1
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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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Rice MC, Janik AJ, Elde NC, Gagnon JA, Balla KM. Microbe transmission from pet shop to lab-reared zebrafish reveals a pathogenic birnavirus. PLoS Biol 2024; 22:e3002606. [PMID: 38814944 PMCID: PMC11139271 DOI: 10.1371/journal.pbio.3002606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 03/27/2024] [Indexed: 06/01/2024] Open
Abstract
Zebrafish are popular research organisms selected for laboratory use due in part to widespread availability from the pet trade. Many contemporary colonies of laboratory zebrafish are maintained in aquaculture facilities that monitor and aim to curb infections that can negatively affect colony health and confound experiments. The impact of laboratory control on the microbial constituents associated with zebrafish in research environments compared to the pet trade are unclear. Diseases of unknown causes are common in both environments. We conducted a metatranscriptomic survey to broadly compare the zebrafish-associated microbes in pet trade and laboratory environments. We detected many microbes in animals from the pet trade that were not found in laboratory animals. Cohousing experiments revealed several transmissible microbes including a newly described non-enveloped, double-stranded RNA virus in the Birnaviridae family we name Rocky Mountain birnavirus (RMBV). Infections were detected in asymptomatic animals from the pet trade, but when transmitted to laboratory animals RMBV was associated with pronounced antiviral responses and hemorrhagic disease. These experiments highlight the pet trade as a distinct source of diverse microbes that associate with zebrafish and establish a paradigm for the discovery of newly described pathogenic viruses and other infectious microbes that can be developed for study in the laboratory.
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Affiliation(s)
- Marlen C. Rice
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Andrew J. Janik
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Nels C. Elde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - James A. Gagnon
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Keir M. Balla
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
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3
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Rice MC, Elde NC, Gagnon JA, Balla KM. Microbe transmission from pet shop to lab-reared zebrafish reveals a pathogenic birnavirus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555169. [PMID: 37693489 PMCID: PMC10491165 DOI: 10.1101/2023.08.28.555169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Zebrafish are popular research organisms selected for laboratory use due in part to widespread availability from the pet trade. Many contemporary colonies of laboratory zebrafish are maintained in aquaculture facilities that monitor and aim to curb infections that can negatively affect colony health and confound experiments. The impact of laboratory control on the microbial constituents associated with zebrafish in research environments compared to the pet trade are unclear. Diseases of unknown causes are common in both environments. We conducted a metagenomic survey to broadly compare the zebrafish-associated microbes in pet trade and laboratory environments. We detected many microbes in animals from the pet trade that were not found in laboratory animals. Co-housing experiments revealed several transmissible microbes including a newly described non-enveloped, double-stranded RNA virus in the Birnaviridae family we name Rocky Mountain birnavirus (RMBV). Infections were detected in asymptomatic animals from the pet trade, but when transmitted to laboratory animals RMBV was associated with pronounced antiviral responses and hemorrhagic disease. These experiments highlight the pet trade as a distinct source of diverse microbes that associate with zebrafish and establish a paradigm for the discovery of newly described pathogenic viruses and other infectious microbes that can be developed for study in the laboratory.
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Affiliation(s)
- Marlen C. Rice
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112 USA
| | - Nels C. Elde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815 USA
| | - James A. Gagnon
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112 USA
| | - Keir M. Balla
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
- Current Address: Chan Zuckerberg Biohub, San Francisco, CA 94158 USA
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4
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Zhou L, Lu X, Zhao C, Zhang Y, Ning S, Zhang W. Characterization of a novel picornavirus prevalent in experimental rabbits ( Oryctolagus cuniculus). Heliyon 2023; 9:e15702. [PMID: 37159695 PMCID: PMC10163628 DOI: 10.1016/j.heliyon.2023.e15702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/11/2023] Open
Abstract
Here, using viral metagenomic method a novel picornavirus (named UJS-2019picorna, GenBank accession number OP821762) was discovered in fecal and blood samples of experimental rabbits (Oryctolagus cuniculus). The complete genome size of UJS-2019picorna is 7832 bp excluding the poly(A)-tail, with GC content of 44.00% and a nucleotide composition of 28.0% A, 28.0% U, 21.5% G, and 22.5% C. The viral genome has a typical picornavirus organization pattern from the 5'-3' direction: VPg-5' UTR-(L)-P1, (VP4-VP2-VP3-VP1)-P2, (2 A-2B-2C)-P3, (3 A-3B-3C-3D)-3' UTR-poly(A). The P1 region of UJS-2019picorna is related to Erbovirus with amino acid identity of 37.31%, while the P2 and P3 regions are the closest to Bopivirus with amino acid identity of 35.66%-39.53%. According to the Picornaviridae Study Group guidelines, UJS-2019picorna should be presumed to be a new genus belonging to the Picornaviridae family. Epidemiologic study revealed that this novel picornavirus was prevalent in a cohort of experimental rabbits, with prevalence rate of 23.68% (9/38) in feces and 18.4% (7/38) in blood samples. Further work is required to elucidate whether this virus is pathogenic to rabbits and whether it has influence on studies using rabbits as experimental animal.
