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Deviatkin AA, Vakulenko YA, Dashian MA, Lukashev AN. Evaluating the Impact of Anthropogenic Factors on the Dissemination of Contemporary Cosmopolitan, Arctic, and Arctic-like Rabies Viruses. Viruses 2021; 14:66. [PMID: 35062270 PMCID: PMC8777955 DOI: 10.3390/v14010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Rabies is a globally prevalent viral zoonosis that causes 59,000 deaths per year and has important economic consequences. Most virus spread is associated with the migration of its primary hosts. Anthropogenic dissemination, mainly via the transportation of rabid dogs, shaped virus ecology a few hundred years ago and is responsible for several current outbreaks. A systematic analysis of aberrant long-distance events in the steppe and Arctic-like groups of rabies virus was performed using statistical (Bayesian) phylogeography and plots of genetic vs. geographic distances. The two approaches produced similar results but had some significant differences and complemented each other. No phylogeographic analysis could be performed for the Arctic group because polar foxes transfer the virus across the whole circumpolar region at high velocity, and there was no correlation between genetic and geographic distances in this virus group. In the Arctic-like group and the steppe subgroup of the cosmopolitan group, a significant number of known sequences (15-20%) was associated with rapid long-distance transfers, which mainly occurred within Eurasia. Some of these events have been described previously, while others have not been documented. Most of the recent long-distance transfers apparently did not result in establishing the introduced virus, but a few had important implications for the phylogeographic history of rabies. Thus, human-mediated long-distance transmission of the rabies virus remains a significant threat that needs to be addressed.
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Affiliation(s)
- Andrei A. Deviatkin
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
- The National Medical Research Center for Endocrinology, 117036 Moscow, Russia
| | - Yulia A. Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (Y.A.V.); (A.N.L.)
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Mariia A. Dashian
- Faculty of Biomedicine, Pirogov Medical University, 117997 Moscow, Russia;
| | - Alexander N. Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (Y.A.V.); (A.N.L.)
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Hyeon JY, Risatti GR, Helal ZH, McGinnis H, Sims M, Hunt A, Chung DH, Kim J, Desiato J, Lee DH. Whole Genome Sequencing and Phylogenetic Analysis of Rabies Viruses from Bats in Connecticut, USA, 2018-2019. Viruses 2021; 13:v13122500. [PMID: 34960769 PMCID: PMC8704678 DOI: 10.3390/v13122500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/04/2021] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
We performed whole genome sequencing and genetic characterization of rabies viruses (RABV) detected in bats submitted to the Connecticut Veterinary Medical Diagnostic Laboratory (CVMDL) during 2018–2019. Among 88 bats submitted to CVMDL, six brain samples (6.8%, 95% confidence interval: 1.6% to 12.1%) tested positive by direct fluorescent antibody test. RABVs were detected in big brown bats (Eptesicus fuscus, n = 4), a hoary bat (Lasiurus cinereus, n = 1), and an unidentified bat species (n = 1). Complete coding sequences of four out of six detected RABVs were obtained. In phylogenetic analysis, the RABVs (18-62, 18-4347, and 19-2274) from big brown bats belong to the bats EF-E1 clade, clustering with RABVs detected from the same bat species in Pennsylvania and New Jersey. The bat RABV (19-2898) detected from the migratory hoary bat belongs to the bats LC clade, clustering with the eleven viruses detected from the same species in Arizona, Washington, Idaho, and Tennessee. The approach used in this study generated novel data regarding genetic relationships of RABV variants, including their reservoirs, and their spatial origin and it would be useful as reference data for future investigations on RABV in North America. Continued surveillance and genome sequencing of bat RABV would be needed to monitor virus evolution and transmission, and to assess the emergence of genetic mutations that may be relevant for public health.
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Affiliation(s)
- Ji-Yeon Hyeon
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (J.-Y.H.); (G.R.R.); (Z.H.H.); (H.M.); (M.S.); (A.H.)
| | - Guillermo R. Risatti
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (J.-Y.H.); (G.R.R.); (Z.H.H.); (H.M.); (M.S.); (A.H.)
| | - Zeinab H. Helal
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (J.-Y.H.); (G.R.R.); (Z.H.H.); (H.M.); (M.S.); (A.H.)
| | - Holly McGinnis
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (J.-Y.H.); (G.R.R.); (Z.H.H.); (H.M.); (M.S.); (A.H.)
| | - Maureen Sims
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (J.-Y.H.); (G.R.R.); (Z.H.H.); (H.M.); (M.S.); (A.H.)
| | - Amelia Hunt
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (J.-Y.H.); (G.R.R.); (Z.H.H.); (H.M.); (M.S.); (A.H.)
| | - David H. Chung
- Genomics and Molecular Epidemiology Research Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (D.H.C.); (J.K.); (J.D.)
| | - Junwon Kim
- Genomics and Molecular Epidemiology Research Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (D.H.C.); (J.K.); (J.D.)
| | - Julia Desiato
- Genomics and Molecular Epidemiology Research Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (D.H.C.); (J.K.); (J.D.)
| | - Dong-Hun Lee
- Genomics and Molecular Epidemiology Research Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (D.H.C.); (J.K.); (J.D.)
- Correspondence: ; Tel.: +1-860-486-1138
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Caraballo DA, Lema C, Novaro L, Gury-Dohmen F, Russo S, Beltrán FJ, Palacios G, Cisterna DM. A Novel Terrestrial Rabies Virus Lineage Occurring in South America: Origin, Diversification, and Evidence of Contact between Wild and Domestic Cycles. Viruses 2021; 13:v13122484. [PMID: 34960753 PMCID: PMC8707302 DOI: 10.3390/v13122484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/30/2021] [Accepted: 12/09/2021] [Indexed: 12/25/2022] Open
Abstract
The rabies virus (RABV) is characterized by a history dominated by host shifts within and among bats and carnivores. One of the main outcomes of long-term RABV maintenance in dogs was the establishment of variants in a wide variety of mesocarnivores. In this study, we present the most comprehensive phylogenetic and phylogeographic analysis, contributing to a better understanding of the origins, diversification, and the role of different host species in the evolution and diffusion of a dog-related variant endemic of South America. A total of 237 complete Nucleoprotein gene sequences were studied, corresponding to wild and domestic species, performing selection analyses, ancestral states reconstructions, and recombination analyses. This variant originated in Brazil and disseminated through Argentina and Paraguay, where a previously unknown lineage was found. A single host shift was identified in the phylogeny, from dog to the crab-eating fox (Cerdocyon thous) in the Northeast of Brazil. Although this process occurred in a background of purifying selection, there is evidence of adaptive evolution -or selection of sub-consensus sequences- in internal branches after the host shift. The interaction of domestic and wild cycles persisted after host switching, as revealed by spillover and putative recombination events.
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Affiliation(s)
- Diego A. Caraballo
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), CONICET-Universidad de Buenos Aires, Ciudad Universitaria-Pabellón II, Buenos Aires C1428EHA, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1053ABH, Argentina
- Correspondence:
| | - Cristina Lema
- Servicio de Neurovirosis, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Instituto Nacional de Enfermedades Infecciosas, “Dr. Carlos G. Malbrán”, Av. Vélez Sarsfield 563, Buenos Aires C1282AFF, Argentina; (C.L.); (D.M.C.)
| | - Laura Novaro
- DILAB, SENASA, Av. Paseo Colón 367, Buenos Aires C1063ACD, Argentina; (L.N.); (S.R.)
| | - Federico Gury-Dohmen
- Instituto de Zoonosis “Dr. Luis Pasteur”, Av. Díaz Vélez 4821, Buenos Aires C1405DCD, Argentina; (F.G.-D.); (F.J.B.)
| | - Susana Russo
- DILAB, SENASA, Av. Paseo Colón 367, Buenos Aires C1063ACD, Argentina; (L.N.); (S.R.)
| | - Fernando J. Beltrán
- Instituto de Zoonosis “Dr. Luis Pasteur”, Av. Díaz Vélez 4821, Buenos Aires C1405DCD, Argentina; (F.G.-D.); (F.J.B.)
| | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Daniel M. Cisterna
- Servicio de Neurovirosis, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Instituto Nacional de Enfermedades Infecciosas, “Dr. Carlos G. Malbrán”, Av. Vélez Sarsfield 563, Buenos Aires C1282AFF, Argentina; (C.L.); (D.M.C.)
