); Tel.: +39-0112686251 (P.P.)
| | - Vasco Menconi
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (V.M.); (M.M.); (L.M.); (M.P.)
| | - Margherita Messina
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (V.M.); (M.M.); (L.M.); (M.P.)
| | - Loretta Masoero
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (V.M.); (M.M.); (L.M.); (M.P.)
| | - Luisa Ceresa
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, 10095 Grugliasco (TO), Italy;
| | | | - Marino Prearo
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (V.M.); (M.M.); (L.M.); (M.P.)
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12
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Mugetti D, Pastorino P, Menconi V, Pedron C, Prearo M. The Old and the New on Viral Diseases in Sturgeon. Pathogens 2020; 9:pathogens9020146. [PMID: 32098100 PMCID: PMC7168591 DOI: 10.3390/pathogens9020146] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/26/2022] Open
Abstract
Although sturgeon production by aquaculture has increased worldwide, a major factor limiting its expansion are infectious diseases, although few data about viral diseases are available however. This review provides a rapid overview of viral agents detected and described to date. Following a general introduction on viral diseases are four sections arranged by virus classification: sturgeon nucleocytoplasmic large DNA viruses, herpesviruses, white sturgeon adenovirus 1, and other viruses. Molecular diagnosis is currently the best tool to detect viral diseases, since cell culture isolation is not yet applicable for the detection of most sturgeon viruses.
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Affiliation(s)
- Davide Mugetti
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (P.P.); (V.M.); (M.P.)
- Correspondence: ; Tel.: +39-0112686251
| | - Paolo Pastorino
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (P.P.); (V.M.); (M.P.)
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, 34127 Trieste, Italy
| | - Vasco Menconi
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (P.P.); (V.M.); (M.P.)
| | | | - Marino Prearo
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (P.P.); (V.M.); (M.P.)
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13
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Schulz F, Roux S, Paez-Espino D, Jungbluth S, Walsh DA, Denef VJ, McMahon KD, Konstantinidis KT, Eloe-Fadrosh EA, Kyrpides NC, Woyke T. Giant virus diversity and host interactions through global metagenomics. Nature 2020; 578:432-436. [PMID: 31968354 PMCID: PMC7162819 DOI: 10.1038/s41586-020-1957-x] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/09/2020] [Indexed: 12/11/2022]
Abstract
Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes from sampling sites across the globe by building on the rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic diversity and a parallel 10-fold expansion in functional diversity. Analysis of 58,023 major capsid proteins from large and giant viruses using metagenomic data revealed the global distribution patterns and cosmopolitan nature of these viruses. The discovered viral genomes encoded a wide range of proteins with putative roles in photosynthesis and diverse substrate transport processes, indicating that host reprogramming is probably a common strategy in the NCLDVs. Furthermore, inferences of horizontal gene transfer connected viral lineages to diverse eukaryotic hosts. We anticipate that the global diversity of NCLDVs that we describe here will establish giant viruses-which are associated with most major eukaryotic lineages-as important players in ecosystems across Earth's biomes.
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Affiliation(s)
- Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Paez-Espino
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sean Jungbluth
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David A Walsh
- Groupe de recherche interuniversitaire en limnologie, Department of Biology, Concordia University, Montréal, Québec, Canada
| | - Vincent J Denef
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Li Y, Endo H, Gotoh Y, Watai H, Ogawa N, Blanc-Mathieu R, Yoshida T, Ogata H. The Earth Is Small for "Leviathans": Long Distance Dispersal of Giant Viruses across Aquatic Environments. Microbes Environ 2019; 34:334-339. [PMID: 31378760 PMCID: PMC6759346 DOI: 10.1264/jsme2.me19037] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Giant viruses of ‘Megaviridae’ have the ability to widely disperse around the globe. We herein examined ‘Megaviridae’ communities in four distinct aquatic environments (coastal and offshore seawater, brackish water, and hot spring freshwater), which are distantly located from each other (between 74 and 1,765 km), using a meta-barcoding method. We identified between 593 and 3,627 OTUs in each sample. Some OTUs were detected in all five samples tested as well as in many of the Tara Oceans metagenomes, suggesting the existence of viruses of this family in a wide range of habitats and the ability to circulate on the planet.
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Affiliation(s)
- Yanze Li
- Institute for Chemical Research, Kyoto University
| | - Hisashi Endo
- Institute for Chemical Research, Kyoto University
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University
| | | | - Nana Ogawa
- Graduate School of Agriculture, Kyoto University
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15
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Doszpoly A, Harrach B, LaPatra S, Benkő M. Unconventional gene arrangement and content revealed by full genome analysis of the white sturgeon adenovirus, the single member of the genus Ichtadenovirus. INFECTION GENETICS AND EVOLUTION 2019; 75:103976. [PMID: 31344490 DOI: 10.1016/j.meegid.2019.103976] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/18/2019] [Accepted: 07/20/2019] [Indexed: 12/29/2022]
Abstract
Adenoviruses are commonly found in members of almost every vertebrate lineage except fish and amphibians, from each of which only a single isolate is available as yet. In this work, the complete genomic sequence of a fish adenovirus, originating from the white sturgeon (Acipenser transmontanus), was determined and analyzed. Several exceptional features were observed including the longest hitherto known genome size (of 48,395 bp) and a strange location of the putative fiber genes resulting in an unconventional organization pattern. The left genome end contained four fiber-like genes, three of them in a tandem position on the r (rightward transcribed) strand, followed by a fourth one on the l strand. Rightward from these, the conserved adenoviral gene cassette, encompassing 16 family-common genes, was identified. In the right-hand part, amounting for >42% of the entire genome, the presence of 28 ORFs, with a coding capacity of larger than 50 amino acids, was revealed. Interestingly, most of these showed no similarity to any adenoviral genes except two ORFs, resembling slightly the parvoviral NS gene, homologues of which occur in certain avian adenoviruses. These specific traits, together with the results of phylogeny reconstructions, fully justified the separation of the white sturgeon adenovirus into the recently established new genus Ichtadenovirus. Targeted attempts to find additional adenoviruses in any other fish species were to no avail as yet. Thus the founding member, WSAdV-1 still remains the only representative of ichtadenoviruses.
