1
|
Yu XD, Ke F, Zhang QY, Gui JF. Genome Characteristics of Two Ranavirus Isolates from Mandarin Fish and Largemouth Bass. Pathogens 2023; 12:pathogens12050730. [PMID: 37242400 DOI: 10.3390/pathogens12050730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/10/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Ranaviruses are promiscuous pathogens that threaten lower vertebrates globally. In the present study, two ranaviruses (SCRaV and MSRaV) were isolated from two fishes of the order Perciformes: mandarin fish (Siniperca chuatsi) and largemouth bass (Micropterus salmoides). The two ranaviruses both induced cytopathic effects in cultured cells from fish and amphibians and have the typical morphologic characteristics of ranaviruses. Complete genomes of the two ranaviruses were then sequenced and analyzed. Genomes of SCRaV and MSRaV have a length of 99, 405, and 99, 171 bp, respectively, and both contain 105 predicted open reading frames (ORFs). Eleven of the predicted proteins have differences between SCRaV and MSRaV, in which only one (79L) possessed a relatively large difference. A comparison of the sequenced six ranaviruses from the two fish species worldwide revealed that sequence identities of the six proteins (11R, 19R, 34L, 68L, 77L, and 103R) were related to the place where the virus was isolated. However, there were obvious differences in protein sequence identities between the two viruses and iridoviruses from other hosts, with more than half lower than 55%. Especially, 12 proteins of the two isolates had no homologs in viruses from other hosts. Phylogenetic analysis revealed that ranaviruses from the two fishes clustered in one clade. Further genome alignment showed five groups of genome arrangements of ranaviruses based on the locally collinear blocks, in which the ranaviruses, including SCRaV and MSRaV, constitute the fifth group. These results provide new information on the ranaviruses infecting fishes of Perciformes and also are useful for further research of functional genomics of the type of ranaviruses.
Collapse
Affiliation(s)
- Xue-Dong Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Ke
- The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Qi-Ya Zhang
- The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jian-Fang Gui
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| |
Collapse
|
2
|
Ke F, Zhang QY. ADRV 12L: A Ranaviral Putative Rad2 Family Protein Involved in DNA Recombination and Repair. Viruses 2022; 14:v14050908. [PMID: 35632650 PMCID: PMC9146916 DOI: 10.3390/v14050908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 02/01/2023] Open
Abstract
The Andrias davidianus ranavirus (ADRV) is a member of the family Iridoviridae and belongs to the nucleocytoplasmic large DNA viruses. Based on genomic analysis, an ADRV-encoding protein, ADRV 12L, and its homologs from other iridoviruses were predicted as Rad2 family proteins based on the conserved amino acids, domains, and secondary structures. Expression analysis showed that the transcription of ADRV 12L started at 4 h post infection, and its expression was not inhibited by a DNA-replication inhibitor. Meanwhile, immunofluorescence localization showed that ADRV 12L mainly localized in viral factories and colocalized with the viral nascent DNA, which hinted at a possible role in DNA replication. Furthermore, a mutant ADRV lacking 12L (ADRV-Δ12L) was constructed. In both luciferase assays based on homologous recombination (HR) and double-strand break repair (DSBR) that followed, ADRV-Δ12L induced less luciferase activity than the wild-type ADRV, indicating that HR and DSBR were impaired in ADRV-Δ12L infected cells. In addition, infection with ADRV-Δ12L resulted in smaller plaque sizes and lower viral titers than that with wild-type ADRV, indicating an important role for 12L in efficient virus infection. Therefore, the results suggest that Rad2 homologs encoded by iridovirus have important roles in HR- and DSBR-process of the viral DNA and, thus, affect virus replication and the production of progeny virions.
Collapse
Affiliation(s)
- Fei Ke
- Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China;
- College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-027-6878-0002
| | - Qi-Ya Zhang
- Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China;
- College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
3
|
Bienentreu JF, Schock DM, Greer AL, Lesbarrères D. Ranavirus Amplification in Low-Diversity Amphibian Communities. Front Vet Sci 2022; 9:755426. [PMID: 35224079 PMCID: PMC8863596 DOI: 10.3389/fvets.2022.755426] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
In an era where emerging infectious diseases are a serious threat to biodiversity, epidemiological patterns need to be identified, particularly the complex mechanisms driving the dynamics of multi-host pathogens in natural communities. Many amphibian species have faced unprecedented population declines associated with diseases. Yet, specific processes shaping host-pathogen relationships within and among communities for amphibian pathogens such as ranaviruses (RV) remain poorly understood. To address this gap, we conducted a comprehensive study of RV in low-diversity amphibian communities in north-western Canada to assess the effects of biotic factors (species identity, species richness, abundance) and abiotic factors (conductivity, pH) on the pathogen prevalence and viral loads. Across 2 years and 18 sites, with communities of up to three hosts (wood frog, Rana sylvatica; boreal chorus frog, Pseudacris maculata; Canadian toad, Anaxyrus hemiophrys), we observed that RV prevalence nearly doubled with each additional species in a community, suggesting an amplification effect in aquatic, as well as terrestrial life-history stages. Infection intensity among infected wood frogs and boreal chorus frogs also significantly increased with an increase in species richness. Interestingly, we did not observe any effects of host abundance or abiotic factors, highlighting the importance of including host identity and species richness when investigating multi-host pathogens. Ultimately, only such a comprehensive approach can improve our understanding of complex and often highly context-dependent host-pathogen interactions.
Collapse
Affiliation(s)
- Joe-Felix Bienentreu
- Department of Biology, Laurentian University, Sudbury, ON, Canada
- *Correspondence: Joe-Felix Bienentreu
| | - Danna M. Schock
- Sciences and Environmental Technology, Keyano College, Fort McMurray, AB, Canada
| | - Amy L. Greer
- Department of Population Medicine, University of Guelph, Guelph, ON, Canada
| | | |
Collapse
|
4
|
FATAL RANAVIRUS INFECTION IN A GROUP OF ZOO-HOUSED MELLER'S CHAMELEONS ( TRIOCEROS MELLERI). J Zoo Wildl Med 2021; 50:696-705. [PMID: 33517641 DOI: 10.1638/2018-0044] [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] [Accepted: 04/05/2019] [Indexed: 11/21/2022] Open
Abstract
A group of five juvenile Meller's chameleons (Trioceros melleri) experienced 100% mortality over a period of 1 mo due to ranavirus infection. The index case was found dead without premonitory signs. The three subsequent cases presented with nonspecific clinical signs (lethargy, decreased appetite, ocular discharge) and were ultimately euthanatized. The final case died after initially presenting with skin lesions. Postmortem examination revealed thin body condition in all five animals and mild coelomic effusion and petechiae affecting the tongue and kidneys of one animal. Microscopically, all animals had multifocal necrosis of the spleen, liver, and kidney; four of five animals had necrosis of the nasal cavity; and two of five had necrosis of adrenal tissue, bone marrow, and skin. Numerous basophilic intracytoplasmic inclusions were present in the liver of all animals and nasal mucosa of three of the five animals. Consensus polymerase chain reaction for herpesvirus and adenovirus were negative, whereas ranavirus quantitative polymerase chain reaction was positive. Virus isolation followed by whole genome sequencing and Bayesian phylogenetic analysis classified the isolates as a strain of frog virus 3 (FV3) most closely related to an FV3 isolate responsible for a previous outbreak in the zoo's eastern box turtle (Terrapene carolina carolina) group. This case series documents the first known occurrence of ranavirus-associated disease in chameleons and demonstrates the potential for interspecies transmission between chelonian and squamate reptiles.
Collapse
|
5
|
Genome Sequence of a Ranavirus Isolated from a Red-Eared Slider (Trachemys scripta elegans) in Poland. Microbiol Resour Announc 2020; 9:9/47/e00781-20. [PMID: 33214291 PMCID: PMC7679084 DOI: 10.1128/mra.00781-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The red-eared slider (RES) ranavirus (RESRV) was isolated from a free-ranging RES turtle that died with evidence of respiratory disease. The RESRV genome sequence (106,878 bp) was determined, and phylogenetic analysis revealed that it is a common midwife toad virus (CMTV) strain. This study is the first report of CMTV in RES.
