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Parrish K, Kirkland P, Horwood P, Chessman B, Ruming S, McGilvray G, Rose K, Hall J, Skerratt L. Delving into the Aftermath of a Disease-Associated Near-Extinction Event: A Five-Year Study of a Serpentovirus (Nidovirus) in a Critically Endangered Turtle Population. Viruses 2024; 16:653. [PMID: 38675993 PMCID: PMC11055124 DOI: 10.3390/v16040653] [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: 03/29/2024] [Revised: 04/17/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024] Open
Abstract
Bellinger River virus (BRV) is a serpentovirus (nidovirus) that was likely responsible for the catastrophic mortality of the Australian freshwater turtle Myuchelys georgesi in February 2015. From November 2015 to November 2020, swabs were collected from turtles during repeated river surveys to estimate the prevalence of BRV RNA, identify risk factors associated with BRV infection, and refine sample collection. BRV RNA prevalence at first capture was significantly higher in M. georgesi (10.8%) than in a coexisting turtle, Emydura macquarii (1.0%). For M. georgesi, various risk factors were identified depending on the analysis method, but a positive BRV result was consistently associated with a larger body size. All turtles were asymptomatic when sampled and conjunctival swabs were inferred to be optimal for ongoing monitoring. Although the absence of disease and recent BRV detections suggests a reduced ongoing threat, the potential for the virus to persist in an endemic focus or resurge in cyclical epidemics cannot be excluded. Therefore, BRV is an ongoing potential threat to the conservation of M. georgesi, and strict adherence to biosecurity principles is essential to minimise the risk of reintroduction or spread of BRV or other pathogens.
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Affiliation(s)
- Kate Parrish
- Virology Laboratory, Elizabeth Macarthur Agriculture Institute, Department of Primary Industries, Menangle, NSW 2568, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4810, Australia
| | - Peter Kirkland
- Virology Laboratory, Elizabeth Macarthur Agriculture Institute, Department of Primary Industries, Menangle, NSW 2568, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4810, Australia
| | - Paul Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4810, Australia
| | | | - Shane Ruming
- Biodiversity Conservation and Science, New South Wales Department of Climate Change, Energy, the Environment and Water, Coffs Harbour, NSW 2450, Australia
| | - Gerry McGilvray
- Biodiversity Conservation and Science, New South Wales Department of Climate Change, Energy, the Environment and Water, Coffs Harbour, NSW 2450, Australia
| | - Karrie Rose
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, NSW 2088, Australia
| | - Jane Hall
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, NSW 2088, Australia
| | - Lee Skerratt
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Werribee, VIC 3030, Australia
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Liao Y, Wang H, Liao H, Sun Y, Tan L, Song C, Qiu X, Ding C. Classification, replication, and transcription of Nidovirales. Front Microbiol 2024; 14:1291761. [PMID: 38328580 PMCID: PMC10847374 DOI: 10.3389/fmicb.2023.1291761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 02/09/2024] Open
Abstract
Nidovirales is one order of RNA virus, with the largest single-stranded positive sense RNA genome enwrapped with membrane envelope. It comprises four families (Arterividae, Mesoniviridae, Roniviridae, and Coronaviridae) and has been circulating in humans and animals for almost one century, posing great threat to livestock and poultry,as well as to public health. Nidovirales shares similar life cycle: attachment to cell surface, entry, primary translation of replicases, viral RNA replication in cytoplasm, translation of viral proteins, virion assembly, budding, and release. The viral RNA synthesis is the critical step during infection, including genomic RNA (gRNA) replication and subgenomic mRNAs (sg mRNAs) transcription. gRNA replication requires the synthesis of a negative sense full-length RNA intermediate, while the sg mRNAs transcription involves the synthesis of a nested set of negative sense subgenomic intermediates by a discontinuous strategy. This RNA synthesis process is mediated by the viral replication/transcription complex (RTC), which consists of several enzymatic replicases derived from the polyprotein 1a and polyprotein 1ab and several cellular proteins. These replicases and host factors represent the optimal potential therapeutic targets. Hereby, we summarize the Nidovirales classification, associated diseases, "replication organelle," replication and transcription mechanisms, as well as related regulatory factors.