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Bouslama Z, Kharmachi H, Basdouri N, Ben Salem J, Ben Maiez S, Handous M, Saadi M, Ghram A, Turki I. Molecular Epidemiology of Rabies in Wild Canidae in Tunisia. Viruses 2021; 13:v13122473. [PMID: 34960742 PMCID: PMC8703460 DOI: 10.3390/v13122473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 12/25/2022] Open
Abstract
Rabies is a viral zoonosis that is transmissible to humans via domestic and wild animals. There are two epidemiological cycles for rabies, the urban and the sylvatic cycles. In an attempt to study the epidemiological role of wild canidae in rabies transmission, the present study aimed to analyze the genetic characteristics of virus isolates and confirm prior suggestions that rabies is maintained through a dog reservoir in Tunisia. Virus strains isolated from wild canidae were subject to viral sequencing, and Bayesian phylogenetic analysis was performed using Beast2 software. Essentially, the virus strains isolated from wild canidae belonged to the Africa-1 clade, which clearly diverges from fox-related strains. Our study also demonstrated that genetic characteristics of the virus isolates were not as distinct as could be expected if a wild reservoir had already existed. On the contrary, the geographic landscape is responsible for the genetic diversity of the virus. The landscape itself could have also acted as a natural barrier to the spread of the virus.
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Affiliation(s)
- Zied Bouslama
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
- Faculty of Sciences, Université Tunis El Manar, Tunis 2092, Tunisia
- Correspondence:
| | - Habib Kharmachi
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Nourhene Basdouri
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Jihen Ben Salem
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Samia Ben Maiez
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Mariem Handous
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Mohamed Saadi
- Laboratory for Rabies Diagnostics, Institute Pasteur of Tunis, Belvedere, Tunis 1002, Tunisia; (H.K.); (N.B.); (J.B.S.); (S.B.M.); (M.H.); (M.S.)
| | - Abdeljalil Ghram
- Laboratory of Epidemiology and Veterinary Microbiology, LR 16 IPT 03, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 2092, Tunisia;
| | - Imed Turki
- Service des Maladies Contagieuses, Ecole Nationale de Médecine Vétérinaire-Sidi Thabet, Université Manouba, Sidi Thabet 2020, Tunisia;
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Browne AS, Cranford HM, Morgan CN, Ellison JA, Berentsen A, Wiese N, Medley A, Rossow J, Jankelunas L, McKinley AS, Lombard CD, Angeli NF, Kelley T, Valiulus J, Bradford B, Burke-France VJ, Harrison CJ, Guendel I, Taylor M, Blanchard GL, Doty JB, Worthington DJ, Horner D, Garcia KR, Roth J, Ellis BR, Bisgard KM, Wallace R, Ellis EM. Determination of freedom-from-rabies for small Indian mongoose populations in the United States Virgin Islands, 2019-2020. PLoS Negl Trop Dis 2021; 15:e0009536. [PMID: 34264951 PMCID: PMC8282080 DOI: 10.1371/journal.pntd.0009536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/03/2021] [Indexed: 11/29/2022] Open
Abstract
Mongooses, a nonnative species, are a known reservoir of rabies virus in the Caribbean region. A cross-sectional study of mongooses at 41 field sites on the US Virgin Islands of St. Croix, St. John, and St. Thomas captured 312 mongooses (32% capture rate). We determined the absence of rabies virus by antigen testing and rabies virus exposure by antibody testing in mongoose populations on all three islands. USVI is the first Caribbean state to determine freedom-from-rabies for its mongoose populations with a scientifically-led robust cross-sectional study. Ongoing surveillance activities will determine if other domestic and wildlife populations in USVI are rabies-free. Mongooses in the Caribbean region are known to carry rabies and infect and kill humans with the deadly virus. While many countries in the Caribbean region assume they are rabies-free, there is a lack of scientifically based surveillance. We prospectively designed a statistically valid study to determine that mongoose populations in the US Virgin Islands are rabies-free and pose no risk of transmission to human or animal populations. We are pursuing further surveillance efforts to establish rabies freedom in all wildlife and domestic animal population in the US Virgin Islands.
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Affiliation(s)
- A. Springer Browne
- Epidemic Intelligence Service, Division of Scientific Education and Professional Development, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- US Virgin Islands Department of Health, Christiansted, US Virgin Islands, United States of America
- * E-mail:
| | - Hannah M. Cranford
- US Virgin Islands Department of Health, Christiansted, US Virgin Islands, United States of America
| | - Clint N. Morgan
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - James A. Ellison
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Are Berentsen
- National Wildlife Research Center, APHIS Wildlife Services, United States Department of Agriculture, Fort Collins, Colorado, United States of America
| | - Nicholas Wiese
- Laboratory Leadership Service, Division of Scientific Education and Professional Development, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Alexandra Medley
- Epidemic Intelligence Service, Division of Scientific Education and Professional Development, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - John Rossow
- Epidemic Intelligence Service, Division of Scientific Education and Professional Development, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Leanne Jankelunas
- Epidemiology Elective Program, Division of Scientific Education and Professional Development, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Alan S. McKinley
- Carribbean District, APHIS Wildlife Services, United States Department of Agriculture, Auburn, Alabama, United States of America
| | - Claudia D. Lombard
- Sandy Point National Wildlife Refuge, US Fish & Wildlife Service, Fredericksted, US Virgin Islands, United States of America
| | - Nicole F. Angeli
- US Virgin Islands Department of Planning and Natural Resources, Fredericksted, US Virgin Islands, United States of America
| | - Thomas Kelley
- National Park Service, St. John, US Virgin Islands, United States of America
| | - Jennifer Valiulus
- St. Croix Environmental Association, Christiansted, US Virgin Islands, United States of America
| | - Bethany Bradford
- US Virgin Islands Department of Agriculture, Kingshill, US Virgin Islands, United States of America
| | - Valicia J. Burke-France
- US Virgin Islands Department of Health, Christiansted, US Virgin Islands, United States of America
| | - Cosme J. Harrison
- US Virgin Islands Department of Health, Christiansted, US Virgin Islands, United States of America
| | - Irene Guendel
- US Virgin Islands Department of Health, Christiansted, US Virgin Islands, United States of America
| | - Marissa Taylor
- US Virgin Islands Department of Health, Christiansted, US Virgin Islands, United States of America
| | - Gerard L. Blanchard
- Carribbean District, APHIS Wildlife Services, United States Department of Agriculture, Auburn, Alabama, United States of America
| | - Jeffrey B. Doty
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - David Horner
- National Park Service, St. John, US Virgin Islands, United States of America
| | - Keith R. Garcia
- Carribbean District, APHIS Wildlife Services, United States Department of Agriculture, Auburn, Alabama, United States of America
| | - Joseph Roth
- US Virgin Islands Department of Health, Christiansted, US Virgin Islands, United States of America
| | - Brett R. Ellis
- US Virgin Islands Department of Health, Christiansted, US Virgin Islands, United States of America
| | - Kristine M. Bisgard
- Center for Surveillance, Epidemiology, and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Ryan Wallace
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Esther M. Ellis
- US Virgin Islands Department of Health, Christiansted, US Virgin Islands, United States of America
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AL-Eitan LN, Wu G, Golding M, Tang Y, Goharriz H, Marston DA, Fooks AR, McElhinney LM. Whole-genome sequencing and phylogenetic analysis of rabies viruses from Jordan. PLoS Negl Trop Dis 2021; 15:e0009431. [PMID: 34014930 PMCID: PMC8171950 DOI: 10.1371/journal.pntd.0009431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/02/2021] [Accepted: 04/30/2021] [Indexed: 12/21/2022] Open
Abstract
Human fatalities caused by rabies are rarely reported in Jordan; however, domestic animals are more likely to fall victim to rabies compared to wild animals, at least this is the case in Jordan due to the presence of canine rabies. In this study, twelve brain samples from domestic and wild animals suspected of being infected with rabies virus from different regions of Jordan were collected during 2019. Seven of them tested positive using the fluorescent antibody test and real-time SYBR RT-PCR assay. Five specimens were from stray dogs and two from foxes. The whole genome sequences were obtained from the positive samples. Sequence analysis showed that one dog virus from Al Quwaysimah city located in Amman governorate, was closely related to an Israeli strain belonging to a Cosmopolitan ME1a clade. The genomes of the remaining six viruses (four from dogs and two from foxes) collected from different areas of Jordan were genetically-related to each other and clustered together with sequences from Iran and Turkey; all belong to Cosmopolitan ME2 clade. These sequences were analyzed with six other Jordanian rabies virus nucleoprotein (N) gene sequences available in the public database, five of them belong to ME1a clade and one belongs to ME1b clade. Rabies virus whole genome data is scarce across the Middle East. This study provides a better understanding of the molecular epidemiology of rabies virus in the region. In this study, we performed whole genome sequencing (WGS) for rabies virus (RABV) isolates from seven samples, five of which were of stray dogs, and the other two were from foxes. Specimens were collected from animals across Jordan, including Balqa, Amman, Irbid, Tafilah, and Madaba governorates. Six out of the seven isolates were belonging to the Cosmopolitan ME2 clade, which related to the Iranian and Turkish sequences. This is not the case previously, where the majority of the Jordanian isolates belong to Cosmopolitan ME1a clade and closely related to the sequences from Israel. This shift might be due to the applied regulations across borders between Jordan and Israel. Besides the growth in travel and trade movement between Jordan and Turkey, where the latter is a border country with Iran. These collected data, where such studies are not common in the Middle East countries, will enhance our understanding of the RABV evolution and epidemiology in the region for rapid and effective response for rabies virus outbreaks.