Collapse
|
6
|
Deng L, Geng Y, Zhao R, Gray MJ, Wang K, Ouyang P, Chen D, Huang X, Chen Z, Huang C, Zhong Z, Guo H, Fang J. CMTV-like ranavirus infection associated with high mortality in captive catfish-like loach, Triplophysa siluorides, in China. Transbound Emerg Dis 2020; 67:1330-1335. [PMID: 31904194 DOI: 10.1111/tbed.13473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 11/11/2019] [Accepted: 01/02/2020] [Indexed: 11/27/2022]
Abstract
Ranaviruses are important emerging pathogens of ectothermic vertebrates that threaten aquaculture and wildlife worldwide. A mortality event occurred in a cultured population of catfish-like loach (Triplophysa siluorides) in Sichuan Province, China. Gross clinical signs of the affected fish included skin lesions and haemorrhagic ulcers, which are often associated with ranaviruses. Inoculation of liver, kidney and spleen tissue homogenates in epithelioma papulosum cyprini (EPC) cells at 25°C resulted in cytopathic effect within 24 hr. Transmission electron microscopy of infected EPC cells revealed hexagonal viral arrays in the cytoplasm and icosahedral geometry of the virions. Following exposure of T. siluroides to the isolated virus, similar clinical signs were observed and the fish experienced 40% and 90% mortality after 21 days at 103.58 and 107.8 TCID50 /0.1 ml doses, respectively, providing evidence the isolated virus was the main causative agent of the mortality event. Diagnostic PCR of the major capsid protein gene of ranavirus showed that all samples of diseased fish and isolated virus were positive. Phylogenetic analysis revealed that the isolated virus, designated as FYLl40220, was associated with the Common Midwife Toad Virus (CMTV)-like ranavirus clade. To our knowledge, this case represents the first report of CMTV-associated mortality in a fish species. Collectively, these results suggest that the host range of CMTV-like ranaviruses is greater than previously thought, and this clade of ranaviruses could have significant economic and biodiversity impacts.
Collapse
Affiliation(s)
- Lishuang Deng
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, China
| | - Yi Geng
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, China
| | - Ruoxuan Zhao
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, China
| | - Matthew J Gray
- Center for Wildlife Health, University of Tennessee Institute of Agriculture, Knoxville, TN, USA
| | - Kaiyu Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, China
| | - Ping Ouyang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, China
| | - Defang Chen
- Department of Aquaculture, Sichuan Agricultural University, Wenjiang, China
| | - Xiaoli Huang
- Department of Aquaculture, Sichuan Agricultural University, Wenjiang, China
| | - Zhengli Chen
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, China
| | - Chao Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, China
| | - Zhijun Zhong
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, China
| | - Hongrui Guo
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, China
| | - Jing Fang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, China
| |
Collapse
|
7
|
Bienentreu JF, Grayfer L, Schock DM, Guerreiro M, Mehes-Smith M, DeWitte-Orr SJ, Robert J, Brunetti CR, Lesbarrères D. Sublethal effects of wild-type and a vIF-2α-knockout Frog virus 3 on postmetamorphic wood frogs (Rana sylvatica): potential for a stage-specific reservoir. Facets (Ott) 2020. [DOI: 10.1139/facets-2020-0001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ranaviruses have been associated with rising numbers of mass die-offs in amphibian populations around the globe. However, most studies on ranaviruses to date focused on larval amphibians. To assess the role of postmetamorphic amphibians in the epidemiology of ranaviruses and to determine the role of viral immune-suppression genes, we performed a bath-exposure study on post-metamorphic wood frogs ( Rana sylvatica) using environmentally relevant concentrations of wild-type Frog virus 3 (WT FV3), and a gene-knockout mutant (KO FV3), deficient for the putative immune-suppression gene vIF-2α. We observed a 42% infection rate and 5% mortality across the virus challenges, with infection rates and viral loads following a dose-dependent pattern. Individuals exposed to the knockout variant exhibited significantly decreased growth and increased lethargy compared with wild-type treatments. Although 85% of exposed individuals exhibited common signs of ranavirosis throughout the experiment, most of these individuals did not exhibit signs of infection by 40 d post-exposure. Overall, we showed that even a single short time exposure to environmentally relevant concentrations of ranavirus may cause sublethal infections in postmetamorphic amphibians, highlighting the importance of this life stage in the epidemiology of ranaviruses. Our study also supports the importance of the vIF-2α gene in immune-suppression in infected individuals.
Collapse
Affiliation(s)
| | - Leon Grayfer
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA
| | - Danna M. Schock
- University Studies and Environmental Technology, Keyano College, Fort McMurray, AB T9H 2H7, Canada
| | - Matthew Guerreiro
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
| | | | | | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA
| | - Craig R. Brunetti
- Department of Biology, Trent University, Peterborough, ON K9J 7B8, Canada
| | - David Lesbarrères
- Department of Biology, Laurentian University, Sudbury, ON P3E 2C6, Canada
| |
Collapse
|
8
|
Vilaça ST, Bienentreu JF, Brunetti CR, Lesbarrères D, Murray DL, Kyle CJ. Frog Virus 3 Genomes Reveal Prevalent Recombination between Ranavirus Lineages and Their Origins in Canada. J Virol 2019; 93:e00765-19. [PMID: 31341053 PMCID: PMC6798099 DOI: 10.1128/jvi.00765-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/10/2019] [Indexed: 12/14/2022] Open
Abstract
Ranaviruses are pathogens associated with the decline of amphibian populations across much of their distribution. In North America, frog virus 3 (FV3) is a widely distributed pathogen with wild populations of amphibians harboring different lineages and putative recombinants between FV3 and common midwife toad virus (CMTV). These recombinants have higher pathogenicity, and CMTV-derived genes associated with virulence are reported in wild strains in Canada. However, while FV3 is linked to amphibian die-offs in North America, CMTVs have been reported only in commercial frog farms in North America. We sequenced complete genomes of 18 FV3 isolates from three amphibian species to characterize genetic diversity of the lineages in Canada and infer possible recombinant regions. The 18 FV3 isolates displayed different signals of recombination, varying from none to interspersed recombination with previously isolated CMTV-like viruses. In general, most recombination breakpoints were located within open reading frames (ORFs), generating new ORFs and proteins that were a mixture between FV3 and CMTV. A combined spatial and temporal phylogeny suggests the presence of the FV3 lineage in Canada is relatively contemporary (<100 years), corroborating the hypothesis that both CMTV- and FV3-like viruses spread to North America when the international commercial amphibian trade started. Our results highlight the importance of pathogen surveillance and viral dynamics using full genomes to more clearly understand the mechanisms of disease origin and spread.IMPORTANCE Amphibian populations are declining worldwide, and these declines have been linked to a number of anthropogenic factors, including disease. Among the pathogens associated with amphibian mortality, ranaviruses have caused massive die-offs across continents. In North America, frog virus 3 (FV3) is a widespread ranavirus that can infect wild and captive amphibians. In this study, we sequenced full FV3 genomes isolated from frogs in Canada. We report widespread recombination between FV3 and common midwife toad virus (CMTV). Phylogenies indicate a recent origin for FV3 in Canada, possibly as a result of international amphibian trade.
Collapse
Affiliation(s)
- Sibelle T Vilaça
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Joe-Felix Bienentreu
- Genetics and Ecology of Amphibian Research Group (GEARG), Department of Biology, Laurentian University, Sudbury, Ontario, Canada
| | - Craig R Brunetti
- Biology Department, Trent University, Peterborough, Ontario, Canada
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - David Lesbarrères
- Genetics and Ecology of Amphibian Research Group (GEARG), Department of Biology, Laurentian University, Sudbury, Ontario, Canada
| | - Dennis L Murray
- Biology Department, Trent University, Peterborough, Ontario, Canada
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Christopher J Kyle
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Forensic Science Department, Trent University, Peterborough, Ontario, Canada
- Natural Resources DNA Profiling and Forensics Centre, Trent University, Peterborough, Ontario, Canada
| |
Collapse
|
9
|
A highly invasive chimeric ranavirus can decimate tadpole populations rapidly through multiple transmission pathways. Ecol Modell 2019. [DOI: 10.1016/j.ecolmodel.2019.108777] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
10
|
Miaud C, Arnal V, Poulain M, Valentini A, Dejean T. eDNA Increases the Detectability of Ranavirus Infection in an Alpine Amphibian Population. Viruses 2019; 11:E526. [PMID: 31174349 PMCID: PMC6631829 DOI: 10.3390/v11060526] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/23/2019] [Accepted: 06/04/2019] [Indexed: 01/12/2023] Open
Abstract
The early detection and identification of pathogenic microorganisms is essential in order to deploy appropriate mitigation measures. Viruses in the Iridoviridae family, such as those in the Ranavirus genus, can infect amphibian species without resulting in mortality or clinical signs, and they can also infect other hosts than amphibian species. Diagnostic techniques allowing the detection of the pathogen outside the period of host die-off would thus be of particular use. In this study, we tested a method using environmental DNA (eDNA) on a population of common frogs (Rana temporaria) known to be affected by a Ranavirus in the southern Alps in France. In six sampling sessions between June and September (the species' activity period), we collected tissue samples from dead and live frogs (adults and tadpoles), as well as insects (aquatic and terrestrial), sediment, and water. At the beginning of the breeding season in June, one adult was found dead; at the end of July, a mass mortality of tadpoles was observed. The viral DNA was detected in both adults and tadpoles (dead or alive) and in water samples, but it was not detected in insects or sediment. In live frog specimens, the virus was detected from June to September and in water samples from August to September. Dead tadpoles that tested positive for Ranavirus were observed only on one date (at the end of July). Our results indicate that eDNA can be an effective alternative to tissue/specimen sampling and can detect Ranavirus presence outside die-offs. Another advantage is that the collection of water samples can be performed by most field technicians. This study confirms that the use of eDNA can increase the performance and accuracy of wildlife health status monitoring and thus contribute to more effective surveillance programs.
