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Niner MD, Stepien CA, Gorgoglione B, Leaman DW. Genomic and immunogenic changes of Piscine novirhabdovirus (Viral Hemorrhagic Septicemia Virus) over its evolutionary history in the Laurentian Great Lakes. PLoS One 2021; 16:e0232923. [PMID: 34048438 PMCID: PMC8162641 DOI: 10.1371/journal.pone.0232923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 04/22/2021] [Indexed: 01/21/2023] Open
Abstract
A unique and highly virulent subgenogroup (-IVb) of Piscine novirhabdovirus, also known as Viral Hemorrhagic Septicemia Virus (VHSV), suddenly appeared in the Laurentian Great Lakes, causing large mortality outbreaks in 2005 and 2006, and affecting >32 freshwater fish species. Periods of apparent dormancy have punctuated smaller and more geographically-restricted outbreaks in 2007, 2008, and 2017. In this study, we conduct the largest whole genome sequencing analysis of VHSV-IVb to date, evaluating its evolutionary changes from 48 isolates in relation to immunogenicity in cell culture. Our investigation compares genomic and genetic variation, selection, and rates of sequence changes in VHSV-IVb, in relation to other VHSV genogroups (VHSV-I, VHSV-II, VHSV-III, and VHSV-IVa) and with other Novirhabdoviruses. Results show that the VHSV-IVb isolates we sequenced contain 253 SNPs (2.3% of the total 11,158 nucleotides) across their entire genomes, with 85 (33.6%) of them being non-synonymous. The most substitutions occurred in the non-coding region (NCDS; 4.3%), followed by the Nv- (3.8%), and M- (2.8%) genes. Proportionally more M-gene substitutions encoded amino acid changes (52.9%), followed by the Nv- (50.0%), G- (48.6%), N- (35.7%) and L- (23.1%) genes. Among VHSV genogroups and subgenogroups, VHSV-IVa from the northeastern Pacific Ocean has shown the fastest substitution rate (2.01x10-3), followed by VHSV-IVb (6.64x10-5) and by the VHSV-I, -II and-III genogroups from Europe (4.09x10-5). A 2016 gizzard shad (Dorosoma cepedianum) from Lake Erie possessed the most divergent VHSV-IVb sequence. The in vitro immunogenicity analysis of that sample displayed reduced virulence (as did the other samples from 2016), in comparison to the original VHSV-IVb isolate (which had been traced back to 2003, as an origin date). The 2016 isolates that we tested induced milder impacts on fish host cell innate antiviral responses, suggesting altered phenotypic effects. In conclusion, our overall findings indicate that VHSV-IVb has undergone continued sequence change and a trend to lower virulence over its evolutionary history (2003 through present-day), which may facilitate its long-term persistence in fish host populations.
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Affiliation(s)
- Megan D. Niner
- Department of Environmental Sciences, University of Toledo, Toledo, Ohio, United States of America
| | - Carol A. Stepien
- School of Oceanography, University of Washington, Seattle, WA, United States of America
- Genetics and Genomics Group, NOAA Pacific Marine Environmental Laboratory, Seattle, Washington, United States of America
- * E-mail: ,
| | - Bartolomeo Gorgoglione
- Department of Biological Sciences, University of Toledo, Toledo, Ohio, United States of America
| | - Douglas W. Leaman
- Department of Biological Sciences, University of Toledo, Toledo, Ohio, United States of America
- Department of Biological Sciences, Wright State University, Dayton, Ohio, United States of America
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Stepien CA, Niner MD. Evolutionary trajectory of fish Piscine novirhabdovirus (=Viral Hemorrhagic Septicemia Virus) across its Laurentian Great Lakes history: Spatial and temporal diversification. Ecol Evol 2020; 10:9740-9775. [PMID: 33005343 PMCID: PMC7520192 DOI: 10.1002/ece3.6611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/04/2020] [Accepted: 05/10/2020] [Indexed: 02/05/2023] Open
Abstract
Piscine novirhabdovirus = Viral Hemorrhagic Septicemia Virus (VHSV) first appeared in the Laurentian Great Lakes with large outbreaks from 2005 to 2006, as a new and novel RNA rhabdovirus subgenogroup (IVb) that killed >30 fish species. Interlude periods punctuated smaller more localized outbreaks in 2007, 2010, and 2017, although some fishes tested positive in the intervals. There have not been reports of outbreaks or positives from 2018, 2019, or 2020. Here, we employ a combined population genetics and phylogenetic approach to evaluate spatial and temporal evolutionary trajectory on its G-gene sequence variation, in comparison with whole-genome sequences (11,083 bp) from a subset of 44 individual isolates (including 40 newly sequenced ones). Our results show that IVb (N = 184 individual fish isolates) diversified into 36 G-gene haplotypes from 2003 to 2017, stemming from two originals ("a" and "b"). G-gene haplotypes "a" and "b" differed by just one synonymous single-nucleotide polymorphism (SNP) substitution, remained the most abundant until 2011, then disappeared. Group "a" descendants (14 haplotypes) remained most prevalent in the Upper and Central Great Lakes, with eight (51%) having nonsynonymous substitutions. Group "b" descendants primarily have occurred in the Lower Great Lakes, including 22 haplotypes, of which 15 (68%) contained nonsynonymous changes. Evolutionary patterns of the whole-genome sequences (which had 34 haplotypes among 44 isolates) appear congruent with those from the G-gene. Virus populations significantly diverged among the Upper, Central, and Lower Great Lakes, diversifying over time. Spatial divergence was apparent in the overall patterns of nucleotide substitutions, while amino acid changes increased temporally. VHSV-IVb thus significantly differentiated across its less than two decades in the Great Lakes, accompanied by declining outbreaks and virulence. Continuing diversification likely allowed the virus to persist at low levels in resident fish populations, and may facilitate its potential for further and future spread to new habitats and nonacclimated hosts.
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Affiliation(s)
- Carol A. Stepien
- Genetics and Genomics Group (G3)NOAA Pacific Marine Environmental Laboratory (PMEL)SeattleWAUSA
| | - Megan D. Niner
- Genetics and Genomics Group (G3), Department of Environmental SciencesUniversity of ToledoToledoOHUSA
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Gorgoglione B, Ringiesn JL, Pham LH, Shepherd BS, Leaman DW. Comparative effects of Novirhabdovirus genes on modulating constitutive transcription and innate antiviral responses, in different teleost host cell types. Virol J 2020; 17:110. [PMID: 32690033 PMCID: PMC7369537 DOI: 10.1186/s12985-020-01372-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/30/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Infectious hematopoietic necrosis virus (IHNV) and viral hemorrhagic septicemia virus (VHSV) are highly contagious, pathogenic Novirhabdoviruses affecting fish and are thusly notifiable diseases with the World Organization for Animal Health. This study assessed the relative capacities of IHNV and VHSV genes to modulate host general transcription and explores the abilities of specific IHNV genes to interfere with the interferon pathway in heterogenous teleost cell-lines. METHODS Optimized protocols allowed for efficient transient transfections in EPC, BF-2, RTG-2 and RTgill-W1 cell lines of plasmids encoding IHNV (M genogroup) and VHSV (-IVb genotype) genes, including N, P, M, G and NV. Their impact on general cellular transcription was measured 48 hours post transfection (hpt) with luciferase constructs driven by a modified β-Actin promoter (pCAG). Their modulation of the innate antiviral immune response was characterized 72 hpt, using luciferase constructs measuring rainbow trout Type I IFN or MX-1 promoter augmentation, upon MAVS co-transfection. RESULTS M was generally confirmed as the strongest constitutive transcriptional suppressor while IHNV P, but not VHSV P, augmented constitutive transcription in fibroblastic cell types. Cell-specific effects were observed for viral G gene, with VHSV G exhibiting suppression of basal transcription in EPC and BF-2 but not in trout cells; while IHNV G was stimulatory in RTG-2, but inhibitory in RTgill-W1. NV consistently stimulated constitutive transcription, with higher augmentation patterns seen in fibroblastic compared to epithelial cells, and for IHNV NV compared to VHSV NV. The innate antiviral immune response, focusing on the IFN pathway, was silenced by IHNV M in all cell lines tested. IHNV N showed a dose-dependent suppression of type I IFN, but with minor effects on MX-1. IHNV P and G played minor IFN-inhibitory roles, consistent and dose-dependent only for G in rainbow trout cells. IHNV NV mediated a consistent stimulatory effect on either Type I IFN or MX-1, but much less pronounced in RTgill-W1. CONCLUSIONS This study extends our understanding of Novirhabdoviruses-host interaction, showing differential innate immune responses in heterogenous cell types. Viral regulators of innate immune signaling are identified, either as dose-dependent suppressors (such as M and N) or stimulators (mainly NV), indicating novel targets for the design of more efficient vaccination strategies.