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Affiliation(s)
- Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huiyu Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
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Flies AS, Flies EJ, Fountain-Jones NM, Musgrove RE, Hamede RK, Philips A, Perrott MRF, Dunowska M. Wildlife nidoviruses: biology, epidemiology, and disease associations of selected nidoviruses of mammals and reptiles. mBio 2023; 14:e0071523. [PMID: 37439571 PMCID: PMC10470586 DOI: 10.1128/mbio.00715-23] [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] [Indexed: 07/14/2023] Open
Abstract
Wildlife is the source of many emerging infectious diseases. Several viruses from the order Nidovirales have recently emerged in wildlife, sometimes with severe consequences for endangered species. The order Nidovirales is currently classified into eight suborders, three of which contain viruses of vertebrates. Vertebrate coronaviruses (suborder Cornidovirineae) have been extensively studied, yet the other major suborders have received less attention. The aim of this minireview was to summarize the key findings from the published literature on nidoviruses of vertebrate wildlife from two suborders: Arnidovirineae and Tornidovirineae. These viruses were identified either during investigations of disease outbreaks or through molecular surveys of wildlife viromes, and include pathogens of reptiles and mammals. The available data on key biological features, disease associations, and pathology are presented, in addition to data on the frequency of infections among various host populations, and putative routes of transmission. While nidoviruses discussed here appear to have a restricted in vivo host range, little is known about their natural life cycle. Observational field-based studies outside of the mortality events are needed to facilitate an understanding of the virus-host-environment interactions that lead to the outbreaks. Laboratory-based studies are needed to understand the pathogenesis of diseases caused by novel nidoviruses and their evolutionary histories. Barriers preventing research progress include limited funding and the unavailability of virus- and host-specific reagents. To reduce mortalities in wildlife and further population declines, proactive development of expertise, technologies, and networks should be developed. These steps would enable effective management of future outbreaks and support wildlife conservation.
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Affiliation(s)
- Andrew S. Flies
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Emily J. Flies
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
- Healthy Landscapes Research Group, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Ruth E. Musgrove
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Rodrigo K. Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Annie Philips
- Natural Resources and Environment Tasmania, Hobart, Tasmania, Australia
| | | | - Magdalena Dunowska
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
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Schilliger L, Paillusseau C, François C, Bonwitt J. Major Emerging Fungal Diseases of Reptiles and Amphibians. Pathogens 2023; 12:pathogens12030429. [PMID: 36986351 PMCID: PMC10053826 DOI: 10.3390/pathogens12030429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/16/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Emerging infectious diseases (EIDs) are caused by pathogens that have undergone recent changes in terms of geographic spread, increasing incidence, or expanding host range. In this narrative review, we describe three important fungal EIDs with keratin trophism that are relevant to reptile and amphibian conservation and veterinary practice. Nannizziopsis spp. have been mainly described in saurians; infection results in thickened, discolored skin crusting, with eventual progression to deep tissues. Previously only reported in captive populations, it was first described in wild animals in Australia in 2020. Ophidiomyces ophidiicola (formely O. ophiodiicola) is only known to infect snakes; clinical signs include ulcerating lesions in the cranial, ventral, and pericloacal regions. It has been associated with mortality events in wild populations in North America. Batrachochytrium spp. cause ulceration, hyperkeratosis, and erythema in amphibians. They are a major cause of catastrophic amphibian declines worldwide. In general, infection and clinical course are determined by host-related characteristics (e.g., nutritional, metabolic, and immune status), pathogens (e.g., virulence and environmental survival), and environment (e.g., temperature, hygrometry, and water quality). The animal trade is thought to be an important cause of worldwide spread, with global modifications in temperature, hygrometry, and water quality further affecting fungal pathogenicity and host immune response.