Collapse
Affiliation(s)
- Claude Miaud
- CEFE, EPHE-PSL, CNRS, Univ. Montpellier, Univ Paul Valéry Montpellier 3, IRD, Biogeography and Vertebrate Ecology, 1919 route de Mende, 34293 Montpellier, France.
| | - Véronique Arnal
- CEFE, EPHE-PSL, CNRS, Univ. Montpellier, Univ Paul Valéry Montpellier 3, IRD, Biogeography and Vertebrate Ecology, 1919 route de Mende, 34293 Montpellier, France.
| | - Marie Poulain
- CEFE, EPHE-PSL, CNRS, Univ. Montpellier, Univ Paul Valéry Montpellier 3, IRD, Biogeography and Vertebrate Ecology, 1919 route de Mende, 34293 Montpellier, France.
| | - Alice Valentini
- SPYGEN, 17 Rue du Lac Saint-André, 73370 Le Bourget-du-Lac, France.
| | - Tony Dejean
- SPYGEN, 17 Rue du Lac Saint-André, 73370 Le Bourget-du-Lac, France.
| |
Collapse
|
11
|
Grant SA, Bienentreu JF, Vilaça ST, Brunetti CR, Lesbarrères D, Murray DL, Kyle CJ. Low intraspecific variation of Frog virus 3 with evidence for novel FV3-like isolates in central and northwestern Canada. DISEASES OF AQUATIC ORGANISMS 2019; 134:1-13. [PMID: 32132268 DOI: 10.3354/dao03354] [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] [Indexed: 06/10/2023]
Abstract
Frog virus 3 (FV3) and FV3-like ranaviruses can infect a variety of cold-blooded aquatic species and present a primary threat to amphibians across the globe. Previous studies of FV3-like viruses have largely investigated higher-level phylogenetic distinctions of these pathogens via portions of the conserved major capsid protein (MCP), and the putative virulence gene vIF-2α. Few studies, however, have investigated the spatial distribution of FV3 variants at the population level3-data that can be used to further understand the spatial epidemiology of this disease. In this study, we sequenced the MCP and vIF-2α of 127 FV3-positive amphibians sampled from Canadian water bodies in Ontario, northeastern Alberta, and southern Northwest Territories to explore whether intraspecific genetic variation exists within FV3. There was a lack of variation at the 2 markers across these regions, suggesting that there is a lack of FV3 sequence diversity in Canada, which may hint at a single source of infection that has spread. However, an undocumented variant termed Wood Buffalo ranavirus (WBRV) was detected in samples from 3 sites in Alberta and Northwest Territories that clustered within the FV3-like lineage with 99.3% sequence homology for MCP. For vIF-2α, all sequences were the expected truncated variant except for 6 samples in Ontario. These latter sequences were suggestive of recombination with common midwife toad virus (CMTV). The lack of variation suggests that higher-resolution genome analyses will be required to further explore the spatial spread and intraspecific variation of the disease.
Collapse
Affiliation(s)
- Samantha A Grant
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario K9J 7B8, Canada
| | | | | | | | | | | | | |
Collapse
|
12
|
Stilwell NK, Whittington RJ, Hick PM, Becker JA, Ariel E, van Beurden S, Vendramin N, Olesen NJ, Waltzek TB. Partial validation of a TaqMan real-time quantitative PCR for the detection of ranaviruses. DISEASES OF AQUATIC ORGANISMS 2018; 128:105-116. [PMID: 29733025 DOI: 10.3354/dao03214] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ranaviruses are globally emerging pathogens negatively impacting wild and cultured fish, amphibians, and reptiles. Although conventional and diagnostic real-time PCR (qPCR) assays have been developed to detect ranaviruses, these assays often have not been tested against the known diversity of ranaviruses. Here we report the development and partial validation of a TaqMan real-time qPCR assay. The primers and TaqMan probe targeted a conserved region of the major capsid protein (MCP) gene. A series of experiments using a 10-fold dilution series of Frog virus 3 (FV3) MCP plasmid DNA revealed linearity over a range of 7 orders of magnitude (107-101), a mean correlation coefficient (R2) of >0.99, and a mean efficiency of 96%. The coefficient of variation of intra- and inter-assay variability ranged from <0.1-3.5% and from 1.1-2.3%, respectively. The analytical sensitivity was determined to be 10 plasmid copies of FV3 DNA. The qPCR assay detected a panel of 33 different ranaviral isolates originating from fish, amphibian, and reptile hosts from all continents excluding Africa and Antarctica, thereby representing the global diversity of ranaviruses. The assay did not amplify highly divergent ranaviruses, members of other iridovirus genera, or members of the alloherpesvirus genus Cyprinivirus. DNA from fish tissue homogenates previously determined to be positive or negative for the ranavirus Epizootic hematopoietic necrosis virus by virus isolation demonstrated a diagnostic sensitivity of 95% and a diagnostic specificity of 100%. The reported qPCR assay provides an improved expedient diagnostic tool and can be used to elucidate important aspects of ranaviral pathogenesis and epidemiology in clinically and sublinically affected fish, amphibians, and reptiles.
Collapse
Affiliation(s)
- Natalie K Stilwell
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Ranavirus genotypes in the Netherlands and their potential association with virulence in water frogs (Pelophylax spp.). Emerg Microbes Infect 2018; 7:56. [PMID: 29615625 PMCID: PMC5882854 DOI: 10.1038/s41426-018-0058-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/04/2017] [Accepted: 02/25/2018] [Indexed: 12/15/2022]
Abstract
Ranaviruses are pathogenic viruses for poikilothermic vertebrates worldwide. The identification of a common midwife toad virus (CMTV) associated with massive die-offs in water frogs (Pelophylax spp.) in the Netherlands has increased awareness for emerging viruses in amphibians in the country. Complete genome sequencing of 13 ranavirus isolates collected from ten different sites in the period 2011–2016 revealed three CMTV groups present in distinct geographical areas in the Netherlands. Phylogenetic analysis showed that emerging viruses from the northern part of the Netherlands belonged to CMTV-NL group I. Group II and III viruses were derived from the animals located in the center-east and south of the country, and shared a more recent common ancestor to CMTV-amphibian associated ranaviruses reported in China, Italy, Denmark, and Switzerland. Field monitoring revealed differences in water frog host abundance at sites where distinct ranavirus groups occur; with ranavirus-associated deaths, host counts decreasing progressively, and few juveniles found in the north where CMTV-NL group I occurs but not in the south with CMTV-NL group III. Investigation of tandem repeats of coding genes gave no conclusive information about phylo-geographical clustering, while genetic analysis of the genomes revealed truncations in 17 genes across CMTV-NL groups II and III compared to group I. Further studies are needed to elucidate the contribution of these genes as well as environmental variables to explain the observed differences in host abundance.
Collapse
|
14
|
Invertebrate Iridoviruses: A Glance over the Last Decade. Viruses 2018; 10:v10040161. [PMID: 29601483 PMCID: PMC5923455 DOI: 10.3390/v10040161] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 02/06/2023] Open
Abstract
Members of the family Iridoviridae (iridovirids) are large dsDNA viruses that infect both invertebrate and vertebrate ectotherms and whose symptoms range in severity from minor reductions in host fitness to systemic disease and large-scale mortality. Several characteristics have been useful for classifying iridoviruses; however, novel strains are continuously being discovered and, in many cases, reliable classification has been challenging. Further impeding classification, invertebrate iridoviruses (IIVs) can occasionally infect vertebrates; thus, host range is often not a useful criterion for classification. In this review, we discuss the current classification of iridovirids, focusing on genomic and structural features that distinguish vertebrate and invertebrate iridovirids and viral factors linked to host interactions in IIV6 (Invertebrate iridescent virus 6). In addition, we show for the first time how complete genome sequences of viral isolates can be leveraged to improve classification of new iridovirid isolates and resolve ambiguous relations. Improved classification of the iridoviruses may facilitate the identification of genus-specific virulence factors linked with diverse host phenotypes and host interactions.
