1
|
Parry RH, Slonchak A, Campbell LJ, Newton ND, Debat HJ, Gifford RJ, Khromykh AA. A novel tamanavirus ( Flaviviridae) of the European common frog ( Rana temporaria) from the UK. J Gen Virol 2023; 104:001927. [PMID: 38059479 PMCID: PMC10770923 DOI: 10.1099/jgv.0.001927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/19/2023] [Indexed: 12/08/2023] Open
Abstract
Flavivirids are small, enveloped, positive-sense RNA viruses from the family Flaviviridae with genomes of ~9-13 kb. Metatranscriptomic analyses of metazoan organisms have revealed a diversity of flavivirus-like or flavivirid viral sequences in fish and marine invertebrate groups. However, no flavivirus-like virus has been identified in amphibians. To remedy this, we investigated the virome of the European common frog (Rana temporaria) in the UK, utilizing high-throughput sequencing at six catch locations. De novo assembly revealed a coding-complete virus contig of a novel flavivirid ~11.2 kb in length. The virus encodes a single ORF of 3456 aa and 5' and 3' untranslated regions (UTRs) of 227 and 666 nt, respectively. We named this virus Rana tamanavirus (RaTV), as BLASTp analysis of the polyprotein showed the closest relationships to Tamana bat virus (TABV) and Cyclopterus lumpus virus from Pteronotus parnellii and Cyclopterus lumpus, respectively. Phylogenetic analysis of the RaTV polyprotein compared to Flavivirus and Flavivirus-like members indicated that RaTV was sufficiently divergent and basal to the vertebrate Tamanavirus clade. In addition to the Mitcham strain, partial but divergent RaTV, sharing 95.64-97.39 % pairwise nucleotide identity, were also obtained from the Poole and Deal samples, indicating that RaTV is widespread in UK frog samples. Bioinformatic analyses of predicted secondary structures in the 3'UTR of RaTV showed the presence of an exoribonuclease-resistant RNA (xrRNA) structure standard in flaviviruses and TABV. To examine this biochemically, we conducted an in vitro Xrn1 digestion assay showing that RaTV probably forms a functional Xrn1-resistant xrRNA.
Collapse
Affiliation(s)
- Rhys H. Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Andrii Slonchak
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
| | - Lewis J. Campbell
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Institute of Zoology, Zoological Society of London, London, UK
- Environment and Sustainability Institute, University of Exeter, Penryn, UK
| | - Natalee D. Newton
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
| | - Humberto J. Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola (UFYMA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5020ICA, Argentina
| | | | - Alexander A. Khromykh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
- AIDRC Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
| |
Collapse
|
2
|
Coutinho CD, Ford CE, Trafford JD, Duarte A, Rebelo R, Rosa GM. Non-Lethal Detection of Ranavirus in Fish. Viruses 2023; 15:471. [PMID: 36851684 PMCID: PMC9964643 DOI: 10.3390/v15020471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Emergent infectious diseases have an increasing impact on both farmed animals and wildlife. The ability to screen for pathogens is critical for understanding host-pathogen dynamics and informing better management. Ranavirus is a pathogen of concern, associated with disease outbreaks worldwide, affecting a broad range of fish, amphibian, and reptile hosts, but research has been limited. The traditional screening of internal tissues, such as the liver, has been regarded as the most effective for detecting and quantifying Ranavirus. However, such methodology imposes several limitations from ethical and conservation standpoints. Non-lethal sampling methods of viral detection were explored by comparing the efficacy of both buccal swabbing and fin clipping. The study was conducted on two Iberian, threatened freshwater fish (Iberochondrostoma lusitanicum and Cobitis paludica), and all samples were screened using qPCR. While for C. paludica both methods were reliable in detecting Ranavirus, on I. lusitanicum, there was a significantly higher detection rate in buccal swabs than in fin tissue. This study, therefore, reports that fin clipping may yield false Ranavirus negatives when in small-bodied freshwater fish. Overall, buccal swabbing is found to be good as an alternative to more invasive procedures, which is of extreme relevance, particularly when dealing with a threatened species.
