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Hess SC, Weiss KCB, Custer JM, Lewis JS, Kraberger S, Varsani A. Identification of small circular DNA viruses in coyote fecal samples from Arizona (USA). Arch Virol 2023; 169:12. [PMID: 38151635 DOI: 10.1007/s00705-023-05937-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023]
Abstract
Coyotes (Canis latrans) have a broad geographic distribution across North and Central America. Despite their widespread presence in urban environments in the USA, there is limited information regarding viruses associated with coyotes in the USA and in particular the state of Arizona. To explore viruses associated with coyotes, particularly small DNA viruses, 44 scat samples were collected (April-June 2021 and November 2021-January 2022) along the Salt River near Phoenix, Arizona (USA), along 43 transects (500 m). From these samples, we identified 11 viral genomes: two novel circoviruses, six unclassified cressdnaviruses, and two anelloviruses. One of the circoviruses is most closely related to a circovirus sequence identified from an aerosolized dust sample in Arizona, USA. The second circovirus is most closely related to a rodent-associated circovirus and canine circovirus. Of the unclassified cressdnaviruses, three encode replication-associated proteins that are similar to those found in protists (Histomonas meleagridis and Monocercomonoides exilis), implying an evolutionary relationship with or a connection to similar unidentified protist hosts. The two anelloviruses are most closely related to those found in rodents, and this suggests a diet-related identification.
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Affiliation(s)
- Savage C Hess
- The School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, 85281, USA
| | - Katherine C B Weiss
- The School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, 85281, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287, USA
| | - Jesse S Lewis
- College of Integrative Sciences and Arts, Arizona State University, Polytechnic Campus, 6073 South Backus Mall, Mesa, AZ, 85212, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- The School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, 85281, USA.
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287, USA.
- Center of Evolution and Medicine, Arizona State University, 427 E Tyler Mall, Tempe, AZ, 85281, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa.
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Velasco-Villa A. On skunk rabies and its prevention in North America. EQUINE VET EDUC 2023; 35:589-593. [PMID: 38651084 PMCID: PMC11034821 DOI: 10.1111/eve.13843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 04/25/2024]
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Data-Driven Management-A Dynamic Occupancy Approach to Enhanced Rabies Surveillance Prioritization. Viruses 2021; 13:v13091795. [PMID: 34578376 PMCID: PMC8472164 DOI: 10.3390/v13091795] [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: 08/06/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/17/2022] Open
Abstract
Rabies lyssavirus (RABV) is enzootic in raccoons across the eastern United States. Intensive management of RABV by oral rabies vaccination (ORV) has prevented its spread westward and shown evidence of local elimination in raccoon populations of the northeastern US. The USDA, Wildlife Services, National Rabies Management Program (NRMP) collaborates with other agencies to implement broad-scale ORV and conducts extensive monitoring to measure the effectiveness of the management. Enhanced Rabies Surveillance (ERS) was initiated during 2005 and updated in 2016 to direct surveillance efforts toward higher-value specimens by assigning points to different methods of encountering specimens for collection (strange-acting, roadkill, surveillance-trapped, etc.; specimen point values ranged from 1 to 15). We used the 2016–2019 data to re-evaluate the point values using a dynamic occupancy model. Additionally, we used ERS data from 2012–2015 and 2016–2019 to examine the impact that the point system had on surveillance data. Implementation of a point system increased positivity rates among specimens by 64%, indicating a substantial increase in the efficiency of the ERS to detect wildlife rabies. Our re-evaluation found that most points accurately reflect the value of the surveillance specimens. The notable exception was that samples from animals found dead were considerably more valuable for rabies detection than originally considered (original points = 5, new points = 20). This work demonstrates how specimen prioritization strategies can be used to refine and improve ERS in support of wildlife rabies management.