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Affiliation(s)
- Lionel Schilliger
- Argos Veterinary Clinic of Paris Auteuil, 35 Rue Leconte de Lisle, 75016 Paris, France
- SpéNac Referral Center, 100 Boulevard de la Tour Maubourg, 75007 Paris, France
- Correspondence: ; Tel.: +33-188-616-831
| | - Clément Paillusseau
- Argos Veterinary Clinic of Paris Auteuil, 35 Rue Leconte de Lisle, 75016 Paris, France
- SpéNac Referral Center, 100 Boulevard de la Tour Maubourg, 75007 Paris, France
| | - Camille François
- Argos Veterinary Clinic of Paris Auteuil, 35 Rue Leconte de Lisle, 75016 Paris, France
- SpéNac Referral Center, 100 Boulevard de la Tour Maubourg, 75007 Paris, France
| | - Jesse Bonwitt
- Department of Anthropology, Durham University, South Rd., Durham DH1 3LE, UK
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Leineweber C, Marschang RE. Detection of nidoviruses in samples collected from captive snakes in Europe between 2016 and 2021. Vet Rec 2023; 192:e2588. [PMID: 36719283 DOI: 10.1002/vetr.2588] [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: 11/01/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND Nidoviruses are increasingly detected in various snake species worldwide, but much remains to be learned about their distribution and the factors influencing their epidemiology. METHODS This retrospective study evaluated the results of routine nidovirus testing, by PCR, of 5210 swab samples from pet snakes from various European countries that were submitted to a commercial veterinary laboratory in Germany between 2016 and 2021. RESULTS The overall detection rate was 19.96%. However, the detection rate varied significantly depending on the snake species (p < 0.0001), with the highest rate in Indian pythons (Python molurus) (42.24%). Rates also varied depending on the season of sample collection (p < 0.0001), with the highest rate in winter (24.46%), and the country of sample origin (p < 0.0001), with the highest rate in Austria (36.69%). The detection rate also decreased significantly (p = 0.0003) over the 6-year observation period, from 26.43% to 17.64%. LIMITATION No information on clinical signs was available for most of the sampled snakes. CONCLUSION The present study supplies new information on the distribution of python nidoviruses (subgenus Roypretovirus) in pet snakes in Europe and indicates a dynamic situation with possible changes in prevalence over time.
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Guzy JC, Falk BG, Smith BJ, Willson JD, Reed RN, Aumen NG, Avery ML, Bartoszek IA, Campbell E, Cherkiss MS, Claunch NM, Currylow AF, Dean T, Dixon J, Engeman R, Funck S, Gibble R, Hengstebeck KC, Humphrey JS, Hunter ME, Josimovich JM, Ketterlin J, Kirkland M, Mazzotti FJ, McCleery R, Miller MA, McCollister M, Parker MR, Pittman SE, Rochford M, Romagosa C, Roybal A, Snow RW, Spencer MM, Waddle JH, Yackel Adams AA, Hart KM. Burmese pythons in Florida: A synthesis of biology, impacts, and management tools. NEOBIOTA 2023. [DOI: 10.3897/neobiota.80.90439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Burmese pythons (Python molurus bivittatus) are native to southeastern Asia, however, there is an established invasive population inhabiting much of southern Florida throughout the Greater Everglades Ecosystem. Pythons have severely impacted native species and ecosystems in Florida and represent one of the most intractable invasive-species management issues across the globe. The difficulty stems from a unique combination of inaccessible habitat and the cryptic and resilient nature of pythons that thrive in the subtropical environment of southern Florida, rendering them extremely challenging to detect. Here we provide a comprehensive review and synthesis of the science relevant to managing invasive Burmese pythons. We describe existing control tools and review challenges to productive research, identifying key knowledge gaps that would improve future research and decision making for python control.