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Affiliation(s)
- Liye Zhou
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Xiang Lu
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Chunyan Zhao
- Medical School, Wuxi Taihu University, Wuxi, Jiangsu, China
| | - Yu Zhang
- Key Laboratory of Cellular Physiology, Ministry of Education, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Songyi Ning
- School of Medicine, Jiangsu University, Zhenjiang, China
- Corresponding author.
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
- Corresponding author.
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5
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Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122048. [PMID: 36556413 PMCID: PMC9784588 DOI: 10.3390/life12122048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.
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Affiliation(s)
- Cristian Bassi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Paola Guerriero
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Marina Pierantoni
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Elisa Callegari
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Silvia Sabbioni
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-053-245-5319
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6
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Levraud JP, Rawls JF, Clatworthy AE. Using zebrafish to understand reciprocal interactions between the nervous and immune systems and the microbial world. J Neuroinflammation 2022; 19:170. [PMID: 35765004 PMCID: PMC9238045 DOI: 10.1186/s12974-022-02506-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
Animals rely heavily on their nervous and immune systems to perceive and survive within their environment. Despite the traditional view of the brain as an immunologically privileged organ, these two systems interact with major consequences. Furthermore, microorganisms within their environment are major sources of stimuli and can establish relationships with animal hosts that range from pathogenic to mutualistic. Research from a variety of human and experimental animal systems are revealing that reciprocal interactions between microbiota and the nervous and immune systems contribute significantly to normal development, homeostasis, and disease. The zebrafish has emerged as an outstanding model within which to interrogate these interactions due to facile genetic and microbial manipulation and optical transparency facilitating in vivo imaging. This review summarizes recent studies that have used the zebrafish for analysis of bidirectional control between the immune and nervous systems, the nervous system and the microbiota, and the microbiota and immune system in zebrafish during development that promotes homeostasis between these systems. We also describe how the zebrafish have contributed to our understanding of the interconnections between these systems during infection in fish and how perturbations may result in pathology.
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Affiliation(s)
- Jean-Pierre Levraud
- Université Paris-Saclay, CNRS, Institut Pasteur, Université Paris-Cité, Institut des Neurosciences Paris-Saclay, 91400, Saclay, France.
| | - John F. Rawls
- grid.26009.3d0000 0004 1936 7961Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, 213 Research Drive, Durham, NC 27710 USA
| | - Anne E. Clatworthy
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA ,grid.32224.350000 0004 0386 9924Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114 USA
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7
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Stenglein MD. The Case for Studying New Viruses of New Hosts. Annu Rev Virol 2022; 9:157-172. [PMID: 35671564 DOI: 10.1146/annurev-virology-100220-112915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Virology has largely focused on viruses that are pathogenic to humans or to the other species that we care most about. There is no doubt that this has been a worthwhile investment. But many transformative advances have been made through the in-depth study of relatively obscure viruses that do not appear on lists of prioritized pathogens. In this review, I highlight the benefits that can accrue from the study of viruses and hosts off the beaten track. I take stock of viral sequence diversity across host taxa as an estimate of the bias that exists in our understanding of host-virus interactions. I describe the gains that have been made through the metagenomic discovery of thousands of new viruses in previously unsampled hosts as well as the limitations of metagenomic surveys. I conclude by suggesting that the study of viruses that naturally infect existing and emerging model organisms represents an opportunity to push virology forward in useful and hard to predict ways.Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Mark D Stenglein
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA;
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8
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Mocho JP, Collymore C, Farmer SC, Leguay E, Murray KN, Pereira N. FELASA-AALAS Recommendations for Monitoring and Reporting of Laboratory Fish Diseases and Health Status, with an Emphasis on Zebrafish ( Danio Rerio). Comp Med 2022; 72:127-148. [PMID: 35513000 PMCID: PMC9334007 DOI: 10.30802/aalas-cm-22-000034] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/02/2022] [Indexed: 11/05/2022]
Abstract
The exchange of fish for research may expose an aquatic laboratory to pathogen contamination as incoming fish can introduce bacteria, fungi, parasites, and viruses capable of affecting both experimental results and fish and personnel health and welfare. To develop risk mitigation strategies, FELASA and AALAS established a joint working group to recommend good practices for health monitoring of laboratory fish. The recommendations address all fish species used for research, with a particular focus on zebrafish (Danio rerio). First, the background of the working group and key definitions are provided. Next, fish diseases of high impact are described. Third, recommendations are made for health monitoring of laboratory fishes. The recommendations emphasize the importance of daily observation of the fish and strategies to determine fish colony health status. Finally, report templates are proposed for historical screening data and aquatic facility description to facilitate biohazard risk assessment when exchanging fish.