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Affiliation(s)
- Laith N. AL-Eitan
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid, Jordan
- * E-mail:
| | - Guanghui Wu
- Animal and Plant Health Agency (APHA, Weybridge), Surrey, United Kingdom
| | - Megan Golding
- Animal and Plant Health Agency (APHA, Weybridge), Surrey, United Kingdom
| | - Yue Tang
- Animal and Plant Health Agency (APHA, Weybridge), Surrey, United Kingdom
| | - Hooman Goharriz
- Animal and Plant Health Agency (APHA, Weybridge), Surrey, United Kingdom
| | - Denise A. Marston
- Animal and Plant Health Agency (APHA, Weybridge), Surrey, United Kingdom
| | - Anthony R. Fooks
- Animal and Plant Health Agency (APHA, Weybridge), Surrey, United Kingdom
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Sauvé CC, Rees EE, Gilbert AT, Berentsen AR, Allibert A, Leighton PA. Modeling Mongoose Rabies in the Caribbean: A Model-Guided Fieldwork Approach to Identify Research Priorities. Viruses 2021; 13:v13020323. [PMID: 33672496 PMCID: PMC7923793 DOI: 10.3390/v13020323] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 12/25/2022] Open
Abstract
We applied the model-guided fieldwork framework to the Caribbean mongoose rabies system by parametrizing a spatially-explicit, individual-based model, and by performing an uncertainty analysis designed to identify parameters for which additional empirical data are most needed. Our analysis revealed important variation in output variables characterizing rabies dynamics, namely rabies persistence, exposure level, spatiotemporal distribution, and prevalence. Among epidemiological parameters, rabies transmission rate was the most influential, followed by rabies mortality and location, and size of the initial infection. The most influential landscape parameters included habitat-specific carrying capacities, landscape heterogeneity, and the level of resistance to dispersal associated with topography. Movement variables, including juvenile dispersal, adult fine-scale movement distances, and home range size, as well as life history traits such as age of independence, birth seasonality, and age- and sex-specific mortality were other important drivers of rabies dynamics. We discuss results in the context of mongoose ecology and its influence on disease transmission dynamics. Finally, we suggest empirical approaches and study design specificities that would provide optimal contributing data addressing the knowledge gaps identified by our approach, and would increase our potential to use epidemiological models to guide mongoose rabies control and management in the Caribbean.
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Affiliation(s)
- Caroline C. Sauvé
- Epidemiology of Zoonoses and Public Health Research Group (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, 3190 Rue Sicotte, Saint-Hyacinthe, QC J2S 2M2, Canada; (E.E.R.); (A.A.); (P.A.L.)
- Centre de Recherche en Santé Publique, 7101 Avenue du Parc, Montréal, QC H3N 1X9, Canada
- Correspondence:
| | - Erin E. Rees
- Epidemiology of Zoonoses and Public Health Research Group (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, 3190 Rue Sicotte, Saint-Hyacinthe, QC J2S 2M2, Canada; (E.E.R.); (A.A.); (P.A.L.)
- Centre de Recherche en Santé Publique, 7101 Avenue du Parc, Montréal, QC H3N 1X9, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, 3190 Rue Sicotte, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Amy T. Gilbert
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, United Sates Department of Agriculture, 4101 LaPorte Avenue, Fort Collins, CO 80521, USA; (A.T.G.); (A.R.B.)
| | - Are R. Berentsen
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, United Sates Department of Agriculture, 4101 LaPorte Avenue, Fort Collins, CO 80521, USA; (A.T.G.); (A.R.B.)
| | - Agathe Allibert
- Epidemiology of Zoonoses and Public Health Research Group (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, 3190 Rue Sicotte, Saint-Hyacinthe, QC J2S 2M2, Canada; (E.E.R.); (A.A.); (P.A.L.)
- Centre de Recherche en Santé Publique, 7101 Avenue du Parc, Montréal, QC H3N 1X9, Canada
| | - Patrick A. Leighton
- Epidemiology of Zoonoses and Public Health Research Group (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, 3190 Rue Sicotte, Saint-Hyacinthe, QC J2S 2M2, Canada; (E.E.R.); (A.A.); (P.A.L.)
- Centre de Recherche en Santé Publique, 7101 Avenue du Parc, Montréal, QC H3N 1X9, Canada
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Bergner LM, Mollentze N, Orton RJ, Tello C, Broos A, Biek R, Streicker DG. Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats. Viruses 2021; 13:252. [PMID: 33562073 PMCID: PMC7914986 DOI: 10.3390/v13020252] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/25/2021] [Accepted: 02/03/2021] [Indexed: 12/17/2022] Open
Abstract
The contemporary surge in metagenomic sequencing has transformed knowledge of viral diversity in wildlife. However, evaluating which newly discovered viruses pose sufficient risk of infecting humans to merit detailed laboratory characterization and surveillance remains largely speculative. Machine learning algorithms have been developed to address this imbalance by ranking the relative likelihood of human infection based on viral genome sequences, but are not yet routinely applied to viruses at the time of their discovery. Here, we characterized viral genomes detected through metagenomic sequencing of feces and saliva from common vampire bats (Desmodus rotundus) and used these data as a case study in evaluating zoonotic potential using molecular sequencing data. Of 58 detected viral families, including 17 which infect mammals, the only known zoonosis detected was rabies virus; however, additional genomes were detected from the families Hepeviridae, Coronaviridae, Reoviridae, Astroviridae and Picornaviridae, all of which contain human-infecting species. In phylogenetic analyses, novel vampire bat viruses most frequently grouped with other bat viruses that are not currently known to infect humans. In agreement, machine learning models built from only phylogenetic information ranked all novel viruses similarly, yielding little insight into zoonotic potential. In contrast, genome composition-based machine learning models estimated different levels of zoonotic potential, even for closely related viruses, categorizing one out of four detected hepeviruses and two out of three picornaviruses as having high priority for further research. We highlight the value of evaluating zoonotic potential beyond ad hoc consideration of phylogeny and provide surveillance recommendations for novel viruses in a wildlife host which has frequent contact with humans and domestic animals.
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Affiliation(s)
- Laura M. Bergner
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (N.M.); (R.B.); (D.G.S.)
- MRC–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; (R.J.O.); (A.B.)
| | - Nardus Mollentze
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (N.M.); (R.B.); (D.G.S.)