Collapse
Affiliation(s)
- Catarina D. Coutinho
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Charlotte E. Ford
- Zoological Society of London, Institute of Zoology, Nuffield Building, Outer Circle, London NW8 7LS, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Joseph D. Trafford
- Zoological Society of London, Institute of Zoology, Nuffield Building, Outer Circle, London NW8 7LS, UK
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Ana Duarte
- Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), 2780-157 Oeiras, Portugal
| | - Rui Rebelo
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Gonçalo M. Rosa
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Zoological Society of London, Institute of Zoology, Nuffield Building, Outer Circle, London NW8 7LS, UK
| |
Collapse
|
3
|
Thumsová B, Price SJ, González-Cascón V, Vörös J, Martínez-Silvestre A, Rosa GM, Machordom A, Bosch J. Climate warming triggers the emergence of native viruses in Iberian amphibians. iScience 2022; 25:105541. [PMID: 36590463 PMCID: PMC9801250 DOI: 10.1016/j.isci.2022.105541] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/19/2022] [Accepted: 11/07/2022] [Indexed: 12/02/2022] Open
Abstract
The number of epizootics in amphibian populations caused by viruses of the genus Ranavirus is increasing worldwide. Yet, causes for pathogen emergence are poorly understood. Here, we confirmed that the Common midwife toad virus (CMTV) and Frog virus 3 (FV3) are responsible for mass mortalities in Iberia since the late 1980s. Our results illustrate the Iberian Peninsula as a diversity hotspot for the highly virulent CMTV. Although this pattern of diversity in Europe is consistent with spread by natural dispersal, the exact origin of the emergence of CMTV remains uncertain. Nevertheless, our data allow hypothesizing that the Iberian Peninsula might harbor the ancestral population of CMTVs that could have spread into the rest of Europe. In addition, we found that climate warming could be triggering the CMTV outbreaks, supporting its endemic status in the Iberian Peninsula.
Collapse
Affiliation(s)
- Barbora Thumsová
- Asociación Herpetológica Española (AHE), Madrid, Spain,Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | | | | | - Judit Vörös
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary,Laboratory for Molecular Taxonomy, Hungarian Natural History Museum, Budapest, Hungary
| | | | - Gonçalo M. Rosa
- Institute of Zoology, Zoological Society of London, Regents Park, LondonNW1 4RY, UK,Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Annie Machordom
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Jaime Bosch
- IMIB-Biodiversity Research Institute (University of Oviedo-CSIC-Principality of Asturias), Mieres, Spain,Corresponding author
| |
Collapse
|
4
|
Ford CE, Brookes LM, Skelly E, Sergeant C, Jordine T, Balloux F, Nichols RA, Garner TWJ. Non-Lethal Detection of Frog Virus 3-Like (RUK13) and Common Midwife Toad Virus-Like (PDE18) Ranaviruses in Two UK-Native Amphibian Species. Viruses 2022; 14:v14122635. [PMID: 36560639 PMCID: PMC9786228 DOI: 10.3390/v14122635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Ranaviruses have been involved in amphibian mass mortality events worldwide. Effective screening to control this pathogen is essential; however, current sampling methods are unsuitable for the detection of subclinical infections. Non-lethal screening is needed to prevent both further spread of ranavirus and losses of at-risk species. To assess non-lethal sampling methods, we conducted two experiments: bath exposing common frogs to RUK13 ranavirus at three concentrations, and exposing common toads to RUK13 or PDE18. Non-lethal sampling included buccal, digit, body and tank swabs, along with toe clips and stool taken across three time-points post-exposure. The presence/load of ranavirus was examined using quantitative PCR in 11 different tissues obtained from the same euthanised animals (incl. liver, gastro-intestinal tract and kidney). Buccal swab screening had the highest virus detection rate in both species (62% frogs; 71% toads) and produced consistently high virus levels compared to other non-lethal assays. The buccal swab was effective across multiple stages of infection and differing infection intensities, though low levels of infection were more difficult to detect. Buccal swab assays competed with, and even outperformed, lethal sampling in frogs and toads, respectively. Successful virus detection in the absence of clinical signs was observed (33% frogs; 50% toads); we found no difference in detectability for RUK13 and PDE18. Our results suggest that buccal swabbing could replace lethal sampling for screening and be introduced as standard practice for ranavirus surveillance.