Collapse
|
15
|
Chinchar V, Waltzek TB, Subramaniam K. Ranaviruses and other members of the family Iridoviridae: Their place in the virosphere. Virology 2017. [DOI: 10.1016/j.virol.2017.06.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
16
|
Price SJ, Wadia A, Wright ON, Leung WTM, Cunningham AA, Lawson B. Screening of a long-term sample set reveals two Ranavirus lineages in British herpetofauna. PLoS One 2017; 12:e0184768. [PMID: 28931029 PMCID: PMC5607163 DOI: 10.1371/journal.pone.0184768] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/30/2017] [Indexed: 11/18/2022] Open
Abstract
Reports of severe disease outbreaks in amphibian communities in mainland Europe due to strains of the common midwife toad virus (CMTV)-like clade of Ranavirus are increasing and have created concern due to their considerable population impacts. In Great Britain, viruses in another clade of Ranavirus-frog virus 3 (FV3)-like-have caused marked declines of common frog (Rana temporaria) populations following likely recent virus introductions. The British public has been reporting mortality incidents to a citizen science project since 1992, with carcasses submitted for post-mortem examination, resulting in a long-term tissue archive spanning 25 years. We screened this archive for ranavirus (458 individuals from 228 incidents) using molecular methods and undertook preliminary genotyping of the ranaviruses detected. In total, ranavirus was detected in 90 individuals from 41 incidents focused in the north and south of England. The majority of detections involved common frogs (90%) but also another anuran, a caudate and a reptile. Most incidents were associated with FV3-like viruses but two, separated by 300 km and 16 years, involved CMTV-like viruses. These British CMTV-like viruses were more closely related to ranaviruses from mainland Europe than to each other and were estimated to have diverged at least 458 years ago. This evidence of a CMTV-like virus in Great Britain in 1995 represents the earliest confirmed case of a CMTV associated with amphibians and raises important questions about the history of ranavirus in Great Britain and the epidemiology of CMTV-like viruses. Despite biases present in the opportunistic sample used, this study also demonstrates the role of citizen science projects in generating resources for research and the value of maintaining long-term wildlife tissue archives.
Collapse
Affiliation(s)
- Stephen J. Price
- UCL Genetics Institute, Gower Street, London, United Kingdom
- Institute of Zoology, ZSL, Regents Park, London, United Kingdom
- * E-mail:
| | - Alexandra Wadia
- Institute of Zoology, ZSL, Regents Park, London, United Kingdom
- University of York, York, United Kingdom
| | - Owen N. Wright
- Institute of Zoology, ZSL, Regents Park, London, United Kingdom
- School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | | | | | - Becki Lawson
- Institute of Zoology, ZSL, Regents Park, London, United Kingdom
| |
Collapse
|
17
|
Claytor SC, Subramaniam K, Landrau-Giovannetti N, Chinchar VG, Gray MJ, Miller DL, Mavian C, Salemi M, Wisely S, Waltzek TB. Ranavirus phylogenomics: Signatures of recombination and inversions among bullfrog ranaculture isolates. Virology 2017; 511:330-343. [PMID: 28803676 DOI: 10.1016/j.virol.2017.07.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 07/12/2017] [Accepted: 07/24/2017] [Indexed: 01/23/2023]
Abstract
Ranaviruses are emerging pathogens of fish, amphibians, and reptiles that threaten aquatic animal industries and wildlife worldwide. Our objective was to genetically characterize ranaviruses isolated during separate bullfrog Lithobates catesbeianus die-offs that occurred eight years apart on the same North American farm. The earlier outbreak was due to a highly pathogenic strain of common midwife toad virus (CMTV) previously known only from Europe and China. The later outbreak was due to a chimeric ranavirus that displayed a novel genome arrangement and a DNA backbone typical for Frog virus 3 (FV3) strains except for interspersed fragments acquired through recombination with the CMTV isolated earlier. Both bullfrog ranaviruses are more pathogenic than wild-type FV3 suggesting recombination may have resulted in the increased pathogenicity observed in the ranavirus isolated in the later outbreak. Our study underscores the role international trade in farmed bullfrogs may have played in the global dissemination of highly pathogenic ranaviruses.
Collapse
Affiliation(s)
- Sieara C Claytor
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
| | - Kuttichantran Subramaniam
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, USA
| | | | | | - Matthew J Gray
- Center for Wildlife Health, University of Tennessee, Knoxville, TN, USA
| | - Debra L Miller
- Center for Wildlife Health, University of Tennessee, Knoxville, TN, USA
| | - Carla Mavian
- Department of Pathology, Immunology, and Laboratory Medicine, and Emerging Pathogens Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, and Emerging Pathogens Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Samantha Wisely
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
| | - Thomas B Waltzek
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, USA.
| |
Collapse
|
18
|
DETECTION AND REPORTING OF RANAVIRUS IN AMPHIBIANS: EVALUATION OF THE ROLES OF THE WORLD ORGANISATION FOR ANIMAL HEALTH AND THE PUBLISHED LITERATURE. J Wildl Dis 2017; 53:509-520. [PMID: 28402726 DOI: 10.7589/2016-08-176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pathogens of wildlife can have direct impacts on human and livestock health as well as on biodiversity, as causative factors in population declines and extinctions. The World Organization for Animal Health (OIE) seeks to facilitate rapid sharing of information about animal diseases to enable up-to-date risk assessments of translocations of animals and animal products. The OIE also produces manuals of recommended methods to standardize diagnostic testing. Ranaviruses are important amphibian pathogens that may have spread through international trade, and infections became notifiable to OIE in 2009. We surveyed and reviewed published literature for data on sampling, diagnostic testing, and reporting of ranavirus during 2009-14. We also investigated attitudes and awareness of the OIE and its recommendations for best practice. We found that sampling effort is uneven and concentrated in the northern hemisphere. We also identified citizen science projects that have the potential to improve the quantity and quality of data on the incidence of ranavirus infection and the circumstances surrounding disease outbreaks. We found reporting of infection to be inconsistent: reporting was split between the published literature (where it was subject to a 2-yr lag) and the OIE with little overlap, results of negative diagnostic tests were underreported, and scientific researchers lacked awareness of the role of the OIE. Approaches to diagnostic screening were poorly harmonized and heavily reliant on molecular methods. These flaws in the mechanisms of ranavirus detection and reporting hamper the construction of a comprehensive disease information database.
Collapse
|
19
|
Genome Sequence of a Ranavirus Isolated from Pike-Perch Sander lucioperca. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01295-16. [PMID: 27856591 PMCID: PMC5114383 DOI: 10.1128/genomea.01295-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The pike-perch iridovirus (PPIV) was isolated in Finland from apparently healthy pike-perch fingerlings during routine disease surveillance. Our phylogenomic analysis revealed that PPIV is the first fish member of a clade of ranaviruses previously described from European and Chinese amphibians.
Collapse
|
20
|
Price SJ. Comparative Genomics of Amphibian-like Ranaviruses, Nucleocytoplasmic Large DNA Viruses of Poikilotherms. Evol Bioinform Online 2016; 11:71-82. [PMID: 27812275 PMCID: PMC5081246 DOI: 10.4137/ebo.s33490] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/12/2016] [Accepted: 09/15/2016] [Indexed: 12/15/2022] Open
Abstract
Recent research on genome evolution of large DNA viruses has highlighted a number of incredibly dynamic processes that can facilitate rapid adaptation. The genomes of amphibian-like ranaviruses – double-stranded DNA viruses infecting amphibians, reptiles, and fish (family Iridoviridae) – were examined to assess variation in genome content and evolutionary processes. The viruses studied were closely related, but their genome content varied considerably, with 29 genes identified that were not present in all of the major clades. Twenty-one genes had evidence of recombination, while a virus isolated from a captive reptile appeared to be a mosaic of two divergent parents. Positive selection was also found to be acting on more than a quarter of Ranavirus genes and was found most frequently in the Spanish common midwife toad virus, which has had a severe impact on amphibian host communities. Efforts to resolve the root of this group by inclusion of an outgroup were inconclusive, but a set of core genes were identified, which recovered a well-supported species tree.