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Affiliation(s)
| | - Chereen Collymore
- Veterinary Care and Services, Charles River Laboratories, Senneville, Quebec, Canada
| | - Susan C Farmer
- Zebrafish Research Facility, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Katrina N Murray
- Zebrafish International Resource Center, University of Oregon, Eugene, Oregon, USA
| | - Nuno Pereira
- Chronic Diseases Research Center (CEDOC), Nova Medical School, Lisbon; Faculty of Veterinary Medicine, Lusophone University of Humanities and Technologies, Lisbon, Portugal; Gulbenkian Institute of Science, Oeiras. Portugal; ISPA - University Institute of Psychological, Social and Life Sciences, Lisbon, Portugal; Lisbon Oceanarium, Lisbon, Portugal
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9
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Maleski ALA, Rosa JGS, Bernardo JTG, Astray RM, Walker CIB, Lopes-Ferreira M, Lima C. Recapitulation of Retinal Damage in Zebrafish Larvae Infected with Zika Virus. Cells 2022; 11:1457. [PMID: 35563763 PMCID: PMC9100881 DOI: 10.3390/cells11091457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/24/2022] [Accepted: 04/07/2022] [Indexed: 02/06/2023] Open
Abstract
Zebrafish are increasingly being utilized as a model to investigate infectious diseases and to advance the understanding of pathogen-host interactions. Here, we take advantage of the zebrafish to recapitulate congenital ZIKV infection and, for the first time, demonstrate that it can be used to model infection and reinfection and monitor anti-viral and inflammatory immune responses, as well as brain growth and eye abnormalities during embryonic development. By injecting a Brazilian strain of ZIKV into the yolk sac of one-cell stage embryos, we confirmed that, after 72 h, ZIKV successfully infected larvae, and the physical condition of the virus-infected hosts included gross morphological changes in surviving embryos (84%), with a reduction in larval head size and retinal damage characterized by increased thickness of the lens and inner nuclear layer. Changes in locomotor activity and the inability to perceive visual stimuli are a result of changes in retinal morphology caused by ZIKV. Furthermore, we demonstrated the ability of ZIKV to replicate in zebrafish larvae and infect new healthy larvae, impairing their visual and neurological functions. These data reinforce the deleterious activity of ZIKV in the brain and visual structures and establish the zebrafish as a model to study the molecular mechanisms involved in the pathology of the virus.
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Affiliation(s)
- Adolfo Luis Almeida Maleski
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CeTICs/FAPESP), Butantan Institute, São Paulo 05503-900, Brazil; (A.L.A.M.); (J.G.S.R.); (J.T.G.B.); (M.L.-F.)
- Laboratory of Neuropharmacological Studies (LABEN), Post-Graduation Program of Pharmaceutical Science, Federal University of Sergipe, São Paulo 05503-009, Brazil;
| | - Joao Gabriel Santos Rosa
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CeTICs/FAPESP), Butantan Institute, São Paulo 05503-900, Brazil; (A.L.A.M.); (J.G.S.R.); (J.T.G.B.); (M.L.-F.)
| | - Jefferson Thiago Gonçalves Bernardo
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CeTICs/FAPESP), Butantan Institute, São Paulo 05503-900, Brazil; (A.L.A.M.); (J.G.S.R.); (J.T.G.B.); (M.L.-F.)
| | | | - Cristiani Isabel Banderó Walker
- Laboratory of Neuropharmacological Studies (LABEN), Post-Graduation Program of Pharmaceutical Science, Federal University of Sergipe, São Paulo 05503-009, Brazil;
| | - Monica Lopes-Ferreira
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CeTICs/FAPESP), Butantan Institute, São Paulo 05503-900, Brazil; (A.L.A.M.); (J.G.S.R.); (J.T.G.B.); (M.L.-F.)
| | - Carla Lima
- Immunoregulation Unit of the Laboratory of Applied Toxinology (CeTICs/FAPESP), Butantan Institute, São Paulo 05503-900, Brazil; (A.L.A.M.); (J.G.S.R.); (J.T.G.B.); (M.L.-F.)
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10
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Reuter G, Pankovics P, László Z, Gáspár G, Hui A, Delwart E, Boros Á. Human-stool-associated tusavirus (Parvoviridae) in domestic goats and sheep. Arch Virol 2022; 167:1307-1310. [PMID: 35355143 PMCID: PMC9038789 DOI: 10.1007/s00705-022-05424-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/10/2022] [Indexed: 11/24/2022]
Abstract
In this study, genetic counterparts of the human-stool-associated tusavirus (subfamily Parvovirinae, family Parvoviridae) with >97% and 95-100% amino acid sequence identity in the parvoviral NS1 and VP1 protein were identified in faecal specimens from domestic goats (Capra hircus) and sheep (Ovis aries) in Hungary. Eleven (17.8%) of the 62 faecal specimens from goats and 12 (25.5%) of the 47 from sheep both from less than 12 months old animals were positive for tusavirus DNA by PCR, while none of the specimens collected from cattle and swine were positive. Thus, it cannot be ruled out that tusavirus infection in humans is of zoonotic origin.
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Affiliation(s)
- Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., Pécs, 7624, Hungary.
