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Aduriz A, Lanthier I, Lair S, Vergneau-Grosset C. EVALUATION OF MORTALITY CAUSES AND PREVALENCE OF RENAL LESIONS IN ZOO-HOUSED CHAMELEONS: 2011-2022. J Zoo Wildl Med 2024; 55:381-392. [PMID: 38875194 DOI: 10.1638/2023-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2024] [Indexed: 06/16/2024] Open
Abstract
Of the 202 species of Chamaeleonidae, 38.6% are globally threatened. Currently, nearly a thousand individual chameleons from 36 different species are kept in zoological institutions worldwide. The objectives of this study were to assess the main mortality causes of chameleons in zoological institutions, the prevalence of renal lesions at necropsy, and the environmental factors associated with renal lesions. An online survey was sent to 245 zoological institutions worldwide to collect information about species and sex distribution, necropsy results, and husbandry parameters. Necropsy reports of the last 10 yr were requested from participating institutions (n = 65) when available. Mortality causes were classified into three categories (open diagnosis, infectious, and noninfectious), and noninfectious causes were further subdivided into seven categories (renal, reproductive, myoarthroskeletal, digestive, ophthalmologic, denutrition/multisystemic, and neoplastic). The prevalence of renal lesions was recorded. Multiple linear regression models were used with the prevalence of renal diseases as the dependent variable, and exhibit minimum and maximum hygrometry; exhibit highest and coolest temperature; as well as minimum, mean, and maximum hygrometry of the geographical area as independent variables, combining all chameleon species with similar environmental requirements. Results were obtained for 14 species (n = 412 individuals). The main mortality causes were infectious (46.8%), noninfectious renal (11.4%), and noninfectious reproductive (10.7%) diseases, with all cases of fatal reproductive diseases reported in females. Of the individuals that underwent renal histopathology, 41.7% displayed renal lesions. There was a tendency towards higher renal lesion prevalence in zoos located in areas with lower mean hygrometry (P = 0.05). Further research studies about infectious, renal, and reproductive diseases of Chamaeleonidae are warranted.
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Affiliation(s)
- Amélie Aduriz
- Faculté de médecine vétérinaire, Département des sciences cliniques, Université de Montréal, Saint-Hyacinthe, QC, J2S 2M2 Canada
| | - Isabelle Lanthier
- Département de pathologie et microbiologie, Université de Montréal, Saint-Hyacinthe, QC, J2S 2M2 Canada
| | - Stéphane Lair
- Faculté de médecine vétérinaire, Département des sciences cliniques, Université de Montréal, Saint-Hyacinthe, QC, J2S 2M2 Canada
| | - Claire Vergneau-Grosset
- Faculté de médecine vétérinaire, Département des sciences cliniques, Université de Montréal, Saint-Hyacinthe, QC, J2S 2M2 Canada,
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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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Lauber C, Zhang X, Vaas J, Klingler F, Mutz P, Dubin A, Pietschmann T, Roth O, Neuman BW, Gorbalenya AE, Bartenschlager R, Seitz S. Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates. PLoS Pathog 2024; 20:e1012163. [PMID: 38648214 PMCID: PMC11065284 DOI: 10.1371/journal.ppat.1012163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 05/02/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
Virus discovery by genomics and metagenomics empowered studies of viromes, facilitated characterization of pathogen epidemiology, and redefined our understanding of the natural genetic diversity of viruses with profound functional and structural implications. Here we employed a data-driven virus discovery approach that directly queries unprocessed sequencing data in a highly parallelized way and involves a targeted viral genome assembly strategy in a wide range of sequence similarity. By screening more than 269,000 datasets of numerous authors from the Sequence Read Archive and using two metrics that quantitatively assess assembly quality, we discovered 40 nidoviruses from six virus families whose members infect vertebrate hosts. They form 13 and 32 putative viral subfamilies and genera, respectively, and include 11 coronaviruses with bisegmented genomes from fishes and amphibians, a giant 36.1 kilobase coronavirus genome with a duplicated spike glycoprotein (S) gene, 11 tobaniviruses and 17 additional corona-, arteri-, cremega-, nanhypo- and nangoshaviruses. Genome segmentation emerged in a single evolutionary event in the monophyletic lineage encompassing the subfamily Pitovirinae. We recovered the bisegmented genome sequences of two coronaviruses from RNA samples of 69 infected fishes and validated the presence of poly(A) tails at both segments using 3'RACE PCR and subsequent Sanger sequencing. We report a genetic linkage between accessory and structural proteins whose phylogenetic relationships and evolutionary distances are incongruent with the phylogeny of replicase proteins. We rationalize these observations in a model of inter-family S recombination involving at least five ancestral corona- and tobaniviruses of aquatic hosts. In support of this model, we describe an individual fish co-infected with members from the families Coronaviridae and Tobaniviridae. Our results expand the scale of the known extraordinary evolutionary plasticity in nidoviral genome architecture and call for revisiting fundamentals of genome expression, virus particle biology, host range and ecology of vertebrate nidoviruses.