Collapse
Affiliation(s)
- Stephen J Price
- Genetics, Evolution and Environment department, UCL Genetics Institute, London, UK.; Institute of Zoology, Zoological Society of London (ZSL), London, UK
| |
Collapse
|
21
|
Dizman YA, Muratoglu H, Sandalli C, Nalcacioglu R, Demirbag Z. Chilo iridescent virus (CIV) ORF 012L encodes a protein with both exonuclease and endonuclease functions. Arch Virol 2016; 161:3029-37. [PMID: 27496102 DOI: 10.1007/s00705-016-3007-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/01/2016] [Indexed: 10/21/2022]
Abstract
Chilo iridescent virus (CIV) is the type member of the genus Iridovirus within the family Iridoviridae. The virions of CIV contain a single linear dsDNA molecule that is circularly permuted and terminally redundant. The genome of CIV contains an open reading frame (ORF 012L) encoding a protein homologous to exonuclease II of Schizosaccharomyces pombe. In this study, we focused on the characterization of CIV ORF 012L. The target ORF was cloned into the pET28a vector, expressed in E. coli strain BL21 (DE3) pLysS with an N-terminal His tag and purified to homogeneity by using Ni-NTA affinity chromatography. Biochemical characterization of the purified CIV 012L confirmed that this viral protein is a functional 5'-3' exonuclease that digests 3'-biotin-labelled oligonucleotides and linear double-stranded DNA (dsDNA) molecules from their 5' termini in a highly processive manner. CIV 012L also has a potent endonuclease activity on dsDNA in vitro. In addition, CIV 012L converted supercoiled plasmid DNA (replicative form I, RFI) into the open circular form (RFII) and then open circular form into linear form (RFIII). Endonuclease activity of CIV 012L was optimal in the presence of 10 mM Mg(2+) or 30 mM Mn(2+) ions and at 150 mM NaCl or KCl salt concentrations. The highest endonuclease activity was obtained at pH 8, and it reached a maximum at 55 °C. The CIV 012L protein showed deficiencies for both double- and single-stranded RNAs.
Collapse
Affiliation(s)
- Yesim Akturk Dizman
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey.,Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, 53100, Rize, Turkey
| | - Hacer Muratoglu
- Department of Molecular Biology and Genetic, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Cemal Sandalli
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, 53100, Rize, Turkey
| | - Remziye Nalcacioglu
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey.
| | - Zihni Demirbag
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey
| |
Collapse
|
22
|
Rijks JM, Saucedo B, Spitzen-van der Sluijs A, Wilkie GS, van Asten AJAM, van den Broek J, Boonyarittichaikij R, Stege M, van der Sterren F, Martel A, Pasmans F, Hughes J, Gröne A, van Beurden SJ, Kik MJL. Investigation of Amphibian Mortality Events in Wildlife Reveals an On-Going Ranavirus Epidemic in the North of the Netherlands. PLoS One 2016; 11:e0157473. [PMID: 27315226 PMCID: PMC4912076 DOI: 10.1371/journal.pone.0157473] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 05/30/2016] [Indexed: 12/15/2022] Open
Abstract
In the four years following the first detection of ranavirus (genus Ranavirus, family Iridoviridae) infection in Dutch wildlife in 2010, amphibian mortality events were investigated nationwide to detect, characterize and map ranaviruses in amphibians over time, and to establish the affected host species and the clinico-pathological presentation of the disease in these hosts. The ultimate goal was to obtain more insight into ranavirus disease emergence and ecological risk. In total 155 dead amphibians from 52 sites were submitted between 2011 and 2014, and examined using histopathology, immunohistochemistry, virus isolation and molecular genetic characterization. Ranavirus-associated amphibian mortality events occurred at 18 sites (35%), initially only in proximity of the 2010 index site. Specimens belonging to approximately half of the native amphibian species were infected, including the threatened Pelobates fuscus (spadefoot toad). Clustered massive outbreaks involving dead adult specimens and ranavirus genomic identity indicated that one common midwife toad virus (CMTV)-like ranavirus strain is emerging in provinces in the north of the Netherlands. Modelling based on the spatiotemporal pattern of spread showed a high probability that this emerging virus will continue to be detected at new sites (the discrete reproductive power of this outbreak is 0.35). Phylogenetically distinct CMTV-like ranaviruses were found in the south of the Netherlands more recently. In addition to showing that CMTV-like ranaviruses threaten wild amphibian populations not only in Spain but also in the Netherlands, the current spread and risk of establishment reiterate that understanding the underlying causes of CMTV-like ranavirus emergence requires international attention.
Collapse
Affiliation(s)
- Jolianne M. Rijks
- Dutch Wildlife Health Centre, Utrecht University, Utrecht, The Netherlands
- * E-mail:
| | - Bernardo Saucedo
- Dutch Wildlife Health Centre, Utrecht University, Utrecht, The Netherlands
- Department of Pathobiology, Utrecht University, Utrecht, The Netherlands
| | | | - Gavin S. Wilkie
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Alphons J. A. M. van Asten
- Dutch Wildlife Health Centre, Utrecht University, Utrecht, The Netherlands
- Department of Pathobiology, Utrecht University, Utrecht, The Netherlands
| | - Jan van den Broek
- Department of Farm Animal Health, Utrecht University, Utrecht, The Netherlands
| | | | - Marisca Stege
- Department of Pathobiology, Utrecht University, Utrecht, The Netherlands
| | | | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Andrea Gröne
- Dutch Wildlife Health Centre, Utrecht University, Utrecht, The Netherlands
- Department of Pathobiology, Utrecht University, Utrecht, The Netherlands
| | | | - Marja J. L. Kik
- Dutch Wildlife Health Centre, Utrecht University, Utrecht, The Netherlands
- Department of Pathobiology, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
23
|
Abstract
Pathogenic fungi and viruses cause mortality outbreaks in wild amphibians worldwide. In the summer of 2012, dead tadpoles and adults of the European common frog Rana temporaria were reported in alpine lakes in the southwestern Alps (Mercantour National Park, France). A preliminary investigation using molecular diagnostic techniques identified a Ranavirus as the potential pathogenic agent. Three mortality events were recorded in the park, and samples were collected. The amphibian chytrid fungus Batrachochytrium dendrobatidis was not detected in any of the dead adult and juvenile frogs sampled (n=16) whereas all specimens were positive for a Ranavirus. The genome sequence of this Ranavirus was identical to previously published sequences of the common midwife toad virus (CMTV), a Ranavirus that has been associated with amphibian mortalities throughout Europe. We cultured virus from the organs of the dead common frogs and infecting adult male common frogs collected in another alpine region where no frog mortality had been observed. The experimentally infected frogs suffered 100% mortality (n=10). The alpine die-off is the first CMTV outbreak associated with mass mortality in wild amphibians in France. We describe the lesions observed and summarize amphibian populations affected by Ranaviruses in Europe. In addition, we discuss the ecologic specificities of mountain amphibians that may contribute to increasing their risk of exposure to and transmission of Ranaviruses.
Collapse
|
24
|
Warne RW, LaBumbard B, LaGrange S, Vredenburg VT, Catenazzi A. Co-Infection by Chytrid Fungus and Ranaviruses in Wild and Harvested Frogs in the Tropical Andes. PLoS One 2016; 11:e0145864. [PMID: 26726999 PMCID: PMC4701007 DOI: 10.1371/journal.pone.0145864] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
While global amphibian declines are associated with the spread of Batrachochytrium dendrobatidis (Bd), undetected concurrent co-infection by other pathogens may be little recognized threats to amphibians. Emerging viruses in the genus Ranavirus (Rv) also cause die-offs of amphibians and other ectotherms, but the extent of their distribution globally, or how co-infections with Bd impact amphibians are poorly understood. We provide the first report of Bd and Rv co-infection in South America, and the first report of Rv infections in the amphibian biodiversity hotspot of the Peruvian Andes, where Bd is associated with extinctions. Using these data, we tested the hypothesis that Bd or Rv parasites facilitate co-infection, as assessed by parasite abundance or infection intensity within individual adult frogs. Co-infection occurred in 30% of stream-dwelling frogs; 65% were infected by Bd and 40% by Rv. Among terrestrial, direct-developing Pristimantis frogs 40% were infected by Bd, 35% by Rv, and 20% co-infected. In Telmatobius frogs harvested for the live-trade 49% were co-infected, 92% were infected by Bd, and 53% by Rv. Median Bd and Rv loads were similar in both wild (Bd = 101.2 Ze, Rv = 102.3 viral copies) and harvested frogs (Bd = 103.1 Ze, Rv = 102.7 viral copies). While neither parasite abundance nor infection intensity were associated with co-infection patterns in adults, these data did not include the most susceptible larval and metamorphic life stages. These findings suggest Rv distribution is global and that co-infection among these parasites may be common. These results raise conservation concerns, but greater testing is necessary to determine if parasite interactions increase amphibian vulnerability to secondary infections across differing life stages, and constitute a previously undetected threat to declining populations. Greater surveillance of parasite interactions may increase our capacity to contain and mitigate the impacts of these and other wildlife diseases.