Collapse
Affiliation(s)
- Charlotte E. Ford
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
- Zoological Society of London, Institute of Zoology, Nuffield Building, Outer Circle, London NW8 7LS, UK
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
- Correspondence: or
| | - Lola M. Brookes
- Zoological Society of London, Institute of Zoology, Nuffield Building, Outer Circle, London NW8 7LS, UK
- RVC Animal Welfare Science and Ethics, The Royal Veterinary College, Hawkshead Lane, Hatfield AL9 7TA, UK
| | - Emily Skelly
- Zoological Society of London, Institute of Zoology, Nuffield Building, Outer Circle, London NW8 7LS, UK
| | - Chris Sergeant
- Zoological Society of London, Institute of Zoology, Nuffield Building, Outer Circle, London NW8 7LS, UK
| | - Tresai Jordine
- Zoological Society of London, Institute of Zoology, Nuffield Building, Outer Circle, London NW8 7LS, UK
| | - Francois Balloux
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Richard A. Nichols
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Trenton W. J. Garner
- Zoological Society of London, Institute of Zoology, Nuffield Building, Outer Circle, London NW8 7LS, UK
| |
Collapse
|
5
|
Bosch J, Mora-Cabello de Alba A, Marquínez S, Price SJ, Thumsová B, Bielby J. Long-Term Monitoring of Amphibian Populations of a National Park in Northern Spain Reveals Negative Persisting Effects of Ranavirus, but Not Batrachochytrium dendrobatidis. Front Vet Sci 2021; 8:645491. [PMID: 34235196 PMCID: PMC8255480 DOI: 10.3389/fvets.2021.645491] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/21/2021] [Indexed: 11/25/2022] Open
Abstract
Amphibians are the most highly threatened vertebrates, and emerging pathogens are a serious threat to their conservation. Amphibian chytrid fungi and the viruses of the Ranavirus genus are causing disease outbreaks worldwide, including in protected areas such as National Parks. However, we lack information about their effect over amphibian populations in the long-term, and sometimes these mortality episodes are considered as transient events without serious consequences over longer time-spans. Here, we relate the occurrence of both pathogens with the population trends of 24 amphibian populations at 15 sites across a national Park in northern Spain over a 14-year period. Just one out 24 populations presents a positive population trend being free of both pathogens, while seven populations exposed to one or two pathogens experienced strong declines during the study period. The rest of the study populations (16) remain stable, and these tend to be of species that are not susceptible to the pathogen present or are free of pathogens. Our study is consistent with infectious diseases playing an important role in dictating amphibian population trends and emphasizes the need to adopt measures to control these pathogens in nature. We highlight that sites housing species carrying Ranavirus seems to have experienced more severe population-level effects compared to those with the amphibian chytrid fungus, and that ranaviruses could be just as, or more important, other more high-profile amphibian emerging pathogens.
Collapse
Affiliation(s)
- Jaime Bosch
- Research Unit of Biodiversity (Consejo Superior de Investigaciones Científicas, Universidad de Oviedo, Principado de Asturias), Oviedo University, Mieres, Spain.,Museo Nacional de Ciencias Naturales-Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | | | - Stephen J Price
- Genetic Institute, University College London, London, United Kingdom
| | - Barbora Thumsová
- Research Unit of Biodiversity (Consejo Superior de Investigaciones Científicas, Universidad de Oviedo, Principado de Asturias), Oviedo University, Mieres, Spain.,Museo Nacional de Ciencias Naturales-Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jon Bielby
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, United Kingdom
| |
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
|
Maclaine A, Wirth WT, McKnight DT, Burgess GW, Ariel E. Ranaviruses in captive and wild Australian lizards. Facets (Ott) 2020. [DOI: 10.1139/facets-2020-0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Ranaviral infections have been associated with mass mortality events in captive and wild amphibian, fish, and reptile populations globally. In Australia, two distinct types of ranaviruses have been isolated: epizootic haematopoietic necrosis virus in fish and a Frog virus 3-like ranavirus in amphibians. Experimental studies and serum surveys have demonstrated that several Australian native fish, amphibian, and reptile species are susceptible to infection and supported the theory that ranavirus is naturally circulating in Australian herpetofauna. However, ranaviral infections have not been detected in captive or wild lizards in Australia. Oral-cloacal swabs were collected from 42 wild lizards from northern Queensland and 83 captive lizards from private collections held across three states/territories. Samples were tested for ranaviral DNA using a quantitative PCR assay. This assay detected ranaviral DNA in 30/83 (36.1%) captive and 33/42 (78.6%) wild lizard samples. This is the first time molecular evidence of ranavirus has been reported in Australian lizards.
Collapse
Affiliation(s)
- Alicia Maclaine
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Wytamma T. Wirth
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Donald T. McKnight
- College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
| | - Graham W. Burgess
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Ellen Ariel
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| |
Collapse
|
8
|
Campbell LJ, Pawlik AH, Harrison XA. Amphibian ranaviruses in Europe: important directions for future research. Facets (Ott) 2020. [DOI: 10.1139/facets-2020-0007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Ranaviruses are an emerging group of pathogens capable of infecting all cold-blooded vertebrates. In Europe, ranaviruses pose a particularly potent threat to wild amphibian populations. Since the 1980s research on amphibian-infecting ranaviruses in Europe has been growing. The wide distribution of amphibian populations in Europe, the ease with which many are monitored, and the tractable nature of counterpart ex situ experimental systems have provided researchers with a unique opportunity to study many aspects of host–ranavirus interactions in the wild. These characteristics of European amphibian populations will also enable researchers to lead the way as the field of host–ranavirus interactions progresses. In this review, we provide a summary of the current key knowledge regarding amphibian infecting ranaviruses throughout Europe. We then outline important areas of further research and suggest practical ways each could be pursued. We address the study of potential interactions between the amphibian microbiome and ranaviruses, how pollution may exacerbate ranaviral disease either as direct stressors of amphibians or indirect modification of the amphibian microbiome. Finally, we discuss the need for continued surveillance of ranaviral emergence in the face of climate change.