- MRC–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; (R.J.O.); (A.B.)
| | - Richard J. Orton
- MRC–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; (R.J.O.); (A.B.)
| | - Carlos Tello
- Association for the Conservation and Development of Natural Resources, Lima 15037, Peru;
- Yunkawasi, Lima 15049, Peru
| | - Alice Broos
- MRC–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; (R.J.O.); (A.B.)
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (N.M.); (R.B.); (D.G.S.)
| | - Daniel G. Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (N.M.); (R.B.); (D.G.S.)
- MRC–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; (R.J.O.); (A.B.)
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Zhao W, Su J, Zhao N, Liu J, Su S. Development of Monoclonal Antibodies for Detection of Conserved and Variable Epitopes of Large Protein of Rabies Virus. Viruses 2021; 13:v13020220. [PMID: 33572652 PMCID: PMC7911920 DOI: 10.3390/v13020220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/18/2021] [Accepted: 01/28/2021] [Indexed: 12/20/2022] Open
Abstract
Rabies virus (RABV) causes fatal neurological encephalitis and results in approximately 6000 human death cases worldwide every year. The large (L) protein of RABV, possessing conserved domains, is considered as the target for detection. In this study, three monoclonal antibodies (mAbs), designated as 3F3, 3A6 and L-C, against L protein were generated by using the recombinant truncated L protein (aa 1431-1754) and the epitopes were also identified using a series of overlapping truncated polypeptides for testing the reactivity of mAbs with different RABV strains. The 1479EIFSIP1484, 1659RALSK1663 and 1724VFNSL1728 were identified as the minimal linear epitopes recognized by mAbs 3F3, 3A6 and L-C, respectively. Amino acid alignment showed epitope 1724VFNSL1728 recognized by mAb L-C is completely conserved among RABV strains, indicating that mAb L-C could be used to detect all of the RABV strains. Epitope 1479EIFSIP1484 is highly conserved among RABV strains except for a P1484S substitution in a China I sub-lineage strain of Asian lineage, which eliminated the reactivity of the epitope with mAb 3F3. However, the epitope 1659RALSK1663 was only completely conserved in the Africa-2 and Indian lineages, and a single A1660T substitution, mainly appeared in strains of the China I belonging to Asian lineage and a Cosmopolitan lineage strain, still retained the reactivity of the epitope with mAb 3A6. While both A1660T and K1663R substitutions in a China I lineage strain, single K1663R/Q substitution in some China II strains of Asian lineage and some Arctic-like lineage strains and R1659Q mutation in a strain of Africa-3 lineage eliminated the reactivity of the epitope with mAb 3A6, suggesting mAb 3A6 could be used for differentiation of variable epitopes of some strains in different lineages. Thus, variability and conservation of the three epitopes of L protein showed the reactive difference of mAbs among RABV strains of different lineages. These results may facilitate future studies in development of detection methods for RABV infection, the structure and function of RABV L protein.
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Caraballo DA, Lombardo MA, Becker P, Sabio MS, Lema C, Martínez LM, Beltrán FJ, Li Y, Cisterna DM. Evaluation of Two Real-Time, TaqMan Reverse Transcription-PCR Assays for Detection of Rabies Virus in Circulating Variants from Argentina: Influence of Sequence Variation. Viruses 2020; 13:v13010023. [PMID: 33375530 PMCID: PMC7823378 DOI: 10.3390/v13010023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 11/16/2022] Open
Abstract
In rabies diagnosis, it is essential to count on a rapid test to give a quick response. The combined sensitivity and robustness of the TaqMan RT-PCR assays (qRT-PCR) have made these methods a valuable alternative for rabies virus (RABV) detection. We conducted a study to compare the applicability of two widely used qRT-PCR assays targeting the nucleoprotein gene (LysGT1 assay) and leader sequences (LN34 qRT-PCR assay) of RABV genomes, in all variants circulating in Argentina. A total of 44 samples obtained from bats, dogs, cattle, and horses, that were previously tested for rabies by FAT and conventional RT-PCR, were used in the study. All variants were successfully detected by the pan-lyssavirus LN34 qRT-PCR assay. The LysGT1 assay failed to detect three bat-related variants. We further sequenced the region targeted by LysGT1 and demonstrated that the presence of three or more mismatches with respect to the primers and probe sequences precludes viral detection. We conclude that the LysGT1 assay is prone to yield variant-dependent false-negative test results, and in consequence, the LN34 assay would ensure more effective detection of RABV in Argentina.
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Affiliation(s)
- Diego A. Caraballo
- Instituto de Zoonosis “Luis Pasteur”, Av. Díaz Vélez 4821, Ciudad Autónoma de Buenos Aires C1405DCD, Argentina; (M.A.L.); (P.B.); (F.J.B.)
- Correspondence:
| | - María A. Lombardo
- Instituto de Zoonosis “Luis Pasteur”, Av. Díaz Vélez 4821, Ciudad Autónoma de Buenos Aires C1405DCD, Argentina; (M.A.L.); (P.B.); (F.J.B.)
| | - Paula Becker
- Instituto de Zoonosis “Luis Pasteur”, Av. Díaz Vélez 4821, Ciudad Autónoma de Buenos Aires C1405DCD, Argentina; (M.A.L.); (P.B.); (F.J.B.)
| | - María S. Sabio
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), “Dr. Carlos G. Malbrán”, Av. Vélez Sarsfield 563, Ciudad Autónoma de Buenos Aires C1282AFF, Argentina; (M.S.S.); (C.L.); (L.M.M.); (D.M.C.)
| | - Cristina Lema
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), “Dr. Carlos G. Malbrán”, Av. Vélez Sarsfield 563, Ciudad Autónoma de Buenos Aires C1282AFF, Argentina; (M.S.S.); (C.L.); (L.M.M.); (D.M.C.)
| | - Leila M. Martínez
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), “Dr. Carlos G. Malbrán”, Av. Vélez Sarsfield 563, Ciudad Autónoma de Buenos Aires C1282AFF, Argentina; (M.S.S.); (C.L.); (L.M.M.); (D.M.C.)
| | - Fernando J. Beltrán
- Instituto de Zoonosis “Luis Pasteur”, Av. Díaz Vélez 4821, Ciudad Autónoma de Buenos Aires C1405DCD, Argentina; (M.A.L.); (P.B.); (F.J.B.)
| | - Yu Li
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30329, USA;
| | - Daniel M. Cisterna
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), “Dr. Carlos G. Malbrán”, Av. Vélez Sarsfield 563, Ciudad Autónoma de Buenos Aires C1282AFF, Argentina; (M.S.S.); (C.L.); (L.M.M.); (D.M.C.)
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12
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Gigante CM, Yale G, Condori RE, Costa NC, Long NV, Minh PQ, Chuong VD, Tho ND, Thanh NT, Thin NX, Hanh NTH, Wambura G, Ade F, Mito O, Chuchu V, Muturi M, Mwatondo A, Hampson K, Thumbi SM, Thomae BG, de Paz VH, Meneses S, Munyua P, Moran D, Cadena L, Gibson A, Wallace RM, Pieracci EG, Li Y. Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION. Viruses 2020; 12:v12111255. [PMID: 33158200 PMCID: PMC7694271 DOI: 10.3390/v12111255] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022] Open
Abstract
As countries with endemic canine rabies progress towards elimination by 2030, it will become necessary to employ techniques to help plan, monitor, and confirm canine rabies elimination. Sequencing can provide critical information to inform control and vaccination strategies by identifying genetically distinct virus variants that may have different host reservoir species or geographic distributions. However, many rabies testing laboratories lack the resources or expertise for sequencing, especially in remote or rural areas where human rabies deaths are highest. We developed a low-cost, high throughput rabies virus sequencing method using the Oxford Nanopore MinION portable sequencer. A total of 259 sequences were generated from diverse rabies virus isolates in public health laboratories lacking rabies virus sequencing capacity in Guatemala, India, Kenya, and Vietnam. Phylogenetic analysis provided valuable insight into rabies virus diversity and distribution in these countries and identified a new rabies virus lineage in Kenya, the first published canine rabies virus sequence from Guatemala, evidence of rabies spread across an international border in Vietnam, and importation of a rabid dog into a state working to become rabies-free in India. Taken together, our evaluation highlights the MinION's potential for low-cost, high volume sequencing of pathogens in locations with limited resources.