Collapse
Affiliation(s)
- Robin W. Warne
- Southern Illinois University, Department of Zoology, 1125 Lincoln Dr., MC6501, Carbondale, IL, 62901, United States of America
- * E-mail:
| | - Brandon LaBumbard
- Southern Illinois University, Department of Zoology, 1125 Lincoln Dr., MC6501, Carbondale, IL, 62901, United States of America
| | - Seth LaGrange
- Southern Illinois University, Department of Zoology, 1125 Lincoln Dr., MC6501, Carbondale, IL, 62901, United States of America
| | - Vance T. Vredenburg
- Department of Biology, San Francisco State University, San Francisco, CA, 94132, United States of America
| | - Alessandro Catenazzi
- Southern Illinois University, Department of Zoology, 1125 Lincoln Dr., MC6501, Carbondale, IL, 62901, United States of America
| |
Collapse
|
25
|
Epstein B, Storfer A. Comparative Genomics of an Emerging Amphibian Virus. G3 (BETHESDA, MD.) 2015; 6:15-27. [PMID: 26530419 PMCID: PMC4704714 DOI: 10.1534/g3.115.023762] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/22/2015] [Indexed: 11/18/2022]
Abstract
Ranaviruses, a genus of the Iridoviridae, are large double-stranded DNA viruses that infect cold-blooded vertebrates worldwide. Ranaviruses have caused severe epizootics in commercial frog and fish populations, and are currently classified as notifiable pathogens in international trade. Previous work shows that a ranavirus that infects tiger salamanders throughout Western North America (Ambystoma tigrinum virus, or ATV) is in high prevalence among salamanders in the fishing bait trade. Bait ATV strains have elevated virulence and are transported long distances by humans, providing widespread opportunities for pathogen pollution. We sequenced the genomes of 15 strains of ATV collected from tiger salamanders across western North America and performed phylogenetic and population genomic analyses and tests for recombination. We find that ATV forms a monophyletic clade within the rest of the Ranaviruses and that it likely emerged within the last several thousand years, before human activities influenced its spread. We also identify several genes under strong positive selection, some of which appear to be involved in viral virulence and/or host immune evasion. In addition, we provide support for the pathogen pollution hypothesis with evidence of recombination among ATV strains, and potential bait-endemic strain recombination.
Collapse
Affiliation(s)
- Brendan Epstein
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| |
Collapse
|
26
|
Chen Q, Ma J, Fan Y, Meng Y, Xu J, Zhou Y, Liu W, Zeng X, Zeng L. Identification of type I IFN in Chinese giant salamander (Andrias davidianus) and the response to an iridovirus infection. Mol Immunol 2015; 65:350-9. [PMID: 25733388 DOI: 10.1016/j.molimm.2015.02.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 10/23/2022]
Abstract
The type I IFNs play a major role in the first line of defense against virus infections. In this study, the type I IFN gene designated gsIFN was identified and characterized in the Chinese giant salamander (Andrias davidianus). The genomic DNA of gsIFN contains 5 exons and 4 introns and has a total length of 5622 bp. The full-length cDNA sequence of gsIFN is 1113 bp and encodes a putative protein of 186 amino acids that has a 43% identity to type I IFN of Xenopus tropicalis. The deduced amino acid sequence has the C-terminal CAWE motif, that is mostly conserved in the higher vertebrate type I IFNs. Real-time fluorescence quantitative RT-PCR analysis revealed broad expression of gsIFN in vivo and the highest level expression in blood, kidney and spleen. Additionally, the expression of gsIFN at the mRNA level was significantly induced in peripheral blood leucocytes after stimulation with poly I:C and after infection with the Chinese giant salamander iridovirus (GSIV). A plasmid expressing gsIFN was constructed and transfected into the Chinese giant salamander muscle cell line. Expression of the IFN-inducible gene Mx was up-regulated in the gsIFN-overexpressing cells after GSIV infection. The virus load and titer were significantly reduced compared with that in control cells. Additionally, a lower level of virus major capsid protein synthesis was confirmed by immunofluorescence assay compared to the control cells. These results suggest that the gsIFN gene plays an important role in the antiviral innate immune response.
Collapse
Affiliation(s)
- Qian Chen
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, P.R China; Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, P.R. China
| | - Jie Ma
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, P.R. China
| | - Yuding Fan
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, P.R. China
| | - Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, P.R. China
| | - Jin Xu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, P.R. China
| | - Yong Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, P.R. China
| | - Wenzhi Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, P.R. China
| | - Xianhui Zeng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, P.R. China
| | - Lingbing Zeng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, P.R. China.
| |
Collapse
|
27
|
Stöhr AC, López-Bueno A, Blahak S, Caeiro MF, Rosa GM, Alves de Matos AP, Martel A, Alejo A, Marschang RE. Phylogeny and differentiation of reptilian and amphibian ranaviruses detected in Europe. PLoS One 2015; 10:e0118633. [PMID: 25706285 PMCID: PMC4338083 DOI: 10.1371/journal.pone.0118633] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/21/2015] [Indexed: 11/23/2022] Open
Abstract
Ranaviruses in amphibians and fish are considered emerging pathogens and several isolates have been extensively characterized in different studies. Ranaviruses have also been detected in reptiles with increasing frequency, but the role of reptilian hosts is still unclear and only limited sequence data has been provided. In this study, we characterized a number of ranaviruses detected in wild and captive animals in Europe based on sequence data from six genomic regions (major capsid protein (MCP), DNA polymerase (DNApol), ribonucleoside diphosphate reductase alpha and beta subunit-like proteins (RNR-α and -β), viral homolog of the alpha subunit of eukaryotic initiation factor 2, eIF-2α (vIF-2α) genes and microsatellite region). A total of ten different isolates from reptiles (tortoises, lizards, and a snake) and four ranaviruses from amphibians (anurans, urodeles) were included in the study. Furthermore, the complete genome sequences of three reptilian isolates were determined and a new PCR for rapid classification of the different variants of the genomic arrangement was developed. All ranaviruses showed slight variations on the partial nucleotide sequences from the different genomic regions (92.6–100%). Some very similar isolates could be distinguished by the size of the band from the microsatellite region. Three of the lizard isolates had a truncated vIF-2α gene; the other ranaviruses had full-length genes. In the phylogenetic analyses of concatenated sequences from different genes (3223 nt/10287 aa), the reptilian ranaviruses were often more closely related to amphibian ranaviruses than to each other, and most clustered together with previously detected ranaviruses from the same geographic region of origin. Comparative analyses show that among the closely related amphibian-like ranaviruses (ALRVs) described to date, three recently split and independently evolving distinct genetic groups can be distinguished. These findings underline the wide host range of ranaviruses and the emergence of pathogen pollution via animal trade of ectothermic vertebrates.
Collapse
Affiliation(s)
- Anke C. Stöhr
- Fachgebiet für Umwelt- und Tierhygiene, Universität Hohenheim, Stuttgart, Germany
| | - Alberto López-Bueno
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Madrid, Spain
| | - Silvia Blahak
- Chemisches und Veterinäruntersuchungsamt Ostwestfalen Lippe (CVUA-OWL), Detmold, Germany
| | - Maria F. Caeiro
- Centro de Estudos do Ambiente e do Mar (CESAM) Lisboa, Lisbon, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Gonçalo M. Rosa
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, United Kingdom
- Institute of Zoology, Zoological Society of London, Regent’s Park, London, United Kingdom
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - António Pedro Alves de Matos
- Centro de Estudos do Ambiente e do Mar (CESAM) Lisboa, Lisbon, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Monte de Caparica, Portugal
| | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Alí Alejo
- Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Valdeolmos, Spain
| | - Rachel E. Marschang
- Fachgebiet für Umwelt- und Tierhygiene, Universität Hohenheim, Stuttgart, Germany
- Laboklin GmbH & Co. KG, Laboratory for Clinical Diagnostics, Bad Kissingen, Germany
- * E-mail:
| |
Collapse
|
28
|
Virus genomes and virus-host interactions in aquaculture animals. SCIENCE CHINA-LIFE SCIENCES 2015; 58:156-69. [DOI: 10.1007/s11427-015-4802-y] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 10/29/2014] [Indexed: 12/20/2022]
|
29
|
Complete genome sequence of a common midwife toad virus-like ranavirus associated with mass mortalities in wild amphibians in the Netherlands. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01293-14. [PMID: 25540340 PMCID: PMC4276818 DOI: 10.1128/genomea.01293-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A ranavirus associated with mass mortalities in wild water frogs (Pelophylax spp.) and other amphibians in the Netherlands since 2010 was isolated, and its complete genome sequence was determined. The virus has a genome of 107,772 bp and shows 96.5% sequence identity with the common midwife toad virus from Spain.