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Affiliation(s)
- Bartolomeo Gorgoglione
- Aquatic Animal Health Laboratory, Department of Pathobiology and Diagnostic Investigation, CVM & Department of Fisheries and Wildlife, CANR - Michigan State University, East Lansing, MI, 48824, USA.
- Department of Biological Sciences, Wright State University, 235 Diggs Laboratory / 134 Oelman Hall, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, USA.
- Department of Biological Sciences, University of Toledo, 2801 W. Bancroft St, Toledo, OH, 43606, USA.
| | - Jeffery L Ringiesn
- Department of Biological Sciences, Wright State University, 235 Diggs Laboratory / 134 Oelman Hall, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, USA
| | - Loc H Pham
- Department of Biological Sciences, University of Toledo, 2801 W. Bancroft St, Toledo, OH, 43606, USA
| | - Brian S Shepherd
- USDA/ARS/School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E. Greenfield Ave, Milwaukee, WI, 53204, USA
| | - Douglas W Leaman
- Department of Biological Sciences, Wright State University, 235 Diggs Laboratory / 134 Oelman Hall, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, USA.
- Department of Biological Sciences, University of Toledo, 2801 W. Bancroft St, Toledo, OH, 43606, USA.
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Cabon J, Almeras F, Baud M, Pallandre L, Morin T, Louboutin L. Susceptibility of pike Esox lucius to VHSV and IHNV and potential transmission to rainbow trout Oncorhynchus mykiss. DISEASES OF AQUATIC ORGANISMS 2020; 139:175-187. [PMID: 32495744 DOI: 10.3354/dao03474] [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] [Indexed: 06/11/2023]
Abstract
Determining the origin of recurrent outbreaks of fish diseases occurring on fish farms is essential for disease prevention and control measures. In this study, we investigated the potential reservoir role of wild fish species living near salmonid farms which were regularly found to be positive for viral hemorrhagic septicemia virus (VHSV). In addition to VHSV, infectious hematopoietic necrosis virus (IHNV) was also isolated from several pike Esox lucius samples collected from a pond near the salmonid farms of interest. All isolates of VHSV and IHNV analyzed had 100% identical partial glycoprotein gene sequences. VHSV pike strain OO128-25 belonged to the Ia genotype and shared 99.1 to 99.5% nucleotide identity with strains recently isolated from the farms. IHNV pike strain OO121-8, European genotype, appeared to be different from strains from France characterized since the first isolation in 1987. Isolates representative of both viral species were highly virulent in rainbow trout Oncorhynchus mykiss. OO128-25 induced 65% mortality in pike fingerlings, whereas only weak mortality was observed with OO121-8, despite characteristic symptoms in infected fish. High levels of specific antibodies to VHSV and IHNV were detected in adult pike in the absence of clinical signs. Infection of rainbow trout in contact with experimentally VHSV- or IHNV-infected pike fingerlings indicates possible horizontal transmission. These results suggest that pike could act as a reservoir for VHSV and IHNV in the wild, providing additional evidence to explain viral persistence and resurgence in certain areas.