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Affiliation(s)
- Crystal M. Gigante
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (C.M.G.); (R.E.C.); (R.M.W.); (E.G.P.)
| | - Gowri Yale
- Mission Rabies, Tonca, Panjim, Goa 403001, India;
| | - Rene Edgar Condori
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (C.M.G.); (R.E.C.); (R.M.W.); (E.G.P.)
| | - Niceta Cunha Costa
- Disease Investigation Unit, Directorate of Animal Health and Veterinary Services, Patto, Panjim, Goa 403001, India;
| | - Nguyen Van Long
- Vietnam Department of Animal Health, Hanoi 100000, Vietnam; (N.V.L.); (P.Q.M.); (V.D.C.)
| | - Phan Quang Minh
- Vietnam Department of Animal Health, Hanoi 100000, Vietnam; (N.V.L.); (P.Q.M.); (V.D.C.)
| | - Vo Dinh Chuong
- Vietnam Department of Animal Health, Hanoi 100000, Vietnam; (N.V.L.); (P.Q.M.); (V.D.C.)
| | - Nguyen Dang Tho
- National Center for Veterinary Diseases, Hanoi 100000, Vietnam;
| | - Nguyen Tat Thanh
- Sub-Department of Animal Health, Phú Thọ Province 35000, Vietnam; (N.T.T.); (N.X.T.); (N.T.H.H.)
| | - Nguyen Xuan Thin
- Sub-Department of Animal Health, Phú Thọ Province 35000, Vietnam; (N.T.T.); (N.X.T.); (N.T.H.H.)
| | - Nguyen Thi Hong Hanh
- Sub-Department of Animal Health, Phú Thọ Province 35000, Vietnam; (N.T.T.); (N.X.T.); (N.T.H.H.)
| | - Gati Wambura
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi 00100, Kenya; (G.W.); (F.A.); (O.M.); (V.C.); (S.M.T.)
| | - Frederick Ade
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi 00100, Kenya; (G.W.); (F.A.); (O.M.); (V.C.); (S.M.T.)
| | - Oscar Mito
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi 00100, Kenya; (G.W.); (F.A.); (O.M.); (V.C.); (S.M.T.)
| | - Veronicah Chuchu
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi 00100, Kenya; (G.W.); (F.A.); (O.M.); (V.C.); (S.M.T.)
- Department of Public Health, Pharmacology and Toxicology, University of Nairobi, Nairobi 00100, Kenya
| | - Mathew Muturi
- Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi 00100, Kenya; (M.M.); (A.M.)
| | - Athman Mwatondo
- Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi 00100, Kenya; (M.M.); (A.M.)
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Samuel M. Thumbi
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi 00100, Kenya; (G.W.); (F.A.); (O.M.); (V.C.); (S.M.T.)
- University of Nairobi Institute of Tropical and Infectious Diseases, Nairobi 00100, Kenya
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA 99164, USA
| | - Byron G. Thomae
- Ministry of Agriculture Livestock and Food, Guatemala City 01013, Guatemala;
| | - Victor Hugo de Paz
- National Health Laboratory, MSPAS, Villa Nueva 01064, Guatemala; (V.H.d.P.); (S.M.)
| | - Sergio Meneses
- National Health Laboratory, MSPAS, Villa Nueva 01064, Guatemala; (V.H.d.P.); (S.M.)
| | - Peninah Munyua
- Division of Global Health Protection, Centers for Disease Control, Nairobi 00100, Kenya;
| | - David Moran
- University del Valle de Guatemala, Guatemala City 01015, Guatemala;
| | - Loren Cadena
- Division of Global Health Protection, Centers for Disease Control, Guatemala City 01001, Guatemala;
| | - Andrew Gibson
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, Division of Genetics and Genomics, The University of Edinburgh, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK;
| | - Ryan M. Wallace
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (C.M.G.); (R.E.C.); (R.M.W.); (E.G.P.)
| | - Emily G. Pieracci
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (C.M.G.); (R.E.C.); (R.M.W.); (E.G.P.)
| | - Yu Li
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (C.M.G.); (R.E.C.); (R.M.W.); (E.G.P.)
- Correspondence:
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13
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Ismail MZ, AL- Hamdi NK, AL- Amery AN, Marston DA, McElhinney L, Taylor E, del Rio Vilas V, Dadan TM, Fooks AR, Horton DL. Quantifying and mapping the burden of human and animal rabies in Iraq. PLoS Negl Trop Dis 2020; 14:e0008622. [PMID: 33090993 PMCID: PMC7580899 DOI: 10.1371/journal.pntd.0008622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 07/21/2020] [Indexed: 11/19/2022] Open
Abstract
Rabies was first reported in ancient Iraqi civilizations, yet it remains a poorly quantified and important public health threat in the region. Efforts to control rabies in Iraq including dog population control, and vaccination of livestock and dogs, have increased since 2010. Officially reported data on human rabies, dog bites, and animal rabies cases between 2012 and 2017 are analysed here to assess the effect of existing control efforts, to inform future strategies, and to highlight gaps in surveillance and reporting. The results of molecular characterization of 32 viruses from animal cases from throughout Iraq are presented, to improve the understanding of rabies dynamics in the animal reservoir. Although annual numbers of reported human cases were lower in the period between 2012 and 2017 than prior to 2010, human cases continue. There was a distinct gender and age bias among human cases with nine cases in males for every one female and twice as many cases in children than adults. Spatial clustering analysis and phylogenetic evidence suggests rabies is endemic throughout the country, with no regional variation in risk, but better surveillance and reporting is required to underpin control strategies.
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Affiliation(s)
- Mashair Z. Ismail
- Central Veterinary Laboratory, Veterinary Directorate, Baghdad, Iraq
| | | | - Ali N. AL- Amery
- Central Veterinary Laboratory, Veterinary Directorate, Baghdad, Iraq
| | - Denise A. Marston
- Animal and Plant Health Agency (APHA), Rabies and Viral Zoonoses Group, (WHO Collaborating Centre for the Characterisation of Rabies and Rabies-Related Viruses, OIE Reference Laboratory for Rabies), Weybridge, New Haw, Surrey, United Kingdom
| | - Lorraine McElhinney
- Animal and Plant Health Agency (APHA), Rabies and Viral Zoonoses Group, (WHO Collaborating Centre for the Characterisation of Rabies and Rabies-Related Viruses, OIE Reference Laboratory for Rabies), Weybridge, New Haw, Surrey, United Kingdom
- University of Liverpool, Institute of Infection & Global Health, Liverpool, United Kingdom
| | - Emma Taylor
- University of Surrey, School of Veterinary Medicine, Guildford, United Kingdom
| | | | - Thani M. Dadan
- Center for Disease Control, Zoonosis Section, Ministry of Health, Baghdad, Iraq
| | - Anthony R. Fooks
- Animal and Plant Health Agency (APHA), Rabies and Viral Zoonoses Group, (WHO Collaborating Centre for the Characterisation of Rabies and Rabies-Related Viruses, OIE Reference Laboratory for Rabies), Weybridge, New Haw, Surrey, United Kingdom
- University of Liverpool, Institute of Infection & Global Health, Liverpool, United Kingdom
- University of London, St George's Hospital Medical School, Institute for Infection and Immunity, London, United Kingdom
| | - Daniel L. Horton
- University of Surrey, School of Veterinary Medicine, Guildford, United Kingdom
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Takahashi T, Inukai M, Sasaki M, Potratz M, Jarusombuti S, Fujii Y, Nishiyama S, Finke S, Yamada K, Sakai H, Sawa H, Nishizono A, Sugiyama M, Ito N. Genetic and Phenotypic Characterization of a Rabies Virus Strain Isolated from a Dog in Tokyo, Japan in the 1940s. Viruses 2020; 12:v12090914. [PMID: 32825306 PMCID: PMC7552007 DOI: 10.3390/v12090914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/24/2022] Open
Abstract
The rabies virus strain Komatsugawa (Koma), which was isolated from a dog in Tokyo in the 1940s before eradication of rabies in Japan in 1957, is known as the only existent Japanese field strain (street strain). Although this strain potentially provides a useful model to study rabies pathogenesis, little is known about its genetic and phenotypic properties. Notably, this strain underwent serial passages in rodents after isolation, indicating the possibility that it may have lost biological characteristics as a street strain. In this study, to evaluate the utility of the Koma strain for studying rabies pathogenesis, we examined the genetic properties and in vitro and in vivo phenotypes. Genome-wide genetic analyses showed that, consistent with previous findings from partial sequence analyses, the Koma strain is closely related to a Russian street strain within the Arctic-related phylogenetic clade. Phenotypic examinations in vitro revealed that the Koma strain and the representative street strains are less neurotropic than the laboratory strains. Examination by using a mouse model demonstrated that the Koma strain and the street strains are more neuroinvasive than the laboratory strains. These findings indicate that the Koma strain retains phenotypes similar to those of street strains, and is therefore useful for studying rabies pathogenesis.