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., Pécs, 7624, Hungary
| | - Zoltán László
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., Pécs, 7624, Hungary
| | - Gábor Gáspár
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., Pécs, 7624, Hungary
| | - Alvin Hui
- Vitalant Research Institute, San Francisco, CA, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, USA.,University of California, San Francisco, CA, USA
| | - Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., Pécs, 7624, Hungary
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11
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Hargitai R, Pankovics P, Boros Á, Mátics R, Altan E, Delwart E, Reuter G. Novel picornavirus (family Picornaviridae) from freshwater fishes (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) in Hungary. Arch Virol 2021; 166:2627-2632. [PMID: 34255185 PMCID: PMC8322000 DOI: 10.1007/s00705-021-05167-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/21/2021] [Indexed: 12/01/2022]
Abstract
In this study, a novel picornavirus (perchPV/M9/2015/HUN, GenBank accession no. MW590713) was detected in eight (12.9%) out of 62 faecal samples collected from three (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) out of 13 freshwater fish species tested and genetically characterized using viral metagenomics and RT-PCR methods. The complete genome of perchPV/M9/2015/HUN is 7,741 nt long, excluding the poly(A) tail, and has the genome organization 5'UTRIRES-?/P1(VP0-VP3-VP1)/P2(2A1NPG↓P-2A2H-box/NC-2B-2C)/P3(3A-3BVPg-3CPro-3DPol)/3'UTR-poly(A). The P1, 2C, and 3CD proteins had 41.4%, 38.1%, and 47.3% amino acid sequence identity to the corresponding proteins of Wenling lepidotrigla picornavirus (MG600079), eel picornavirus (NC_022332), and Wenling pleuronectiformes picornavirus (MG600098), respectively, as the closest relatives in the genus Potamipivirus. PerchPV/M9/2015/HUN represents a potential novel fish-origin species in an unassigned genus in the family Picornaviridae.
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Affiliation(s)
- Renáta Hargitai
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., 7624, Pecs, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., 7624, Pecs, Hungary
| | - Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., 7624, Pecs, Hungary
| | | | - Eda Altan
- Vitalant Research Institute, San Francisco, CA, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, USA
- University of California, San Francisco, CA, USA
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., 7624, Pecs, Hungary.
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12
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Sun FJ, Crim MJ, Leblanc M. Edwardsiella ictaluri in a Colony of Zebrafish ( Danio rerio) Used in a Teaching Laboratory. Comp Med 2021; 71:318-322. [PMID: 34187617 DOI: 10.30802/aalas-cm-21-000034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A small colony of zebrafish (Danio rerio) experienced 30% acute mortality within a few days after receipt from a commercial source. A few fish presented with small areas of raised scales or tissue necrosis, primarily near the caudal peduncle. Edwardsiella ictaluri (E. ictaluri) was identified by real-time PCR of pooled zebrafish and swabs of the pre-filter and fine filter pads, with subsequent sequence analysis. E. ictaluri is most commonly associated with an enteric septicemia in catfish species and can have significant economic impact on commercial catfish fisheries. However, several references report naturally occurring E. ictaluri infection of nonictalurid fishes, including zebrafish. Ours is the first report demonstrating the use of environmental sampling to identify E. ictaluri in a zebrafish colony by real-time PCR. Moreover, our report indicates that E. ictaluri is a relevant disease for institutions using zebrafish as research species and emphasizes the importance of carefully considering importation and quarantine practices.
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Affiliation(s)
- Francis J Sun
- Division of Laboratory Animal Resources, Duke University Medical Center, Durham, North Carolina;,
| | | | - Mathias Leblanc
- Division of Laboratory Animal Resources, Duke University Medical Center, Durham, North Carolina
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13
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Sullivan C, Soos BL, Millard PJ, Kim CH, King BL. Modeling Virus-Induced Inflammation in Zebrafish: A Balance Between Infection Control and Excessive Inflammation. Front Immunol 2021; 12:636623. [PMID: 34025644 PMCID: PMC8138431 DOI: 10.3389/fimmu.2021.636623] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/21/2021] [Indexed: 12/16/2022] Open
Abstract
The inflammatory response to viral infection in humans is a dynamic process with complex cell interactions that are governed by the immune system and influenced by both host and viral factors. Due to this complexity, the relative contributions of the virus and host factors are best studied in vivo using animal models. In this review, we describe how the zebrafish (Danio rerio) has been used as a powerful model to study host-virus interactions and inflammation by combining robust forward and reverse genetic tools with in vivo imaging of transparent embryos and larvae. The innate immune system has an essential role in the initial inflammatory response to viral infection. Focused studies of the innate immune response to viral infection are possible using the zebrafish model as there is a 4-6 week timeframe during development where they have a functional innate immune system dominated by neutrophils and macrophages. During this timeframe, zebrafish lack a functional adaptive immune system, so it is possible to study the innate immune response in isolation. Sequencing of the zebrafish genome has revealed significant genetic conservation with the human genome, and multiple studies have revealed both functional conservation of genes, including those critical to host cell infection and host cell inflammatory response. In addition to studying several fish viruses, zebrafish infection models have been developed for several human viruses, including influenza A, noroviruses, chikungunya, Zika, dengue, herpes simplex virus type 1, Sindbis, and hepatitis C virus. The development of these diverse viral infection models, coupled with the inherent strengths of the zebrafish model, particularly as it relates to our understanding of macrophage and neutrophil biology, offers opportunities for far more intensive studies aimed at understanding conserved host responses to viral infection. In this context, we review aspects relating to the evolution of innate immunity, including the evolution of viral pattern recognition receptors, interferons and interferon receptors, and non-coding RNAs.