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Affiliation(s)
- J Cabon
- French Agency for Food, Environmental and Occupational Health and Safety, Ploufragan-Plouzané-Niort Laboratory, Viral Fish Diseases Unit, National Reference Laboratory for Regulated Fish Diseases, 29280 Plouzané, France
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Getchell RG, First EJ, Bogdanowicz SM, Andrés JA, Schulman AT, Kramer J, Eckerlin GE, Farrell JM, Marquis H. Investigation of round goby viral haemorrhagic septicaemia outbreak in New York. JOURNAL OF FISH DISEASES 2019; 42:1023-1033. [PMID: 31025373 DOI: 10.1111/jfd.13003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
Eleven viral haemorrhagic septicaemia virus (VHSV) genotype IVb isolates were sequenced, and their genetic variation explored to determine the source of a VHS outbreak on the eastern shore of Cayuga Lake. An active fish kill of round gobies (Neogobius melanostomus, Pallas) was intensively sampled at King Ferry, NY and nearby Long Point State Park in May 2017. Gross lesions observed on 67 moribund round gobies and two rock bass (Ambloplites rupestris, Rafinesque) included moderately haemorrhagic internal organs and erythematous areas on the head, flank, and fins. RT-qPCR tests for VHSV were positive for all 69 fish. Viral isolation on epithelioma papulosum cyprinid cells showed cytopathic effect characteristic of VHSV for six round goby samples from King Ferry. The complete nucleotide sequence of the VHSV IVb genomes of five Cayuga Lake round goby isolates were derived on an Illumina platform along with 2017 VHSV IVb isolates from round gobies collected from the following: Lake Erie near Dunkirk, NY; the St. Lawrence River near Clayton and Cape Vincent, NY; and Lake St. Lawrence near Massena, NY. The phylogenetic tree created from these aligned sequences and four other complete VHSV IVb genomes shows Cayuga Lake isolates are closely related to the Lake Erie isolates.
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Affiliation(s)
- Rodman G Getchell
- Aquatic Animal Health Program, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Erika J First
- Aquatic Animal Health Program, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Steven M Bogdanowicz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Jose A Andrés
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Adam T Schulman
- Aquatic Animal Health Program, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Jordan Kramer
- Aquatic Animal Health Program, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Geofrey E Eckerlin
- Rome Field Station, New York State Department of Environmental Conservation, Rome, New York
| | - John M Farrell
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, New York
| | - Hélène Marquis
- Aquatic Animal Health Program, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York
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Gotesman M, Menanteau-Ledouble S, Saleh M, Bergmann SM, El-Matbouli M. A new age in AquaMedicine: unconventional approach in studying aquatic diseases. BMC Vet Res 2018; 14:178. [PMID: 29879957 PMCID: PMC5992843 DOI: 10.1186/s12917-018-1501-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/24/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Marine and aquaculture industries are important sectors of the food production and global trade. Unfortunately, the fish food industry is challenged with a plethora of infectious pathogens. The freshwater and marine fish communities are rapidly incorporating novel and most up to date techniques for detection, characterization and treatment strategies. Rapid detection of infectious diseases is important in preventing large disease outbreaks. MAIN TEXT One hundred forty-six articles including reviews papers were analyzed and their conclusions evaluated in the present paper. This allowed us to describe the most recent development research regarding the control of diseases in the aquatic environment as well as promising avenues that may result in beneficial developments. For the characterization of diseases, traditional sequencing and histological based methods have been augmented with transcriptional and proteomic studies. Recent studies have demonstrated that transcriptional based approaches using qPCR are often synergistic to expression based studies that rely on proteomic-based techniques to better understand pathogen-host interactions. Preventative therapies that rely on prophylactics such as vaccination with protein antigens or attenuated viruses are not always feasible and therefore, the development of therapies based on small nucleotide based medicine is on the horizon. Of those, RNAi or CRISPR/Cas- based therapies show great promise in combating various types of diseases caused by viral and parasitic agents that effect aquatic and fish medicine. CONCLUSIONS In our modern times, when the marine industry has become so vital for feed and economic stability, even the most extreme alternative treatment strategies such as the use of small molecules or even the use of disease to control invasive species populations should be considered.
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Affiliation(s)
- Michael Gotesman
- Department of Biology, New York City College of Technology of the City University of New York, Brooklyn, New York, USA
| | - Simon Menanteau-Ledouble
- Clinical Division of Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Mona Saleh
- Clinical Division of Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Sven M Bergmann
- Institute of Infectology, Friedrich-Loffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria.
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