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Affiliation(s)
- Chris Lauber
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence 2155 RESIST, Hannover, Germany
| | - Xiaoyu Zhang
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Josef Vaas
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| | - Franziska Klingler
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| | - Pascal Mutz
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Arseny Dubin
- Marine Evolutionary Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Thomas Pietschmann
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence 2155 RESIST, Hannover, Germany
| | - Olivia Roth
- Marine Evolutionary Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Benjamin W. Neuman
- Department of Biology and Texas A&M Global Health Research Complex, Texas A&M University, College Station, Texas, United States
| | - Alexander E. Gorbalenya
- Leiden University Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
- Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ralf Bartenschlager
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| | - Stefan Seitz
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
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Tillis SB, Ossiboff RJ, Wellehan JFX. Serpentoviruses Exhibit Diverse Organization and ORF Composition with Evidence of Recombination. Viruses 2024; 16:310. [PMID: 38400085 PMCID: PMC10892116 DOI: 10.3390/v16020310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Serpentoviruses are a subfamily of positive sense RNA viruses in the order Nidovirales, family Tobaniviridae, associated with respiratory disease in multiple clades of reptiles. While the broadest viral diversity is reported from captive pythons, other reptiles, including colubrid snakes, turtles, and lizards of captive and free-ranging origin are also known hosts. To better define serpentoviral diversity, eleven novel serpentovirus genomes were sequenced with an Illumina MiSeq and, when necessary, completed with other Sanger sequencing methods. The novel serpentoviral genomes, along with 57 other previously published serpentovirus genomes, were analyzed alongside four outgroup genomes. Genomic analyses included identifying unique genome templates for each serpentovirus clade, as well as analysis of coded protein composition, potential protein function, protein glycosylation sites, differences in phylogenetic history between open-reading frames, and recombination. Serpentoviral genomes contained diverse protein compositions. In addition to the fundamental structural spike, matrix, and nucleoprotein proteins required for virion formation, serpentovirus genomes also included 20 previously uncharacterized proteins. The uncharacterized proteins were homologous to a number of previously characterized proteins, including enzymes, transcription factors, scaffolding, viral resistance, and apoptosis-related proteins. Evidence for recombination was detected in multiple instances in genomes from both captive and free-ranging snakes. These results show serpentovirus as a diverse clade of viruses with genomes that code for a wide diversity of proteins potentially enhanced by recombination events.
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Affiliation(s)
- Steven B. Tillis
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA; (R.J.O.); (J.F.X.W.J.)
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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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6
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Tillis SB, Holt C, Havens S, Logan TD, Julander JG, Ossiboff RJ. In Vitro Characterization and Antiviral Susceptibility of Ophidian Serpentoviruses. Microorganisms 2023; 11:1371. [PMID: 37374873 DOI: 10.3390/microorganisms11061371] [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: 04/06/2023] [Revised: 05/09/2023] [Accepted: 05/20/2023] [Indexed: 06/29/2023] Open
Abstract
Ophidian serpentoviruses, positive-sense RNA viruses in the order Nidovirales, are important infectious agents of both captive and free-ranging reptiles. Although the clinical significance of these viruses can be variable, some serpentoviruses are pathogenic and potentially fatal in captive snakes. While serpentoviral diversity and disease potential are well documented, little is known about the fundamental properties of these viruses, including their potential host ranges, kinetics of growth, environmental stability, and susceptibility to common disinfectants and viricides. To address this, three serpentoviruses were isolated in culture from three unique PCR-positive python species: Ball python (Python regius), green tree python (Morelia viridis), and Stimson's python (Antaresia stimsoni). A median tissue culture infectious dose (TCID50) was established to characterize viral stability, growth, and susceptibility. All isolates showed an environmental stability of 10-12 days at room temperature (20 °C). While all three viruses produced variable peak titers on three different cell lines when incubated at 32 °C, none of the viruses detectably replicated at 35 °C. All viruses demonstrated a wide susceptibility to sanitizers, with 10% bleach, 2% chlorhexidine, and 70% ethanol inactivating the virus in one minute and 7% peroxide and a quaternary ammonium solution within three minutes. Of seven tested antiviral agents, remdesivir, ribavirin, and NITD-008, showed potent antiviral activity against the three viruses. Finally, the three isolates successfully infected 32 unique tissue culture cell lines representing different diverse reptile taxa and select mammals and birds as detected by epifluorescent immunostaining. This study represents the first characterization of in vitro properties of growth, stability, host range, and inactivation for a serpentovirus. The reported results provide the basis for procedures to mitigate the spread of serpentoviruses in captive snake colonies as well as identify potential non-pharmacologic and pharmacologic treatment options for ophidian serpentoviral infections.