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Affiliation(s)
- Con Sullivan
- College of Arts and Sciences, University of Maine at Augusta, Bangor, ME, United States
| | - Brandy-Lee Soos
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, United States
| | - Paul J. Millard
- Department of Environmental and Sustainable Engineering, University at Albany, Albany, NY, United States
| | - Carol H. Kim
- Department of Biomedical Sciences, University at Albany, Albany, NY, United States
- Department of Biological Sciences, University at Albany, Albany, NY, United States
| | - Benjamin L. King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, United States
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, United States
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14
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Deng Z, Delwart E. ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data. BMC Bioinformatics 2021; 22:119. [PMID: 33706720 PMCID: PMC7953547 DOI: 10.1186/s12859-021-04038-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Metagenomics is the study of microbial genomes for pathogen detection and discovery in human clinical, animal, and environmental samples via Next-Generation Sequencing (NGS). Metagenome de novo sequence assembly is a crucial analytical step in which longer contigs, ideally whole chromosomes/genomes, are formed from shorter NGS reads. However, the contigs generated from the de novo assembly are often very fragmented and rarely longer than a few kilo base pairs (kb). Therefore, a time-consuming extension process is routinely performed on the de novo assembled contigs. RESULTS To facilitate this process, we propose a new tool for metagenome contig extension after de novo assembly. ContigExtender employs a novel recursive extending strategy that explores multiple extending paths to achieve highly accurate longer contigs. We demonstrate that ContigExtender outperforms existing tools in synthetic, animal, and human metagenomics datasets. CONCLUSIONS A novel software tool ContigExtender has been developed to assist and enhance the performance of metagenome de novo assembly. ContigExtender effectively extends contigs from a variety of sources and can be incorporated in most viral metagenomics analysis pipelines for a wide variety of applications, including pathogen detection and viral discovery.
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Affiliation(s)
- Zachary Deng
- Vitalant Research Institute, San Francisco, CA, 94118, USA.
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94107, USA.
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, 94118, USA.
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94107, USA.
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15
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Scherbatskoy EC, Subramaniam K, Al-Hussinee L, Imnoi K, Thompson PM, Popov VL, Ng TFF, Kelley KL, Alvarado R, Wolf JC, Pouder DB, Yanong RPE, Waltzek TB. Characterization of a novel picornavirus isolated from moribund aquacultured clownfish. J Gen Virol 2021; 101:735-745. [PMID: 32421489 DOI: 10.1099/jgv.0.001421] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Over the last decade, a number of USA aquaculture facilities have experienced periodic mortality events of unknown aetiology in their clownfish (Amphiprion ocellaris). Clinical signs of affected individuals included lethargy, altered body coloration, reduced body condition, tachypnea, and abnormal positioning in the water column. Samples from outbreaks were processed for routine parasitological, bacteriological, and virological diagnostic testing, but no consistent parasitic or bacterial infections were observed. Histopathological evaluation revealed individual cell necrosis and mononuclear cell inflammation in the branchial cavity, pharynx, oesophagus and/or stomach of four examined clownfish, and large basophilic inclusions within the pharyngeal mucosal epithelium of one fish. Homogenates from pooled external and internal tissues from these outbreaks were inoculated onto striped snakehead (SSN-1) cells for virus isolation and cytopathic effects were observed, resulting in monolayer lysis in the initial inoculation and upon repassage. Transmission electron microscopy of infected SSN-1 cells revealed small round particles (mean diameter=20.0-21.7 nm) within the cytoplasm, consistent with the ultrastructure of a picornavirus. Full-genome sequencing of the purified virus revealed a novel picornavirus most closely related to the bluegill picornavirus and other members of the genus Limnipivirus. Additionally, pairwise protein alignments between the clownfish picornavirus (CFPV) and other known members of the genus Limnipivirus yielded results in accordance with the current International Committee on Taxonomy of Viruses criteria for members of the same genus. Thus, CFPV represents a proposed new limnipivirus species. Future experimental challenge studies are needed to determine the role of CFPV in disease.