Collapse
|
30
|
Collapse of amphibian communities due to an introduced Ranavirus. Curr Biol 2014; 24:2586-91. [PMID: 25438946 DOI: 10.1016/j.cub.2014.09.028] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/13/2014] [Accepted: 09/09/2014] [Indexed: 11/22/2022]
Abstract
The emergence of infectious diseases with a broad host range can have a dramatic impact on entire communities and has become one of the main threats to biodiversity. Here, we report the simultaneous exploitation of entire communities of potential hosts with associated severe declines following invasion by a novel viral pathogen. We found two phylogenetically related, highly virulent viruses (genus Ranavirus, family Iridoviridae) causing mass mortality in multiple, diverse amphibian hosts in northern Spain, as well as a third, relatively avirulent virus. We document host declines in multiple species at multiple sites in the region. Our work reveals a group of pathogens that seem to have preexisting capacity to infect and evade immunity in multiple diverse and novel hosts, and that are exerting massive impacts on host communities. This report provides an exceptional record of host population trends being tracked in real time following emergence of a wildlife disease and a striking example of a novel, generalist pathogen repeatedly crossing the species barrier with catastrophic consequences at the level of host communities.
Collapse
|
31
|
Waltzek TB, Miller DL, Gray MJ, Drecktrah B, Briggler JT, MacConnell B, Hudson C, Hopper L, Friary J, Yun SC, Malm KV, Weber ES, Hedrick RP. New disease records for hatchery-reared sturgeon. I. Expansion of frog virus 3 host range into Scaphirhynchus albus. DISEASES OF AQUATIC ORGANISMS 2014; 111:219-227. [PMID: 25320034 DOI: 10.3354/dao02761] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In 2009, juvenile pallid sturgeon Scaphirhynchus albus, reared at the Blind Pony State Fish Hatchery (Missouri, USA) to replenish dwindling wild stocks, experienced mass mortality. Histological examination revealed extensive necrosis of the haematopoietic tissues, and a virus was isolated from affected organs in cell culture and then observed by electron microscopy. Experimental infection studies revealed that the virus is highly pathogenic to juvenile pallid sturgeon, one of several species of sturgeon currently listed as Endangered. The DNA sequence of the full length major capsid protein gene of the virus was identical to that of the species Frog virus 3 (FV3), the type species for the genus Ranavirus, originally isolated from northern leopard frog Lithobates pipiens. Although FV3 infections and epizootics in amphibians and reptiles are well documented, there is only 1 prior report of a natural infection of FV3 in fish. Our results illustrate the broad potential host range for FV3, with the known potential to cause significant mortality in poikilothermic vertebrates across 3 taxonomic classes including bony fishes, anuran and caudate amphibians, and squamate and testudine reptiles.
Collapse
Affiliation(s)
- Thomas B Waltzek
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Cheng K, Jones MEB, Jancovich JK, Burchell J, Schrenzel MD, Reavill DR, Imai DM, Urban A, Kirkendall M, Woods LW, Chinchar VG, Pessier AP. Isolation of a Bohle-like iridovirus from boreal toads housed within a cosmopolitan aquarium collection. DISEASES OF AQUATIC ORGANISMS 2014; 111:139-152. [PMID: 25266901 DOI: 10.3354/dao02770] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A captive 'survival assurance' population of 56 endangered boreal toads Anaxyrus boreas boreas, housed within a cosmopolitan collection of amphibians originating from Southeast Asia and other locations, experienced high mortality (91%) in April to July 2010. Histological examination demonstrated lesions consistent with ranaviral disease, including multicentric necrosis of skin, kidney, liver, spleen, and hematopoietic tissue, vasculitis, and myriad basophilic intracytoplasmic inclusion bodies. Initial confirmation of ranavirus infection was made by Taqman real-time PCR analysis of a portion of the major capsid protein (MCP) gene and detection of iridovirus-like particles by transmission electron microscopy. Preliminary DNA sequence analysis of the MCP, DNA polymerase, and neurofilament protein (NFP) genes demonstrated highest identity with Bohle iridovirus (BIV). A virus, tentatively designated zoo ranavirus (ZRV), was subsequently isolated, and viral protein profiles, restriction fragment length polymorphism analysis, and next generation DNA sequencing were performed. Comparison of a concatenated set of 4 ZRV genes, for which BIV sequence data are available, with sequence data from representative ranaviruses confirmed that ZRV was most similar to BIV. This is the first report of a BIV-like agent outside of Australia. However, it is not clear whether ZRV is a novel North American variant of BIV or whether it was acquired by exposure to amphibians co-inhabiting the same facility and originating from different geographic locations. Lastly, several surviving toads remained PCR-positive 10 wk after the conclusion of the outbreak. This finding has implications for the management of amphibians destined for use in reintroduction programs, as their release may inadvertently lead to viral dissemination.
Collapse
Affiliation(s)
- Kwang Cheng
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Virion-associated viral proteins of a Chinese giant salamander (Andrias davidianus) iridovirus (genus Ranavirus) and functional study of the major capsid protein (MCP). Vet Microbiol 2014; 172:129-39. [DOI: 10.1016/j.vetmic.2014.05.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 05/01/2014] [Accepted: 05/04/2014] [Indexed: 01/04/2023]
|
34
|
Mavian C, López-Bueno A, Bryant NA, Seeger K, Quail MA, Harris D, Barrell B, Alcami A. The genome sequence of ectromelia virus Naval and Cornell isolates from outbreaks in North America. Virology 2014; 462-463:218-26. [PMID: 24999046 PMCID: PMC4139192 DOI: 10.1016/j.virol.2014.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 04/11/2014] [Accepted: 06/10/2014] [Indexed: 01/01/2023]
Abstract
Ectromelia virus (ECTV) is the causative agent of mousepox, a disease of laboratory mouse colonies and an excellent model for human smallpox. We report the genome sequence of two isolates from outbreaks in laboratory mouse colonies in the USA in 1995 and 1999: ECTV-Naval and ECTV-Cornell, respectively. The genome of ECTV-Naval and ECTV-Cornell was sequenced by the 454-Roche technology. The ECTV-Naval genome was also sequenced by the Sanger and Illumina technologies in order to evaluate these technologies for poxvirus genome sequencing. Genomic comparisons revealed that ECTV-Naval and ECTV-Cornell correspond to the same virus isolated from independent outbreaks. Both ECTV-Naval and ECTV-Cornell are extremely virulent in susceptible BALB/c mice, similar to ECTV-Moscow. This is consistent with the ECTV-Naval genome sharing 98.2% DNA sequence identity with that of ECTV-Moscow, and indicates that the genetic differences with ECTV-Moscow do not affect the virulence of ECTV-Naval in the mousepox model of footpad infection. We describe the genome sequence of two highly virulent ectromelia virus isolates. The outbreak of ectromelia virus in USA was caused by Chinese viral isolates. We describe a clade of ectromelia virus isolates from China. We compare three different sequencing technologies to sequence large DNA viruses.
Collapse
Affiliation(s)
- Carla Mavian
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Nicolas Cabrera 1, Campus de Cantoblanco, Madrid, Spain
| | - Alberto López-Bueno
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Nicolas Cabrera 1, Campus de Cantoblanco, Madrid, Spain
| | - Neil A Bryant
- Department of Medicine, University of Cambridge, United Kingdom
| | - Kathy Seeger
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, United Kingdom
| | - Michael A Quail
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, United Kingdom
| | - David Harris
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, United Kingdom
| | - Bart Barrell
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, United Kingdom
| | - Antonio Alcami
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Nicolas Cabrera 1, Campus de Cantoblanco, Madrid, Spain; Department of Medicine, University of Cambridge, United Kingdom.
| |
Collapse
|
35
|
Ozgen A, Muratoglu H, Demirbag Z, Vlak JM, van Oers MM, Nalcacioglu R. Construction and characterization of a recombinant invertebrate iridovirus. Virus Res 2014; 189:286-92. [PMID: 24930447 DOI: 10.1016/j.virusres.2014.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 05/09/2014] [Accepted: 05/13/2014] [Indexed: 01/04/2023]
Abstract
Chilo iridescent virus (CIV), officially named Insect iridescent virus 6 (IIV6), is the type species of the genus Iridovirus (family Iridoviridae). In this paper we constructed a recombinant CIV, encoding the green fluorescent protein (GFP). This recombinant can be used to investigate viral replication dynamics. We showed that homologous recombination is a valid method to make CIV gene knockouts and to insert foreign genes. The CIV 157L gene, putatively encoding a non-functional inhibitor of apoptosis (IAP), was chosen as target for foreign gene insertion. The gfp open reading frame preceded by the viral mcp promoter was inserted into the 157L locus by homologous recombination in Anthonomus grandis BRL-AG-3A cells. Recombinant virus (rCIV-Δ157L-gfp) was purified by successive rounds of plaque purification. All plaques produced by the purified recombinant virus emitted green fluorescence due to the presence of GFP. One-step growth curves for recombinant and wild-type CIV were similar and the recombinant was fully infectious in vivo. Hence, CIV157L can be inactivated without altering the replication kinetics of the virus. Consequently, the CIV 157L locus can be used as a site for insertion of foreign DNA, e.g. to modify viral properties for insect biocontrol.