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Affiliation(s)
- Steven B Tillis
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Camille Holt
- Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
| | - Spencer Havens
- Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
| | - Tracey D Logan
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Justin G Julander
- Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
| | - Robert J Ossiboff
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
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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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Tillis SB, Josimovich JM, Miller MA, Hoon-Hanks LL, Hartmann AM, Claunch NM, Iredale ME, Logan TD, Yackel Adams AA, Bartoszek IA, Humphrey JS, Kluever BM, Stenglein MD, Reed RN, Romagosa CM, Wellehan JFX, Ossiboff RJ. Divergent Serpentoviruses in Free-Ranging Invasive Pythons and Native Colubrids in Southern Florida, United States. Viruses 2022; 14:v14122726. [PMID: 36560729 PMCID: PMC9782103 DOI: 10.3390/v14122726] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
Burmese python (Python bivittatus) is an invasive snake that has significantly affected ecosystems in southern Florida, United States. Aside from direct predation and competition, invasive species can also introduce nonnative pathogens that can adversely affect native species. The subfamily Serpentovirinae (order Nidovirales) is composed of positive-sense RNA viruses primarily found in reptiles. Some serpentoviruses, such as shingleback nidovirus, are associated with mortalities in wild populations, while others, including ball python nidovirus and green tree python nidovirus can be a major cause of disease and mortality in captive animals. To determine if serpentoviruses were present in invasive Burmese pythons in southern Florida, oral swabs were collected from both free-ranging and long-term captive snakes. Swabs were screened for the presence of serpentovirus by reverse transcription PCR and sequenced. A total serpentovirus prevalence of 27.8% was detected in 318 python samples. Of the initial swabs from 172 free-ranging pythons, 42 (24.4%) were positive for multiple divergent viral sequences comprising four clades across the sampling range. Both sex and snout-vent length were statistically significant factors in virus prevalence, with larger male snakes having the highest prevalence. Sampling location was statistically significant in circulating virus sequence. Mild clinical signs and lesions consistent with serpentovirus infection were observed in a subset of sampled pythons. Testing of native snakes (n = 219, 18 species) in part of the python range found no evidence of python virus spillover; however, five individual native snakes (2.3%) representing three species were PCR positive for unique, divergent serpentoviruses. Calculated pairwise uncorrected distance analysis indicated the newly discovered virus sequences likely represent three novel genera in the subfamily Serpentovirinae. This study is the first to characterize serpentovirus in wild free-ranging pythons or in any free-ranging North America reptile. Though the risk these viruses pose to the invasive and native species is unknown, the potential for spillover to native herpetofauna warrants further investigation.
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Affiliation(s)
- Steven B. Tillis
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Jillian M. Josimovich
- U.S. Geological Survey, Fort Collins Science Center-South Florida Field Station in Everglades National Park, 40001 SR 9336, Homestead, FL 33034, USA
| | - Melissa A. Miller
- Florida Fish and Wildlife Conservation Commission, Davie, FL 33314, USA
| | - Laura L. Hoon-Hanks
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Arik M. Hartmann
- Department of Biology, University of Florida, Gainesville, FL 32608, USA
| | - Natalie M. Claunch
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32608, USA
- School of Natural Resources and Environment, University of Florida, Gainesville, FL 32608, USA
| | - Marley E. Iredale
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Tracey D. Logan
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Amy A. Yackel Adams
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO 80526, USA
| | - Ian A. Bartoszek
- Conservancy of Southwest Florida, Environmental Science Department, Naples, FL 34102, USA
| | - John S. Humphrey
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Gainesville, FL 32641, USA
| | - Bryan M. Kluever
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Gainesville, FL 32641, USA
| | - Mark D. Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Robert N. Reed
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO 80526, USA
| | - Christina M. Romagosa
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32608, USA
| | - James F. X. Wellehan
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Robert J. Ossiboff
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
- Correspondence:
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Allain SJR, Duffus ALJ, Marschang RE. Editorial: Emerging infections and diseases of herpetofauna. Front Vet Sci 2022; 9:909616. [PMID: 36238439 PMCID: PMC9552943 DOI: 10.3389/fvets.2022.909616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Steven J. R. Allain
- Durrell Institute of Conservation and Ecology, University of Kent, Canterbury, United Kingdom
| | - Amanda L. J. Duffus
- Health of Herpetofauna Communities Research Group, Department of Natural Sciences, Gordon State College, Barnesville, GA, United States
- *Correspondence: Amanda L. J. Duffus