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Harding EF, Russo AG, Yan GJH, Mercer LK, White PA. Revealing the uncharacterised diversity of amphibian and reptile viruses. ISME COMMUNICATIONS 2022; 2:95. [PMID: 37938670 PMCID: PMC9723728 DOI: 10.1038/s43705-022-00180-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/18/2022] [Accepted: 09/15/2022] [Indexed: 06/29/2023]
Abstract
Amphibians and non-avian reptiles represent a significant proportion of terrestrial vertebrates, however knowledge of their viruses is not proportional to their abundance. Many amphibians and reptiles have strict habitual environments and localised populations and are vulnerable to viral outbreaks and potential elimination as a result. We sought to identify viruses that were hidden in amphibian and reptile metatranscriptomic data by screening 235 RNA-sequencing datasets from a 122 species covering 25 countries. We identified 26 novel viruses and eight previously characterised viruses from fifteen different viral families. Twenty-five viruses had RNA genomes with identity to Arteriviridae, Tobaniviridae, Hantaviridae, Rhabdoviridae, Astroviridae, Arenaviridae, Hepeviridae, Picornaviridae, Orthomyxoviridae, Reoviridae, Flaviviridae and Caliciviridae. In addition to RNA viruses, we also screened datasets for DNA viral transcripts, which are commonly excluded from transcriptomic analysis. We identified ten DNA viruses with identity to Papillomaviridae, Parvoviridae, Circoviridae and Adomaviridae. With the addition of these viruses, we expand the global amphibian and reptile virome and identify new potentially pathogenic viruses that could challenge populations. We speculate that amphibian viruses often have simpler genomes than those in amniotes, as in the case of the Secondpapillomavirinae and Orthomyxoviridae viruses identified in this study. In addition, we find evidence of inter-family recombination in RNA viruses, and we also identify new members of the recombinant Adomaviridae family. Overall, we provide insights into the uncharacterised diversity of amphibian and reptile viruses with the aim of improving population management, treatment and conservation into the future.
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Affiliation(s)
- Emma F Harding
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Alice G Russo
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
- Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, 2010, Australia
| | - Grace J H Yan
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Lewis K Mercer
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia.
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8
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Xiong Y, Wu Q, Qin X, Yang C, Luo S, He J, Cheng Q, Wu Z. Identification of Pseudomonas aeruginosa From the Skin Ulcer Disease of Crocodile Lizards ( Shinisaurus crocodilurus) and Probiotics as the Control Measure. Front Vet Sci 2022; 9:850684. [PMID: 35529836 PMCID: PMC9069141 DOI: 10.3389/fvets.2022.850684] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/17/2022] [Indexed: 01/02/2023] Open
Abstract
The crocodile lizard (Shinisaurus crocodilurus) is an endangered ancient reptile species. Captive breeding is an important conservation measure for the potential restoration and recovery of their wild populations. However, a skin ulcer disease caused by an unknown pathogen has become a serious threat to captive breeding individuals. In the current study, based on microbial isolation, we identified Pseudomonas aeruginosa as the dominant pathogen in skin ulcer disease. Chinese skinks (Plestiodon chinensis) were used to verify the pathogenicity of P. aeruginosa in skin ulcer disease in vivo. As expected, subcutaneous inoculation of P. aeruginosa induced skin disease in healthy skinks and P. aeruginosa was re-isolated from the induced skin ulcers. Therefore, P. aeruginosa, an opportunistic and ubiquitous pathogen that causes a wide range of infections, appears to be the main pathogen of the skin disease affecting crocodile lizards. In the aquaculture industry, probiotics are widely used in the prevention and control of animal diseases caused by such pathogens. Here, we administered probiotics to the breeding crocodile lizards for 6 months. The three experiment groups treated with different kinds of probiotics showed significance at controlling case incidence. Three of the four groups treated with probiotics showed significant disease prevention (Effective Microorganisms mixed probiotics P = 0.0374; Double-dose Effective Microorganisms, P = 0.0299; Bacillus subtilis, P = 0.0140, T-test), and CFUs in the water of the breeding enclosures were also inhibited after probiotics usage (P < 0.001, T-test). Our study demonstrated the role of Pseudomonas aeruginosa in development of skin ulcer disease of crocodile lizards in a local zoo and offered the probiotic-based method for control measurements, which would be of benefit for the conservation of endangered reptiles.
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Affiliation(s)
- Yi Xiong
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guilin, China.,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, China
| | - Qiong Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guilin, China.,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, China
| | - Xudong Qin
- Daguishan National Nature Reserve for Crocodile Lizards, Hezhou, China
| | - Chengsheng Yang
- Daguishan National Nature Reserve for Crocodile Lizards, Hezhou, China
| | - Shuyi Luo
- Daguishan National Nature Reserve for Crocodile Lizards, Hezhou, China
| | - Jiasong He
- Daguishan National Nature Reserve for Crocodile Lizards, Hezhou, China
| | - Qingzhen Cheng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guilin, China.,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, China
| | - Zhengjun Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guilin, China.,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin, China
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