Collapse
Affiliation(s)
- Arzu Ozgen
- Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, Turkey
| | - Hacer Muratoglu
- Karadeniz Technical University, Faculty of Science, Department of Molecular Biology and Genetics, 61080 Trabzon, Turkey
| | - Zihni Demirbag
- Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, Turkey
| | - Just M Vlak
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Monique M van Oers
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Remziye Nalcacioglu
- Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, Turkey.
| |
Collapse
|
36
|
Complete Genome Sequence of a Ranavirus Isolated from Chinese Giant Salamander (Andrias davidianus). GENOME ANNOUNCEMENTS 2014; 2:2/1/e01032-13. [PMID: 24407629 PMCID: PMC3886942 DOI: 10.1128/genomea.01032-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A ranavirus (RV) was isolated from Chinese giant salamanders (Andrias davidianus) in China in 2010 and provisionally designated Andrias davidianus ranavirus (ADRV). The complete genome sequence is 106,719 nucleotides long. Genomic sequence and phylogenetic analyses showed that ADRV has a high degree of conservation with other RVs.
Collapse
|
37
|
Genome Sequence of WAU86/88-1, a New Variant of Vaccinia Virus Lister Strain from Poland. GENOME ANNOUNCEMENTS 2014; 2:2/1/e01086-13. [PMID: 24407630 PMCID: PMC3886943 DOI: 10.1128/genomea.01086-13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The poxviruses Warsaw Agricultural University 86 (WAU86) and 88-1 (WAU88-1) were isolated in 1986 to 1988 from separate outbreaks in laboratory mice in Poland and described as ectromelia virus isolates. The genome sequences of these poxviruses reveal that they are almost identical and represent a novel variant of the vaccinia virus Lister strain.
Collapse
|
38
|
Huang X, Gong J, Huang Y, Ouyang Z, Wang S, Chen X, Qin Q. Characterization of an envelope gene VP19 from Singapore grouper iridovirus. Virol J 2013; 10:354. [PMID: 24341864 PMCID: PMC3878628 DOI: 10.1186/1743-422x-10-354] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 12/11/2013] [Indexed: 01/22/2023] Open
Abstract
Background Viral envelope proteins are always proposed to exert important function during virus infection and replication. Vertebrate iridoviruses are enveloped large DNA virus, which can cause great economic losses in aquaculture and ecological destruction. Although numerous iridovirus envelope proteins have been identified using bioinformatics and proteomic methods, their roles in virus infection remained largely unknown. Methods Using SMART and TMHMM programs, we investigated the structural characteristics of Singapore grouper iridovirus (SGIV) VP19. A specific antibody against VP19 was generated and the expression profile of VP19 was clarified. The subcellular localization of VP19 in the absence or presence of other viral products was determined via transfection and immune fluorescence assay. In addition, Western blot assay and electron microscopy examination were performed to demonstrate whether SGIV VP19 was an envelope protein or a capsid protein. Results Here, SGIV VP19 was cloned and characterized. Among all sequenced iridoviruses, VP19 and its orthologues shared common features, including 19 invariant cysteines, a proline-rich motif and a predicted transmembrane domain. Subsequently, the protein synthesis of VP19 was only detected at the late stage of SGIV infection and inhibited obviously by treating with AraC, confirming that VP19 was a late expressed protein. Ectopic expression of EGFP-VP19 in vitro displayed a punctate pattern in the cytoplasm. In SGIV infected cells, the newly synthesized VP19 protein was initially localized in the cytoplasm in a punctate pattern, and then aggregated into the virus assembly site at the late stage of SGIV infection, suggesting that other viral protein products were essential for VP19’s function during SGIV infection. In addition, Western blot assay and electron microscopy observation revealed that SGIV VP19 was associated with viral envelope, which was different from major capsid protein (MCP). Conclusion Taken together, the current data suggested that VP19 represented a conserved envelope protein in iridovirus, and might contribute greatly to virus assembly during virus infection.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Qiwei Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
| |
Collapse
|
39
|
Genome architecture changes and major gene variations of Andrias davidianus ranavirus (ADRV). Vet Res 2013; 44:101. [PMID: 24143877 PMCID: PMC4015033 DOI: 10.1186/1297-9716-44-101] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 10/04/2013] [Indexed: 01/08/2023] Open
Abstract
Ranaviruses are emerging pathogens that have led to global impact and public concern. As a rarely endangered species and the largest amphibian in the world, the Chinese giant salamander, Andrias davidianus, has recently undergone outbreaks of epidemic diseases with high mortality. In this study, we isolated and identified a novel ranavirus from the Chinese giant salamanders that exhibited systemic hemorrhage and swelling syndrome with high death rate in China during May 2011 to August 2012. The isolate, designated Andrias davidianus ranavirus (ADRV), not only could induce cytopathic effects in different fish cell lines and yield high viral titers, but also caused severely hemorrhagic lesions and resulted in 100% mortality in experimental infections of salamanders. The complete genome of ADRV was sequenced and compared with other sequenced amphibian ranaviruses. Gene content and phylogenetic analyses revealed that ADRV should belong to an amphibian subgroup in genus Ranavirus, and is more closely related to frog ranaviruses than to other salamander ranaviruses. Homologous gene comparisons show that ADRV contains 99%, 97%, 94%, 93% and 85% homologues in RGV, FV3, CMTV, TFV and ATV genomes respectively. In addition, several variable major genes, such as duplicate US22 family-like genes, viral eukaryotic translation initiation factor 2 alpha gene and novel 75L gene with both motifs of nuclear localization signal (NLS) and nuclear export signal (NES), were predicted to contribute to pathogen virulence and host susceptibility. These findings confirm the etiologic role of ADRV in epidemic diseases of Chinese giant salamanders, and broaden our understanding of evolutionary emergence of ranaviruses.
Collapse
|
40
|
Abrams AJ, Cannatella DC, Hillis DM, Sawyer SL. Recent host-shifts in ranaviruses: signatures of positive selection in the viral genome. J Gen Virol 2013; 94:2082-2093. [PMID: 23784445 DOI: 10.1099/vir.0.052837-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ranaviruses have been implicated in recent declines in global amphibian populations. Compared with the family Iridoviridae, to which the genus Ranavirus belongs, ranaviruses have a wide host range in that species/strains are known to infect fish, amphibians and reptiles, presumably due to recent host-switching events. We used eight sequenced ranavirus genomes and two selection-detection methods (site based and branch based) to identify genes that exhibited signatures of positive selection, potentially due to the selective pressures at play during host switching. We found evidence of positive selection acting on four genes via the site-based method, three of which were newly acquired genes unique to ranavirus genomes. Using the branch-based method, we identified eight additional candidate genes that exhibited signatures of dN/dS (non-synonymous/synonymous substitution rate) >1 in the clade where intense host switching had occurred. We found that these branch-specific patterns of elevated dN/dS were enriched in a small group of viral genes that have been acquired most recently in the ranavirus genome, compared with core genes that are shared among all members of the family Iridoviridae. Our results suggest that the group of newly acquired genes in the ranavirus genome may have undergone recent adaptive changes that have facilitated interspecies and interclass host switching.
Collapse
Affiliation(s)
- A Jeanine Abrams
- Section of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - David C Cannatella
- Section of Integrative Biology and Texas Memorial Museum, University of Texas, Austin, TX 78712, USA
| | - David M Hillis
- Section of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas, Austin, TX 78712, USA
| | - Sara L Sawyer
- Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
| |
Collapse
|
41
|
Nelson OW, Garrity GM. Genome sequences published outside of Standards in Genomic Sciences, January-March 2012. Stand Genomic Sci 2012. [DOI: 10.4056/sigs.1756022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Oranmiyan W. Nelson
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| | - George M. Garrity
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| |
Collapse
|