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Affiliation(s)
- Tatsuki Takahashi
- The United Graduate School of Veterinary Sciences, Gifu University, Gifu 501-1193, Japan; (T.T.); (H.S.); (M.S.)
| | - Maho Inukai
- Laboratory of Zoonotic Disease, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan; (M.I.); (S.N.)
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (M.S.); (H.S.)
| | - Madlin Potratz
- Institute of Molecular Virology and Cell Biology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, 17493 Greifswald, Germany; (M.P.); (S.F.)
| | - Supasiri Jarusombuti
- Graduate School of Bioagricultural Science, Nagoya University, Nagoya 464-8601, Japan;
| | - Yuji Fujii
- Joint Graduate School of Veterinary Sciences, Gifu University, Gifu 501-1193, Japan;
| | - Shoko Nishiyama
- Laboratory of Zoonotic Disease, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan; (M.I.); (S.N.)
| | - Stefan Finke
- Institute of Molecular Virology and Cell Biology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, 17493 Greifswald, Germany; (M.P.); (S.F.)
| | - Kentaro Yamada
- Department of Microbiology, Faculty of Medicine, Oita University, Oita 879-5593, Japan; (K.Y.); (A.N.)
| | - Hiroki Sakai
- The United Graduate School of Veterinary Sciences, Gifu University, Gifu 501-1193, Japan; (T.T.); (H.S.); (M.S.)
- Joint Graduate School of Veterinary Sciences, Gifu University, Gifu 501-1193, Japan;
- Laboratory of Veterinary Pathology, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
- Gifu Center for Highly Advanced Integration of Nanosciences and Life Sciences, Gifu University, Gifu 501-1193, Japan
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (M.S.); (H.S.)
| | - Akira Nishizono
- Department of Microbiology, Faculty of Medicine, Oita University, Oita 879-5593, Japan; (K.Y.); (A.N.)
| | - Makoto Sugiyama
- The United Graduate School of Veterinary Sciences, Gifu University, Gifu 501-1193, Japan; (T.T.); (H.S.); (M.S.)
- Laboratory of Zoonotic Disease, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan; (M.I.); (S.N.)
- Joint Graduate School of Veterinary Sciences, Gifu University, Gifu 501-1193, Japan;
| | - Naoto Ito
- The United Graduate School of Veterinary Sciences, Gifu University, Gifu 501-1193, Japan; (T.T.); (H.S.); (M.S.)
- Laboratory of Zoonotic Disease, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan; (M.I.); (S.N.)
- Joint Graduate School of Veterinary Sciences, Gifu University, Gifu 501-1193, Japan;
- Gifu Center for Highly Advanced Integration of Nanosciences and Life Sciences, Gifu University, Gifu 501-1193, Japan
- Correspondence: ; Tel.: +81-58-293-2949
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Nadin-Davis S, Buchanan T, Nituch L, Fehlner-Gardiner C. A long-distance translocation initiated an outbreak of raccoon rabies in Hamilton, Ontario, Canada. PLoS Negl Trop Dis 2020; 14:e0008113. [PMID: 32210439 PMCID: PMC7135350 DOI: 10.1371/journal.pntd.0008113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 04/06/2020] [Accepted: 02/04/2020] [Indexed: 11/22/2022] Open
Abstract
Despite proactive measures to prevent raccoon rabies entering Canada from the United States, several incursions of this disease have occurred. The largest outbreak, first reported in December 2015 in the city of Hamilton, Ontario, has resulted in the reporting of 449 animal cases as of December 31, 2018. Initial phylogenetic studies on the index case suggested that this outbreak was not due to local cross-border spread from the Niagara region of the United States where raccoon rabies has persisted for several years. Phylogenetic analysis of whole genome sequences of a viral collection from the Hamilton area and several US states indicates that a long-distance translocation of a diseased animal from southeastern New York State was responsible for this incursion. The role of the skunk as a potential secondary host supporting persistence and / or spread of the virus is also examined. Distinct variants of rabies virus are harbored by several wildlife species across North America. The variant associated with the raccoon host is especially problematic given its rapid spread throughout the eastern seaboard of the United States over the second half of the 20th century and the high population density of this species in urban habitats that raises the potential for disease spread to both companion animals and their owners. Accordingly, extensive efforts to control raccoon rabies have been undertaken at many jurisdictional levels. This study uses current methods of genome analysis to explore the origins of a raccoon rabies outbreak in and around the city of Hamilton, Ontario, Canada, located close to the border with western New York state. In contrast to previous Canadian outbreaks of raccoon rabies, which were due to cross-border spread of the virus, this study demonstrates that the incursion into the Hamilton area was the result of a long-distance animal translocation from south-eastern New York. The implications of this event for strategies to control raccoon rabies are discussed.
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Affiliation(s)
- Susan Nadin-Davis
- National Reference Laboratory for Rabies, Ottawa Laboratory–Fallowfield, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
- * E-mail:
| | - Tore Buchanan
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Trent University, Peterborough, Ontario, Canada
| | - Larissa Nituch
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Trent University, Peterborough, Ontario, Canada
| | - Christine Fehlner-Gardiner
- National Reference Laboratory for Rabies, Ottawa Laboratory–Fallowfield, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
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16
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Eze UU, Ngoepe EC, Anene BM, Ezeokonkwo RC, Nwosuh CI, Sabeta CT. Molecular Detection of Rabies Lyssaviruses from Dogs in Southeastern Nigeria: Evidence of TransboundaryTransmission of Rabies in West Africa. Viruses 2020; 12:v12020134. [PMID: 31979379 PMCID: PMC7077224 DOI: 10.3390/v12020134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/20/2019] [Accepted: 09/24/2019] [Indexed: 12/25/2022] Open
Abstract
Despite being the first country to register confirmed cases of Mokola and Lagos bat lyssaviruses (two very distant lyssaviruses), knowledge gaps, particularly on the molecular epidemiology of lyssaviruses, still exist in Nigeria. A total of 278 specimens were collected from dogs in southeastern Nigeria between October 2015 and July 2016, and 23 (8.3%) of these tested positive for lyssaviruses with the direct fluorescent antibody test (DFA). The lyssaviruses were genetically characterized by amplifying the highly conserved nucleoprotein (N) gene of the rabies lyssaviruses (RABVs) of the viral genome. Phylogenetic analyses of the nucleotide sequences showed that all the RABV sequences in this study were of the Africa-2 lineage. Our results demonstrated that transboundary transmission of rabies lyssavirus is a key event, given that one of the RABV sequences (MN196576) clustered with rabies variants from neighboring Niger Republic. Furthermore, three RABVs from dogs from Anambra State clustered separately forming a novel and distinct group. Our results demonstrated that transboundary transmission of RABLVs is a key driver in the spread of rabies in West Africa. In order for the successful control of this zoonotic disease, a multinational stepwise surveillance and elimination of rabies in Africa by 2030 is probably the solution for regional elimination.