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Nahata KD, Bollen N, Gill MS, Layan M, Bourhy H, Dellicour S, Baele G. On the Use of Phylogeographic Inference to Infer the Dispersal History of Rabies Virus: A Review Study. Viruses 2021; 13:v13081628. [PMID: 34452492 PMCID: PMC8402743 DOI: 10.3390/v13081628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/28/2022] Open
Abstract
Rabies is a neglected zoonotic disease which is caused by negative strand RNA-viruses belonging to the genus Lyssavirus. Within this genus, rabies viruses circulate in a diverse set of mammalian reservoir hosts, is present worldwide, and is almost always fatal in non-vaccinated humans. Approximately 59,000 people are still estimated to die from rabies each year, leading to a global initiative to work towards the goal of zero human deaths from dog-mediated rabies by 2030, requiring scientific efforts from different research fields. The past decade has seen a much increased use of phylogeographic and phylodynamic analyses to study the evolution and spread of rabies virus. We here review published studies in these research areas, making a distinction between the geographic resolution associated with the available sequence data. We pay special attention to environmental factors that these studies found to be relevant to the spread of rabies virus. Importantly, we highlight a knowledge gap in terms of applying these methods when all required data were available but not fully exploited. We conclude with an overview of recent methodological developments that have yet to be applied in phylogeographic and phylodynamic analyses of rabies virus.
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Affiliation(s)
- Kanika D. Nahata
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
- Correspondence:
| | - Nena Bollen
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
| | - Mandev S. Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
| | - Maylis Layan
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Sorbonne Université, UMR2000, CNRS, 75015 Paris, France;
| | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, 75015 Paris, France;
- WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, 75015 Paris, France
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
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Melyantono SE, Susetya H, Widayani P, Tenaya IWM, Hartawan DHW. The rabies distribution pattern on dogs using average nearest neighbor analysis approach in the Karangasem District, Bali, Indonesia, in 2019. Vet World 2021; 14:614-624. [PMID: 33935406 PMCID: PMC8076469 DOI: 10.14202/vetworld.2021.614-624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 01/25/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND AND AIM Rabies is a severe progressive encephalitis disease in dogs characterized as a zoonosis. The transmission of rabies between animals in Karangasem District, Bali is still high and continues until today; therefore, rabies in the district still actively circulating. The distribution pattern of rabies, especially in the district, is unknown. This research aimed to describe the spatial distribution of rabies in Karangasem District. The information would help in developing effective control strategies for the disease. MATERIALS AND METHODS An observational study was carried out using 38 positive rabies cases confirmed by the direct fluorescent antibody test diagnosed at the Disease Investigation Centre of Denpasar from September 2018 to September 2019. The Global Positioning System was used to take the geographical coordinates of the places where positive rabies cases had been confirmed in Karangasem District. The ArcGIS version 10.3 (ESRI) was used to determine and analyze the distribution pattern using the average nearest neighbor (ANN) method. RESULTS On the basis of the ANN analysis, the rabies distribution pattern in Karangasem District in 2019 was clustered in groups but not significant (Z-score=-1.670309 [<-1.65], p=0.094858 [<0.1]; nearest neighbor ratio=0.858364). The rabies distribution pattern in each subdistrict of Karangasem was dispersed significantly since it had z-score of more than 2.58, p-value less than 0.1 and nearest neighbor ratio of more than 1. CONCLUSION The rabies distribution in Karangasem District had a clustered pattern, although this was not significant. The grouping of rabies in Karangasem District showed a significant dispersed pattern in the subdistricts Abang, Bebandem, and Karangasem. The dispersed pattern of the rabies cases in the subdistricts was caused by unidentified stray dogs that lived in rice fields and other fields and by the whole district's hilly and mountainous topography. The ANN analysis suggested that for rabies control in Karangasem District, vaccination, elimination, and sterilization of stray dogs should be conducted in densely populated areas.
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Affiliation(s)
| | - Heru Susetya
- Department of Epidemiology and Veterinary Public Health, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta, Indonesia
| | - Prima Widayani
- Department of Geographical Information Science, Faculty of Geography, Gadjah Mada University, Yogyakarta, Indonesia
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Pepin KM, Miller RS, Wilber MQ. A framework for surveillance of emerging pathogens at the human-animal interface: Pigs and coronaviruses as a case study. Prev Vet Med 2021; 188:105281. [PMID: 33530012 PMCID: PMC7839430 DOI: 10.1016/j.prevetmed.2021.105281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/09/2020] [Accepted: 01/19/2021] [Indexed: 12/13/2022]
Abstract
Pigs (Sus scrofa) may be important surveillance targets for risk assessment and risk-based control planning against emerging zoonoses. Pigs have high contact rates with humans and other animals, transmit similar pathogens as humans including CoVs, and serve as reservoirs and intermediate hosts for notable human pandemics. Wild and domestic pigs both interface with humans and each other but have unique ecologies that demand different surveillance strategies. Three fundamental questions shape any surveillance program: where, when, and how can surveillance be conducted to optimize the surveillance objective? Using theory of mechanisms of zoonotic spillover and data on risk factors, we propose a framework for determining where surveillance might begin initially to maximize a detection in each host species at their interface. We illustrate the utility of the framework using data from the United States. We then discuss variables to consider in refining when and how to conduct surveillance. Recent advances in accounting for opportunistic sampling designs and in translating serology samples into infection times provide promising directions for extracting spatio-temporal estimates of disease risk from typical surveillance data. Such robust estimates of population-level disease risk allow surveillance plans to be updated in space and time based on new information (adaptive surveillance) thus optimizing allocation of surveillance resources to maximize the quality of risk assessment insight.