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Lu J, Yang S, Wang C, Wang H, Gong G, Xi Y, Pan J, Wang X, Zeng J, Zhang J, Li P, Shen Q, Shan T, Zhang W. Gut Virome of the World's Highest-Elevation Lizard Species ( Phrynocephalus erythrurus and Phrynocephalus theobaldi) Reveals Versatile Commensal Viruses. Microbiol Spectr 2022; 10:e0187221. [PMID: 35196818 PMCID: PMC8865479 DOI: 10.1128/spectrum.01872-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/29/2022] [Indexed: 12/27/2022] Open
Abstract
The gut virome is a reservoir of diverse symbiotic and pathogenic viruses coevolving with their hosts, and yet limited research has explored the gut viromes of highland-dwelling rare species. Using viral metagenomic analysis, the viral communities of the Phrynocephalus lizards living in the Qinghai-Tibet Plateau were investigated. Phage-encoded functional genes and antibiotic resistance genes (ARGs) were analyzed. The viral communities of different lizard species were all predominated by bacteriophages, especially the Caudovirales order. The virome of Phrynocephalus erythrurus living around the Namtso Lake possessed a unique structure, with the greatest abundance of the Parvoviridae family and the highest number of exclusive viral species. Several vertebrate-infecting viruses were discovered, including caliciviruses, astroviruses, and parvoviruses. Phylogenetic analyses demonstrated that the virus hallmark genes of bacteriophages possessed high genetic diversity. After functional annotation, the majority of phage-associated functional genes were classified in the energy metabolism category. In addition, plenty of ARGs belonging to the multidrug category were discovered, and five ARGs were exclusive to the virome from Phrynocephalus theobaldi. This study provided the first insight into the structure and function of the virome in highland lizards, contributing to the protection of threatened lizard species. Also, our research is of exemplary significance for the gut virome research of lizard species and other cold-blooded and highland-dwelling animals, prompting a better understanding of the interspecific differences and transmission of commensal viruses. IMPORTANCE The Phrynocephalus lizards inhabiting the Qinghai-Tibet Plateau (QTP) are considered to be the highest-altitude lizard species in the world, and they have been added to the IUCN list of threatened species. Living in the QTP with hypoxic, arid, natural conditions, the lizards presented a unique pattern of gut virome, which could provide both positive and negative effects, such as the enrichment of functional genes and the dissemination of antibiotic resistance genes (ARGs). This work provides the foundation for further research on the gut virome in these endangered lizard species and other cold-blooded and highland-dwelling animals, contributing to the maintenance of ecological balance on the plateau.
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Affiliation(s)
- Juan Lu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Chunmei Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hao Wang
- The Affiliated Huai’an Hospital, Xuzhou Medical University, Huai’an, Jiangsu, China
| | - Ga Gong
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, Tibet, China
| | - Yuan Xi
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jiamin Pan
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jian Zeng
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ju Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
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Parrish K, Kirkland PD, Skerratt LF, Ariel E. Nidoviruses in Reptiles: A Review. Front Vet Sci 2021; 8:733404. [PMID: 34621811 PMCID: PMC8490724 DOI: 10.3389/fvets.2021.733404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/19/2021] [Indexed: 12/17/2022] Open
Abstract
Since their discovery in 2014, reptile nidoviruses (also known as serpentoviruses) have emerged as significant pathogens worldwide. They are known for causing severe and often fatal respiratory disease in various captive snake species, especially pythons. Related viruses have been detected in other reptiles with and without respiratory disease, including captive and wild populations of lizards, and wild populations of freshwater turtles. There are many opportunities to better understand the viral diversity, species susceptibility, and clinical presentation in different species in this relatively new field of research. In captive snake collections, reptile nidoviruses can spread quickly and be associated with high morbidity and mortality, yet the potential disease risk to wild reptile populations remains largely unknown, despite reptile species declining on a global scale. Experimental studies or investigations of disease outbreaks in wild reptile populations are scarce, leaving the available literature limited mostly to exploring findings of naturally infected animals in captivity. Further studies into the pathogenesis of different reptile nidoviruses in a variety of reptile species is required to explore the complexity of disease and routes of transmission. This review focuses on the biology of these viruses, hosts and geographic distribution, clinical signs and pathology, laboratory diagnosis and management of reptile nidovirus infections to better understand nidovirus infections in reptiles.
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Affiliation(s)
- Kate Parrish
- Virology Laboratory, Elizabeth Macarthur Agricultural Institute, New South Wales (NSW) Department of Primary Industries, Menangle, NSW, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | - Peter D Kirkland
- Virology Laboratory, Elizabeth Macarthur Agricultural Institute, New South Wales (NSW) Department of Primary Industries, Menangle, NSW, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | - Lee F Skerratt
- Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Melbourne, VIC, Australia
| | - Ellen Ariel
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
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