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Affiliation(s)
- Ukamaka U Eze
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Nigeria, Nsukka 410001, Nigeria;
- Correspondence:
| | - Ernest C Ngoepe
- Agricultural Research Council-Onderstepoort Veterinary Institute, OIE Rabies Reference Laboratory, Onderstepoort 0110, South Africa; (E.C.N.); (C.T.S.)
| | - Boniface M Anene
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Nigeria, Nsukka 410001, Nigeria;
| | - Romanus C Ezeokonkwo
- Department of Veterinary Parasitology and Entomology, Faculty of Veterinary Medicine, University of Nigeria, Nsukka 41001, Nigeria;
| | - Chika I Nwosuh
- National Veterinary Research Institute, Vom, Plateau State 930103, Nigeria;
| | - Claude T Sabeta
- Agricultural Research Council-Onderstepoort Veterinary Institute, OIE Rabies Reference Laboratory, Onderstepoort 0110, South Africa; (E.C.N.); (C.T.S.)
- Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort 0110, South Africa
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17
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Calvelage S, Smreczak M, Orłowska A, Freuling CM, Müller T, Fehlner-Gardiner C, Nadin-Davis S, Höper D, Trębas P. Population- and Variant-Based Genome Analyses of Viruses from Vaccine-Derived Rabies Cases Demonstrate Product Specific Clusters and Unique Patterns. Viruses 2020; 12:v12010115. [PMID: 31963517 PMCID: PMC7020022 DOI: 10.3390/v12010115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 12/24/2022] Open
Abstract
Rabies in wildlife has been successfully controlled in parts of Europe and North America using oral rabies vaccination, i.e., the distribution of baits containing live-attenuated virus strains. Occasionally, these vaccines caused vaccine virus-induced rabies cases. To elucidate the mechanisms of genetic selection and the effect of viral populations on these rabies cases, a next generation sequencing approach as well as comprehensive data analyses of the genetic diversity of Street Alabama Dufferin (SAD) and ERA vaccine virus strains and vaccine-induced rabies cases from Canada and several European countries were conducted. As a result, twelve newly generated sets of sequencing data from Canada and Poland were added to a pool of previously investigated samples. While the population-based analysis showed a segregation of viruses of ERA vaccine-induced rabies cases from those of SAD Bern original (SAD Bernorig)-derived rabies cases, the in-depth variant analysis revealed three distinct combinations of selected variants for the ERA vaccine-induced cases, suggesting the presence of multiple replication-competent haplotypes in the investigated ERA-BHK21 vaccine. Our findings demonstrate the potential of a deep sequencing approach in combination with comprehensive analyses on the consensus, population, and variant level.
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Affiliation(s)
- Sten Calvelage
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (S.C.); (D.H.)
| | - Marcin Smreczak
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (M.S.); (A.O.); (P.T.)
| | - Anna Orłowska
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (M.S.); (A.O.); (P.T.)
| | - Conrad Martin Freuling
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany;
- Correspondence:
| | - Thomas Müller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany;
| | - Christine Fehlner-Gardiner
- National Reference Centre for Rabies, Ottawa Laboratory–Fallowfield, Canadian Food Inspection Agency, Ottawa, ON K2H 8P91, Canada; (C.F.-G.); (S.N.-D.)
| | - Susan Nadin-Davis
- National Reference Centre for Rabies, Ottawa Laboratory–Fallowfield, Canadian Food Inspection Agency, Ottawa, ON K2H 8P91, Canada; (C.F.-G.); (S.N.-D.)
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (S.C.); (D.H.)
| | - Paweł Trębas
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (M.S.); (A.O.); (P.T.)
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18
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Nadin-Davis SA, Fehlner-Gardiner C. Origins of the arctic fox variant rabies viruses responsible for recent cases of the disease in southern Ontario. PLoS Negl Trop Dis 2019; 13:e0007699. [PMID: 31490919 PMCID: PMC6750613 DOI: 10.1371/journal.pntd.0007699] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 09/18/2019] [Accepted: 08/12/2019] [Indexed: 01/03/2023] Open
Abstract
A subpopulation of the arctic fox lineage of rabies virus has circulated extensively in red fox populations of Ontario, Canada, between the 1960s and 1990s. An intensive wildlife rabies control program, in which field operations were initiated in 1989, resulted in elimination of the disease in eastern Ontario. However in southwestern Ontario, as numbers of rabid foxes declined the proportion of skunks confirmed to be infected with this rabies virus variant increased and concerted control efforts targeting this species were employed to eliminate the disease. Since 2012 no cases due to this viral variant were reported in southwestern Ontario until 2015 when a single case of rabies due to the arctic fox variant was reported in a bovine. Several additional cases have been documented subsequently. Since routine antigenic typing cannot discriminate between the variants which previously circulated in Ontario and those from northern Canada it was unknown whether these recent cases were the result of a new introduction of this variant or a continuation of the previous enzootic. To explore the origins of this new outbreak whole genome sequences of a collection of 128 rabies viruses recovered from Ontario between the 1990s to the present were compared with those representative of variants circulating in the Canadian north. Phylogenetic analysis shows that the variant responsible for current cases in southwestern Ontario has evolved from those variants known to circulate in Ontario previously and is not due to a new introduction from northern regions. Thus despite ongoing passive surveillance the persistence of wildlife rabies went undetected in the study area for almost three years. The apparent adaptation of this rabies virus variant to the skunk host provided the opportunity to explore coding changes in the viral genome which might be associated with this host shift. Several such changes were identified including a subset for which the operation of positive selection was supported. The location of a small number of these amino acid substitutions in or close to protein motifs of functional importance suggests that some of them may have played a role in this host shift. Rabies, a serious disease which almost invariably results in death once clinical signs appear, is caused by the rabies virus. The arctic fox lineage of rabies virus persists in fox populations in northern Canada and from the 1960s onwards a sub-population of this virus has circulated in red foxes in the province of Ontario, Canada. By 2000 a provincial wildlife control program attempting to control fox rabies in southern Ontario had eliminated the disease in most of the targeted regions except for a focus of rabies in certain counties in southwestern Ontario which involved mostly skunks. Modified control efforts resulted in apparent rabies elimination with no cases reported in southern Ontario after May 2012 until a rabid bovine was identified in December 2015. Additional cases, mostly in skunks and livestock, have been reported subsequently. To discriminate between a re-introduction of the virus from the north and re-emergence of the Ontario viral variant, we sequenced and compared the genome of multiple viruses from both areas. The sequence data indicate that sub-types of the Ontario variant which eluded control efforts are responsible for these recent cases. These data also permit an examination of potential genetic changes in the virus that may facilitate its circulation in this new wildlife host, the skunk.
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Affiliation(s)
- Susan A. Nadin-Davis
- National Reference Laboratory for Rabies, Ottawa Laboratory–Fallowfield, Canadian Food Inspection Agency, Ottawa, Ontario
- * E-mail:
| | - Christine Fehlner-Gardiner
- National Reference Laboratory for Rabies, Ottawa Laboratory–Fallowfield, Canadian Food Inspection Agency, Ottawa, Ontario
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Nadin-Davis SA. Rapid identification of the raccoon rabies virus variant using a real-time reverse-transcriptase polymerase chain reaction. J Virol Methods 2019; 273:113713. [PMID: 31404575 DOI: 10.1016/j.jviromet.2019.113713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/27/2019] [Accepted: 08/08/2019] [Indexed: 11/18/2022]
Abstract
The raccoon-associated variant of rabies virus (RRV) is enzootic throughout the eastern seaboard of the United States with frequent incursions into Canada. Many wildlife management agencies are actively engaged in control programmes targeting elimination of this disease and rapid identification of raccoon rabies cases is crucial to the success of these operations. This report documents the development of a reverse transcriptase real-time PCR (RT-qPCR) that specifically identifies this rabies virus variant (RRV RT-qPCR) and which can be readily multiplexed with a generic rabies virus RT-qPCR for use as a typing tool. Using a large collection of rabies virus samples representative of the variants circulating around the world, but with a focus on those occurring in the Americas, the RRV RT-qPCR was 100% sensitive and 99.31% specific. To further apply these assays for diagnostic purposes, addition of an RT-qPCR targeting the host β-actin mRNA, which serves as an internal amplification control, in a triplex format was shown to yield highly comparable results using a subset of our viral collection. Use of these assays for early and accurate identification of this viral variant will help to optimize the utilization of resources required for control of this disease.