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Affiliation(s)
- Kim M Pepin
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, 4101 Laporte Ave., Fort Collins, CO, 80526, United States.
| | - Ryan S Miller
- Centers for Epidemiology and Animal Health, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, 2150 Center Ave., Fort Collins, CO, 80526, United States
| | - Mark Q Wilber
- Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, 93106, United States
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Pepin KM, Golnar A, Podgórski T. Social structure defines spatial transmission of African swine fever in wild boar. J R Soc Interface 2021; 18:20200761. [PMID: 33468025 DOI: 10.1098/rsif.2020.0761] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The spatial spread of infectious disease is determined by spatial and social processes such as animal space use and family group structure. Yet, the impacts of social processes on spatial spread remain poorly understood and estimates of spatial transmission kernels (STKs) often exclude social structure. Understanding the impacts of social structure on STKs is important for obtaining robust inferences for policy decisions and optimizing response plans. We fit spatially explicit transmission models with different assumptions about contact structure to African swine fever virus surveillance data from eastern Poland from 2014 to 2015 and evaluated how social structure affected inference of STKs and spatial spread. The model with social structure provided better inference of spatial spread, predicted that approximately 80% of transmission events occurred within family groups, and that transmission was weakly female-biased (other models predicted weakly male-biased transmission). In all models, most transmission events were within 1.5 km, with some rare events at longer distances. Effective reproductive numbers were between 1.1 and 2.5 (maximum values between 4 and 8). Social structure can modify spatial transmission dynamics. Accounting for this additional contact heterogeneity in spatial transmission models could provide more robust inferences of STKs for policy decisions, identify best control targets and improve transparency in model uncertainty.
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Affiliation(s)
- Kim M Pepin
- National Wildlife Research Center, USDA, APHIS, Wildlife Services, 4101 Laporte Avenue, Fort Collins, CO 80526, USA
| | - Andrew Golnar
- National Wildlife Research Center, USDA, APHIS, Wildlife Services, 4101 Laporte Avenue, Fort Collins, CO 80526, USA
| | - Tomasz Podgórski
- Mammal Research Institute, Polish Academy of Sciences, Stoczek 1, 17-230 Białowieża, Poland.,Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamýcká 129, 165 00 Praha 6, Czech Republic
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Davis AJ, Kirby JD, Chipman RB, Nelson KM, Xifara T, Webb CT, Wallace R, Gilbert AT, Pepin KM. Not all surveillance data are created equal—A multi‐method dynamic occupancy approach to determine rabies elimination from wildlife. J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13477] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Amy J. Davis
- United States Department of Agriculture, Animal and Plant Health Inspection Service Wildlife Services National Wildlife Research Center Fort Collins CO USA
| | - Jordona D. Kirby
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Rabies Management Program Concord NH USA
| | - Richard B. Chipman
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Rabies Management Program Concord NH USA
| | - Kathleen M. Nelson
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Rabies Management Program Concord NH USA
| | - Tatiana Xifara
- United States Department of Agriculture, Animal and Plant Health Inspection Service Wildlife Services National Wildlife Research Center Fort Collins CO USA
- Department of Biology Colorado State University Fort Collins CO USA
| | - Colleen T. Webb
- Department of Biology Colorado State University Fort Collins CO USA
| | - Ryan Wallace
- Centers for Disease Control and Prevention Atlanta GA USA
| | - Amy T. Gilbert
- United States Department of Agriculture, Animal and Plant Health Inspection Service Wildlife Services National Wildlife Research Center Fort Collins CO USA
| | - Kim M. Pepin
- United States Department of Agriculture, Animal and Plant Health Inspection Service Wildlife Services National Wildlife Research Center Fort Collins CO USA
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Newton EJ, Pond BA, Tinline RR, Middel K, Bélanger D, Rees EE. Differential impacts of vaccination on wildlife disease spread during epizootic and enzootic phases. J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Erica J. Newton