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Affiliation(s)
- Elizabeth C Scherbatskoy
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Kuttichantran Subramaniam
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Lowia Al-Hussinee
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Kamonchai Imnoi
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Patrick M Thompson
- Present address: Whitney Laboratory for Marine Bioscience, St Augustine, FL, USA
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Vsevolod L Popov
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Terry Fei Fan Ng
- College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Karen L Kelley
- Electron Microscopy Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Rodolfo Alvarado
- Electron Microscopy Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Jeffrey C Wolf
- Experimental Pathology Laboratories, Inc., Sterling, VA, USA
| | - Deborah B Pouder
- Tropical Aquaculture Laboratory, Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, IFAS, University of Florida, Ruskin, FL, USA
| | - Roy P E Yanong
- Tropical Aquaculture Laboratory, Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, IFAS, University of Florida, Ruskin, FL, USA
| | - Thomas B Waltzek
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
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16
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Vila IK, Fretaud M, Vlachakis D, Laguette N, Langevin C. Animal Models for the Study of Nucleic Acid Immunity: Novel Tools and New Perspectives. J Mol Biol 2020; 432:5529-5543. [PMID: 32860771 PMCID: PMC7611023 DOI: 10.1016/j.jmb.2020.08.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/16/2020] [Accepted: 08/18/2020] [Indexed: 02/08/2023]
Abstract
Unresolved inflammation fosters and supports a wide range of human pathologies. There is growing evidence for a role played by cytosolic nucleic acids in initiating and supporting pathological chronic inflammation. In particular, the cGAS-STING pathway has emerged as central to the mounting of nucleic acid-dependent type I interferon responses, leading to the identification of small-molecule modulators of STING that have raised clinical interest. However, several new challenges have emerged, representing potential obstacles to efficient clinical translation. Indeed, the current literature underscores that nucleic acid-induced inflammatory responses are subjected to several layers of regulation, further suggesting complex coordination at the cell-type, tissue or organism level. Untangling the underlying processes is paramount to the identification of specific therapeutic strategies targeting deleterious inflammation. Herein, we present an overview of human pathologies presenting with deregulated interferon levels and with accumulation of cytosolic nucleic acids. We focus on the central role of the STING adaptor protein in these pathologies and discuss how in vivo models have forged our current understanding of nucleic acid immunity. We present our opinion on the advantages and limitations of zebrafish and mice models to highlight their complementarity for the study of inflammatory human pathologies and the development of therapeutics. Finally, we discuss high-throughput screening strategies that generate multi-parametric datasets that allow integrative analysis of heterogeneous information (imaging and omics approaches). These approaches are likely to structure the future of screening strategies for the treatment of human pathologies.
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Affiliation(s)
- Isabelle K Vila
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Molecular Basis of Inflammation Laboratory, Montpellier, France.
| | - Maxence Fretaud
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece; Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; University Research Institute of Maternal and Child Health & Precision Medicine, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Nadine Laguette
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Molecular Basis of Inflammation Laboratory, Montpellier, France
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17
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Kent M, Sanders J, Spagnoli S, Al-Samarrie C, Murray K. Review of diseases and health management in zebrafish Danio rerio (Hamilton 1822) in research facilities. JOURNAL OF FISH DISEASES 2020; 43:637-650. [PMID: 32291793 PMCID: PMC7253333 DOI: 10.1111/jfd.13165] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/27/2020] [Accepted: 02/17/2020] [Indexed: 05/09/2023]
Abstract
The use of zebrafish (Danio rerio) in biomedical research has expanded at a tremendous rate over the last two decades. Along with increases in laboratories using this model, we are discovering new and important diseases. We review here the important pathogens and diseases based on some 20 years of research and findings from our diagnostic service at the NIH-funded Zebrafish International Resource Center. Descriptions of the present status of biosecurity programmes and diagnostic and treatment approaches are included. The most common and important diseases and pathogens are two parasites, Pseudoloma neurophilia and Pseudocapillaria tomentosa, and mycobacteriosis caused by Mycobacterium chelonae, M. marinum and M. haemophilum. Less common but deadly diseases are caused by Edwardsiella ictaluri and infectious spleen and kidney necrosis virus (ISKNV). Hepatic megalocytosis and egg-associated inflammation and fibroplasia are common, apparently non-infectious, in zebrafish laboratories. Water quality diseases include supersaturation and nephrocalcinosis. Common neoplasms are spindle cell sarcomas, ultimobranchial tumours, spermatocytic seminomas and a small-cell carcinoma that is caused by a transmissible agent. Despite the clear biosecurity risk, researchers continue to use fish from pet stores, and here, we document two novel coccidia associated with significant lesions in zebrafish from one of these stores.