Collapse
Affiliation(s)
- Lewis J. Campbell
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Alice H. Pawlik
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Xavier A. Harrison
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| |
Collapse
|
9
|
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
|
10
|
Price SJ, Leung WTM, Owen CJ, Puschendorf R, Sergeant C, Cunningham AA, Balloux F, Garner TWJ, Nichols RA. Effects of historic and projected climate change on the range and impacts of an emerging wildlife disease. GLOBAL CHANGE BIOLOGY 2019; 25:2648-2660. [PMID: 31074105 DOI: 10.1111/gcb.14651] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/13/2019] [Indexed: 06/09/2023]
Abstract
The global trend of increasing environmental temperatures is often predicted to result in more severe disease epidemics. However, unambiguous evidence that temperature is a driver of epidemics is largely lacking, because it is demanding to demonstrate its role among the complex interactions between hosts, pathogens, and their shared environment. Here, we apply a three-pronged approach to understand the effects of temperature on ranavirus epidemics in UK common frogs, combining in vitro, in vivo, and field studies. Each approach suggests that higher temperatures drive increasing severity of epidemics. In wild populations, ranavirosis incidents were more frequent and more severe at higher temperatures, and their frequency increased through a period of historic warming in the 1990s. Laboratory experiments using cell culture and whole animal models showed that higher temperature increased ranavirus propagation, disease incidence, and mortality rate. These results, combined with climate projections, predict severe ranavirosis outbreaks will occur over wider areas and an extended season, possibly affecting larval recruitment. Since ranaviruses affect a variety of ectothermic hosts (amphibians, reptiles, and fish), wider ecological damage could occur. Our three complementary lines of evidence present a clear case for direct environmental modulation of these epidemics and suggest management options to protect species from disease.
Collapse
Affiliation(s)
- Stephen J Price
- UCL Genetics Institute, London, United Kingdom
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - William T M Leung
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | | | - Robert Puschendorf
- School of Biological and Marine Sciences, University of Plymouth, Devon, United Kingdom
| | - Chris Sergeant
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | | | | | - Trenton W J Garner
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | | |
Collapse
|
11
|
Duffus ALJ, Garner TWJ, Nichols RA, Standridge JP, Earl JE. Modelling Ranavirus Transmission in Populations of Common Frogs ( Rana temporaria) in the United Kingdom. Viruses 2019; 11:v11060556. [PMID: 31208063 PMCID: PMC6630962 DOI: 10.3390/v11060556] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/31/2019] [Accepted: 06/04/2019] [Indexed: 12/13/2022] Open
Abstract
Ranaviruses began emerging in common frogs (Rana temporaria) in the United Kingdom in the late 1980s and early 1990s, causing severe disease and declines in the populations of these animals. Herein, we explored the transmission dynamics of the ranavirus(es) present in common frog populations, in the context of a simple susceptible-infected (SI) model, using parameters derived from the literature. We explored the effects of disease-induced population decline on the dynamics of the ranavirus. We then extended the model to consider the infection dynamics in populations exposed to both ulcerative and hemorrhagic forms of the ranaviral disease. The preliminary investigation indicated the important interactions between the forms. When the ulcerative form was present in a population and the hemorrhagic form was later introduced, the hemorrhagic form of the disease needed to be highly contagious, to persist. We highlighted the areas where further research and experimental evidence is needed and hope that these models would act as a guide for further research into the amphibian disease dynamics.
Collapse
Affiliation(s)
- Amanda L J Duffus
- Department of Mathematics and Natural Sciences, Gordon State College, Barnesville, GA 30204, USA.
| | | | - Richard A Nichols
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK.
| | - Joshua P Standridge
- Department of Mathematics and Natural Sciences, Gordon State College, Barnesville, GA 30204, USA.
| | - Julia E Earl
- School of Biological Sciences, Louisiana Tech University, Ruston, LA 71272, USA.
| |
Collapse
|
12
|
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
|
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
|