- Wildlife Research and Monitoring SectionOntario Ministry of Natural Resources and ForestryTrent University Peterborough ON Canada
| | - Bruce A. Pond
- Wildlife Research and Monitoring SectionOntario Ministry of Natural Resources and ForestryTrent University Peterborough ON Canada
| | | | - Kevin Middel
- Wildlife Research and Monitoring SectionOntario Ministry of Natural Resources and ForestryTrent University Peterborough ON Canada
| | - Denise Bélanger
- Département de pathologie et microbiologieGroupe de recherche en épidémiologie des zoonoses et santé publiqueUniversité de Montréal Saint‐Hyacinthe QC Canada
| | - Erin E. Rees
- Département de pathologie et microbiologieGroupe de recherche en épidémiologie des zoonoses et santé publiqueUniversité de Montréal Saint‐Hyacinthe QC Canada
- Public Health Risk Sciences DivisionNational Microbiology LaboratoryPublic Health Agency of Canada Saint‐Hyacinthe Québec Canada
- Land and Sea Systems Analysis Inc. Granby QC Canada
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Isolation of Rabies Virus from the Salivary Glands of Wild and Domestic Carnivores during a Skunk Rabies Epizootic. J Wildl Dis 2018; 55:473-476. [PMID: 30226803 DOI: 10.7589/2018-05-127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Rabies is a fatal zoonotic disease of global importance. Rabies virus is shed in the saliva of infected hosts and is primarily transmitted through bite contact. Canine rabies has been eliminated from the US, but wildlife constitutes more than 90% of the reported cases of animal rabies in the US each year. In the US, several wild carnivore species are reservoirs of distinct variants of rabies virus (RV). After decades of apparent absence, the south-central skunk (SCSK) RV variant was detected in Colorado in 2007 and resulted in a large-scale epizootic in striped skunk ( Mephitis mephitis) populations in northern Colorado starting in 2012. We attempted isolation of RV from salivary gland tissues from confirmed rabid carnivores, comprising 51 striped skunks and seven other wild and domestic carnivores collected during 2013 through 2015 in northern Colorado. We isolated RV from 84.0% (158/188; 95% confidence interval=78.1-88.6%) of striped skunk and 71% (17/24; 95% confidence interval =51-85%) of other carnivore salivary glands. These data suggested that infected reservoir and vector species were equally likely to shed the SCSK RV variant and posed a secondary transmission risk to humans and other animals.
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EVIDENCE OF TWO COCIRCULATING CANINE DISTEMPER VIRUS STRAINS IN MESOCARNIVORES FROM NORTHERN COLORADO, USA. J Wildl Dis 2018; 54:534-543. [PMID: 29498900 DOI: 10.7589/2017-09-238] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Canine distemper virus (CDV) is a highly contagious pathogen that principally infects wildlife and domestic carnivores. Peridomestic species such as raccoons ( Procyon lotor) experience outbreaks with high mortality. Clinical signs of infection include anorexia, fever, respiratory infection, and neurologic complications. Although not zoonotic, CDV poses a high risk to unvaccinated domestic animals and the conservation of endangered species. During 2013-16, we opportunistically collected wild and domestic carnivore specimens through a rabies surveillance program in northern Colorado, US. Brainstem and cerebellar tissue samples were independently tested for rabies and CDV by fluorescent antibody test. We tested a total of 478 animals for CDV, comprised of 10 wild and domestic carnivore species. A total of 15% (72/478) of all animals sampled tested positive for CDV, consisting of 24% (71/300) of raccoons and 4% (1/26) of coyotes ( Canis latrans), but coinfection with rabies virus was not observed among CDV-positive animals. We extracted RNA from positive tissues, and a reverse-transcription PCR was used to create complementary DNA. We amplified and sequenced the hemagglutinin gene from 60 CDV-positive tissues, and a median joining network and maximum likelihood phylogenetic tree revealed two major lineages among samples. Phylogenetic analysis indicated that our sequences were most similar to the America-2 ( n=55) and the America-3 ( n=5) CDV lineages circulating in North America. Our results indicated two distinct and distantly related clades of CDV overlapping geographically and temporally among raccoon populations in northern Colorado.
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