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Affiliation(s)
- M.L Kent
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon 97331
| | - J.L. Sanders
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon 97331
| | - S. Spagnoli
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon 97331
| | - C.E. Al-Samarrie
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331
| | - K.N. Murray
- Zebrafish International Resource Center, Eugene, Oregon 97403
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18
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Kent ML, Sanders JL, Spagnoli S, Al-Samarrie CE, Murray KN. Review of diseases and health management in zebrafish Danio rerio (Hamilton 1822) in research facilities. JOURNAL OF FISH DISEASES 2020; 43:637-650. [PMID: 32291793 DOI: 10.1111/jfd.13165j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/27/2020] [Accepted: 02/17/2020] [Indexed: 05/22/2023]
Abstract
The use of zebrafish (Danio rerio) in biomedical research has expanded at a tremendous rate over the last two decades. Along with increases in laboratories using this model, we are discovering new and important diseases. We review here the important pathogens and diseases based on some 20 years of research and findings from our diagnostic service at the NIH-funded Zebrafish International Resource Center. Descriptions of the present status of biosecurity programmes and diagnostic and treatment approaches are included. The most common and important diseases and pathogens are two parasites, Pseudoloma neurophilia and Pseudocapillaria tomentosa, and mycobacteriosis caused by Mycobacterium chelonae, M. marinum and M. haemophilum. Less common but deadly diseases are caused by Edwardsiella ictaluri and infectious spleen and kidney necrosis virus (ISKNV). Hepatic megalocytosis and egg-associated inflammation and fibroplasia are common, apparently non-infectious, in zebrafish laboratories. Water quality diseases include supersaturation and nephrocalcinosis. Common neoplasms are spindle cell sarcomas, ultimobranchial tumours, spermatocytic seminomas and a small-cell carcinoma that is caused by a transmissible agent. Despite the clear biosecurity risk, researchers continue to use fish from pet stores, and here, we document two novel coccidia associated with significant lesions in zebrafish from one of these stores.
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Affiliation(s)
- M L Kent
- Department of Microbiology, Oregon State University, Corvallis, Oregon
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon
| | - J L Sanders
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon
| | - S Spagnoli
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon
| | - C E Al-Samarrie
- Department of Microbiology, Oregon State University, Corvallis, Oregon
| | - K N Murray
- Zebrafish International Resource Center, Eugene, Oregon
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19
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Balla KM, Rice MC, Gagnon JA, Elde NC. Linking Virus Discovery to Immune Responses Visualized during Zebrafish Infections. Curr Biol 2020; 30:2092-2103.e5. [PMID: 32413307 DOI: 10.1016/j.cub.2020.04.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/28/2020] [Accepted: 04/14/2020] [Indexed: 12/12/2022]
Abstract
The discovery of new viruses currently outpaces our capacity for experimental examination of infection biology. To better couple virus discovery with immunology, we genetically modified zebrafish to visually report on virus infections. After generating a strain that expresses green fluorescent protein (GFP) under an interferon-stimulated gene promoter, we repeatedly observed transgenic larvae spontaneously expressing GFP days after hatching. RNA sequencing comparisons of co-housed GFP-positive and GFP-negative zebrafish revealed a naturally occurring picornavirus that induced a canonical interferon-mediated response and hundreds of antiviral defense genes not observed following immunostimulatory treatments or experimental infections with other viruses. Among the many genes induced by picornavirus infection was a large set encoding guanosine triphosphatase (GTPase) of immunity-associated proteins (GIMAPs). The GIMAP gene family is massively expanded in fish genomes and may also play a crucial role in antiviral responses in mammals, including humans. We subsequently detected zebrafish picornavirus in publicly available sequencing data from seemingly asymptomatic zebrafish in many research institutes and found that it altered gene expression in a previous study of zebrafish development. Experiments revealed a horizontal mode of virus transmission, highlighting a system for studying the spread of picornavirus infections within and between individuals. Our study describes a naturally occurring picornavirus that elicits strong antiviral responses in zebrafish and provides new strategies for simultaneously discovering viruses and their impact on vertebrate hosts.
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Affiliation(s)
- Keir M Balla
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Marlen C Rice
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - James A Gagnon
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Nels C Elde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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20
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Segrist E, Cherry S. Using Diverse Model Systems to Define Intestinal Epithelial Defenses to Enteric Viral Infections. Cell Host Microbe 2020; 27:329-344. [PMID: 32164844 DOI: 10.1016/j.chom.2020.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The intestine is an essential physical and immunological barrier comprised of a monolayer of diverse and specialized epithelial cells that perform functions ranging from nutrient absorption to pathogen sensing and intestinal homeostasis. The intestinal barrier prevents translocation of intestinal microbes into internal compartments. The microbiota is comprised of a complex community largely populated by diverse bacterial species that provide metabolites, nutrients, and immune stimuli that promote intestinal and organismal health. Although commensal organisms promote health, enteric pathogens, including a diverse plethora of enteric viruses, cause acute and chronic diseases. The barrier epithelium plays fundamental roles in immune defenses against enteric viral infections by integrating diverse signals, including those from the microbiota, to prevent disease. Importantly, many model systems have contributed to our understanding of this complex interface. This review will focus on the antiviral mechanisms at play within the intestinal epithelium and how these responses are shaped by the microbiota.