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Affiliation(s)
- Andor Doszpoly
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Balázs Harrach
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Scott LaPatra
- Research Division, Clear Springs Foods Inc., Buhl, ID, USA
| | - Mária Benkő
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
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Pallandre L, Lesne M, de Boisséson C, Charrier A, Daniel P, Tragnan A, Debeuf B, Chesneau V, Bigarré L. Genetic identification of two Acipenser iridovirus-European variants using high-resolution melting analysis. J Virol Methods 2018; 265:105-112. [PMID: 30586558 DOI: 10.1016/j.jviromet.2018.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/23/2018] [Accepted: 12/15/2018] [Indexed: 11/19/2022]
Abstract
Acipenser iridovirus-European (AcIV-E) is an important pathogen of sturgeons. Two variants differing by single-nucleotide polymorphisms (SNP) in the Major Capsid Protein gene have been described, but without any indication as to their prevalence in farms. To facilitate epidemiological studies, we developed a high-resolution melting (HRM) assay to distinguish between two alleles (var1 and var2) differing by five point substitutions. The HRM assay detected as little as 100 copies of plasmids harboring cloned sequences of var1 and var2, which have melting temperatures (Tm) differing by only 1 °C. The assay was specific of AcIV-E as demonstrated by the absence of signal when testing a related, yet distinct, virus as well as DNA from an AcIV-E-negative sturgeon sample. Experiments with mixtures of two distinct plasmids revealed abnormal melting curve patterns, which showed dips just before the main melting peaks. These dips in the curves were interpreted as the dissociation of heteroduplexes fortuitously created during the PCR step. Screening AciV-E-positive field samples of Russian sturgeons from three farms revealed the presence of var2, based on the Tm. However, for a few samples, the melting curves showed patterns typical of var2 as the dominant viral genome, mixed with another minor variant which proved to be var1. In conclusion, HRM is a simple method to screen for AcIV-E var1 and var2 and can be used on a large scale in Europe to trace these two variants which likely represent two genetic lineages.
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Affiliation(s)
- Laurane Pallandre
- Laboratoire de Ploufragan-Plouzané, ANSES, Technopole Brest Iroise, 29280 Plouzané, France
| | - Mélanie Lesne
- Laboratoires des Pyrénées et des Landes, 40004, Mont-de-Marsan, France
| | - Claire de Boisséson
- Laboratoire de Ploufragan-Plouzané, ANSES, rue des fusillés, 22440, Ploufragan, France
| | - Amélie Charrier
- Laboratoires des Pyrénées et des Landes, 40004, Mont-de-Marsan, France
| | - Patrick Daniel
- Laboratoires des Pyrénées et des Landes, 40004, Mont-de-Marsan, France
| | - Arthur Tragnan
- Groupement de Défense Sanitaire Aquacole Aquitain, 40004, Mont-de-Marsan, France
| | | | | | - Laurent Bigarré
- Laboratoire de Ploufragan-Plouzané, ANSES, Technopole Brest Iroise, 29280 Plouzané, France.
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Mimiviridae: An Expanding Family of Highly Diverse Large dsDNA Viruses Infecting a Wide Phylogenetic Range of Aquatic Eukaryotes. Viruses 2018; 10:v10090506. [PMID: 30231528 PMCID: PMC6163669 DOI: 10.3390/v10090506] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 01/22/2023] Open
Abstract
Since 1998, when Jim van Etten’s team initiated its characterization, Paramecium bursaria Chlorella virus 1 (PBCV-1) had been the largest known DNA virus, both in terms of particle size and genome complexity. In 2003, the Acanthamoeba-infecting Mimivirus unexpectedly superseded PBCV-1, opening the era of giant viruses, i.e., with virions large enough to be visible by light microscopy and genomes encoding more proteins than many bacteria. During the following 15 years, the isolation of many Mimivirus relatives has made Mimiviridae one of the largest and most diverse families of eukaryotic viruses, most of which have been isolated from aquatic environments. Metagenomic studies of various ecosystems (including soils) suggest that many more remain to be isolated. As Mimiviridae members are found to infect an increasing range of phytoplankton species, their taxonomic position compared to the traditional Phycodnaviridae (i.e., etymologically “algal viruses”) became a source of confusion in the literature. Following a quick historical review of the key discoveries that established the Mimiviridae family, we describe its current taxonomic structure and propose a set of operational criteria to help in the classification of future isolates.
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