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Affiliation(s)
- Elisha Segrist
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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21
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Flores EM, Nguyen AT, Odem MA, Eisenhoffer GT, Krachler AM. The zebrafish as a model for gastrointestinal tract-microbe interactions. Cell Microbiol 2020; 22:e13152. [PMID: 31872937 DOI: 10.1111/cmi.13152] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/07/2019] [Accepted: 12/19/2019] [Indexed: 02/06/2023]
Abstract
The zebrafish (Danio rerio) has become a widely used vertebrate model for bacterial, fungal, viral, and protozoan infections. Due to its genetic tractability, large clutch sizes, ease of manipulation, and optical transparency during early life stages, it is a particularly useful model to address questions about the cellular microbiology of host-microbe interactions. Although its use as a model for systemic infections, as well as infections localised to the hindbrain and swimbladder having been thoroughly reviewed, studies focusing on host-microbe interactions in the zebrafish gastrointestinal tract have been neglected. Here, we summarise recent findings regarding the developmental and immune biology of the gastrointestinal tract, drawing parallels to mammalian systems. We discuss the use of adult and larval zebrafish as models for gastrointestinal infections, and more generally, for studies of host-microbe interactions in the gut.
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Affiliation(s)
- Erika M Flores
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.,M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas
| | - Anh T Nguyen
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.,M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas
| | - Max A Odem
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - George T Eisenhoffer
- M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas.,Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anne Marie Krachler
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.,M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas
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22
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Miller M, Sabrautzki S, Beyerlein A, Brielmeier M. Combining fish and environmental PCR for diagnostics of diseased laboratory zebrafish in recirculating systems. PLoS One 2019; 14:e0222360. [PMID: 31513657 PMCID: PMC6742364 DOI: 10.1371/journal.pone.0222360] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/27/2019] [Indexed: 01/10/2023] Open
Abstract
Precise knowledge of the health status of experimental fish is crucial to obtain high scientific and ethical standards in biomedical research. In addition to the use of sentinel fish, the examination of diseased fish is a fundamental part of all health monitoring concepts. PCR assays offer excellent sensitivity and the ability to test a broad variety of pathogenic agents in different sample types. Recently, it was shown that analysis of environmental samples such as water, sludge or detritus from static tanks can complement PCR analysis of fish and is actually more reliable for certain pathogens. In our study, we investigated whether the analysis of filtered water mixed with detritus of tanks including fish showing clinical signs of illness is suitable to complement health monitoring programs in recirculating systems. The obtained data indicate that pathogens such as Pseudoloma neurophilia or Myxidium streisingeri were exclusively or mainly found in fish, while mycobacteria were predominantly present in environmental samples. A combination of both sample types seems to be required for the detection of a broad range of infectious agents in zebrafish colonies using real-time PCR technology.
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Affiliation(s)
- Manuel Miller
- Research Unit Comparative Medicine, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- * E-mail:
| | - Sibylle Sabrautzki
- Research Unit Comparative Medicine, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Andreas Beyerlein
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Markus Brielmeier
- Research Unit Comparative Medicine, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
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23
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Boros Á, Orlovácz K, Pankovics P, Szekeres S, Földvári G, Fahsbender E, Delwart E, Reuter G. Diverse picornaviruses are prevalent among free-living and laboratory rats (Rattus norvegicus) in Hungary and can cause disseminated infections. INFECTION GENETICS AND EVOLUTION 2019; 75:103988. [PMID: 31377399 DOI: 10.1016/j.meegid.2019.103988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/24/2019] [Accepted: 07/31/2019] [Indexed: 12/28/2022]
Abstract
In this study, the full length genomes of three phylogenetically distant picornaviruses (family Picornaviridae) belonging to the genus Rosavirus (rat08/rRoB/HUN, MN116648), Kobuvirus (rat08/rAiA/HUN, MN116647), and Cardiovirus (rat08/rCaB/HUN, MN116646) were obtained from a single faecal sample of a free-living Norway rat (Rattus norvegicus) in Hungary using viral metagenomics and RT-PCR/Sanger sequencing. The acquired complete genomes were in silico analyzed in detail revealing the presence of a second minor open reading frame encoding an alternative Leader peptide (L*) in rat08/rCaB/HUN and a ca. 222 nt-long sequence repeat with compact secondary RNA structure in the 3' UTR of rat08/rRoB/HUN. The studied rat picornaviruses were frequently detectable by RT-PCR with relatively high viral loads ranged between 8.99E+02 and 1.29E+06 copies/ml in rat faecal samples collected from five geographically distant locations throughout Hungary. The VP1 sequence-based phylogenetic analyses show the presence of multiple, mostly location-specific lineages for all three picornaviruses. Rat rosavirus and rat cardiovirus were identified in spleen while rat cardiovirus was also detected in liver, muscle and kidney samples with variable copy numbers (6.42E+01-1.90E+05 copies/μg total RNA) suggesting extra-intestinal dissemination. Both viruses were also prevalent (70.0% and 18.2%) among two populations of laboratory rats ("Wistar-type" and "hooded-type") held in different, isolated laboratory animal units.
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Affiliation(s)
- Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs Pécs, Hungary
| | - Katalin Orlovácz
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs Pécs, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs Pécs, Hungary
| | - Sándor Szekeres
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - Gábor Földvári
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary; Evolutionary Systems Research Group MTA Centre for Ecological Research, Tihany, Hungary
| | | | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, USA; University of California, San Francisco, CA, USA
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs Pécs, Hungary.
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