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Affiliation(s)
- S A Nadin-Davis
- Animal Health Microbiology Research, Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Room A222, 3851 Fallowfield Rd., P.O. Box 11300, Station H, K2H 8P9, Ottawa, Ontario, Canada.
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Tao XY, Li ML, Wang Q, Baima C, Hong M, Li W, Wu YB, Li YR, Zhao YM, Rayner S, Zhu WY. The reemergence of human rabies and emergence of an Indian subcontinent lineage in Tibet, China. PLoS Negl Trop Dis 2019; 13:e0007036. [PMID: 30640911 PMCID: PMC6349412 DOI: 10.1371/journal.pntd.0007036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/28/2019] [Accepted: 11/29/2018] [Indexed: 12/25/2022] Open
Abstract
Coordinated surveillance, vaccination and public information efforts have brought the Chinese rabies epizootic under control, but significant numbers of fatalities are still reported annually with some cases occurring in previously rabies free regions. Tibet has remained virtually rabies free for 16 years, but since 2015 one human rabies case has been reported each year. To better understand the origins of these cases, we sequenced three human samples and an additional sample isolated from a dog in 2012. Three genomes were sequenced from brain samples: human case 1 (reported in 2015), human case 3 (2017), and the 2012 dog case. For human case 2 (2016), the rabies N gene was sequenced from a limited saliva sample. Phylogenetic analysis shows that Case 1 (CXZ1501H) and the dog case (CXZ1201D) belong to China IV lineage (equivalent to Arctic-like-2 in global rabies), suggesting an association with a wildlife spillover event. However, Case 2 (CXZ1601H) is placed within the dominant lineage China I, and was most similar with recent strains from neighboring Yunnan province, indicating the current epizootic has finally reached Tibet. Most surprisingly however, was the finding that Case 3 (CXZ1704H) is distinct from other Chinese isolates. This isolate is placed in the Indian Subcontinent clade, similar to recent Nepal strains, indicating that cross-border transmission is a new source for rabies infections. Thus, the complex mixture of the rabies epizootic in Tibet represents a major new challenge for Tibet and national rabies control.
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Affiliation(s)
- Xiao-Yan Tao
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mu-Li Li
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Pathology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Qian Wang
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ciwang Baima
- Tibet Center for Disease Control and Prevention, Lhasa, Tibet, China
| | - Mei Hong
- Tibet Center for Disease Control and Prevention, Lhasa, Tibet, China
| | - Wei Li
- Sichuan Center for Disease Control and Prevention, Chengdu, Sichuan, China
| | - Yong-Biao Wu
- Wuhou District Center for Disease Control and Prevention, Chengdu, Sichuan, China
| | - Yan-Rong Li
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yu-Min Zhao
- Department of Parasitology, Guilin Medical University, Guilin, Guangxi
| | - Simon Rayner
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Hybrid Technology Hub - Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Wu-Yang Zhu
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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21
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Trewby H, Nadin-Davis SA, Real LA, Biek R. Processes Underlying Rabies Virus Incursions across US-Canada Border as Revealed by Whole-Genome Phylogeography. Emerg Infect Dis 2018; 23:1454-1461. [PMID: 28820138 PMCID: PMC5572885 DOI: 10.3201/eid2309.170325] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Disease control programs aim to constrain and reduce the spread of infection. Human disease interventions such as wildlife vaccination play a major role in determining the limits of a pathogen’s spatial distribution. Over the past few decades, a raccoon-specific variant of rabies virus (RRV) has invaded large areas of eastern North America. Although expansion into Canada has been largely prevented through vaccination along the US border, several outbreaks have occurred in Canada. Applying phylogeographic approaches to 289 RRV whole-genome sequences derived from isolates collected in Canada and adjacent US states, we examined the processes underlying these outbreaks. RRV incursions were attributable predominantly to systematic virus leakage of local strains across areas along the border where vaccination has been conducted but also to single stochastic events such as long-distance translocations. These results demonstrate the utility of phylogeographic analysis of pathogen genomes for understanding transboundary outbreaks.
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Ajorloo M, Mirzaei H, Sadeghi Y, Tarban N, Soltani S, Mohammadi FS, Davarinejad P, Amiri Roudy M, Jahantigh HR, Abouhamzeh K, Mohammadhosayni M, Razavi Nikoo H, Alamdary A, Norouzi M. Evaluation and Phylogenetic Analysis of Regular Rabies Virus Vaccine Strains. Arch Iran Med 2018; 21:101-110. [PMID: 29688735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 11/29/2017] [Indexed: 06/08/2023]
Abstract
BACKGROUND This study aimed to evaluate Rabies virus vaccine strains. The obtained results may be helpful for vaccine producers and researchers to compare the strains with wild type and other vaccine strains and select the correct strain to challenge their products. METHODS Fourteen rabies virus vaccine strains were compared with each other. The full genomes of the selected strains were taken from the GenBank and the N, P and G genes were labeled. The major and minor antigenic sites of these sequences were identified and contrasted with each other. The identity matrix was designed for rabies virus full genome, N and G genes. In addition, the phylogenetic tree was drawn based on rabies virus N gene for deep analysis. RESULTS Although there were no significant differences between antigenic sites in N, P, and G genes, there were noticeable differences for full genome identity matrix and this significant difference can also be observed in N and G identity matrix. In the phylogenetic tree, the Iranian sequences were distant from currently applied vaccine strains. CONCLUSION It is necessary to pay attention to the results shown in phylogenetic tree because they warn us about distance between the Iranian sequences and current strains used in applied vaccines. In addition, the obtained results help vaccine producers to choose a correct strain to challenge their product and evaluate their vaccine potency.
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Affiliation(s)
- Mehdi Ajorloo
- Hepatitis Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
- School of Allied Medical Sciences, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Habibollah Mirzaei
- Hepatitis Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
- Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Yasaman Sadeghi
- Department of Pathobiology School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Nastaran Tarban
- Department of Biology, Kish international campus, university of Tehran, Kish, Iran
| | - Saber Soltani
- Department of Pathobiology School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Sadat Mohammadi
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Medical School, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Pardis Davarinejad
- Department Biology, Faculty of Biology Sciences, Islamic Azad University, Tehran North Branch, Tehran, Iran
| | - Maedeh Amiri Roudy
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Jahantigh
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Medical School, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kosar Abouhamzeh
- Department of Clinical Laboratory Sciences, Faculty of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Hadi Razavi Nikoo
- Laboratory Science Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ashkan Alamdary
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mehdi Norouzi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
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Fischer S, Freuling CM, Müller T, Pfaff F, Bodenhofer U, Höper D, Fischer M, Marston DA, Fooks AR, Mettenleiter TC, Conraths FJ, Homeier-Bachmann T. Defining objective clusters for rabies virus sequences using affinity propagation clustering. PLoS Negl Trop Dis 2018; 12:e0006182. [PMID: 29357361 PMCID: PMC5794188 DOI: 10.1371/journal.pntd.0006182] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 02/01/2018] [Accepted: 12/19/2017] [Indexed: 11/18/2022] Open
Abstract
Rabies is caused by lyssaviruses, and is one of the oldest known zoonoses. In recent years, more than 21,000 nucleotide sequences of rabies viruses (RABV), from the prototype species rabies lyssavirus, have been deposited in public databases. Subsequent phylogenetic analyses in combination with metadata suggest geographic distributions of RABV. However, these analyses somewhat experience technical difficulties in defining verifiable criteria for cluster allocations in phylogenetic trees inviting for a more rational approach. Therefore, we applied a relatively new mathematical clustering algorythm named ‘affinity propagation clustering’ (AP) to propose a standardized sub-species classification utilizing full-genome RABV sequences. Because AP has the advantage that it is computationally fast and works for any meaningful measure of similarity between data samples, it has previously been applied successfully in bioinformatics, for analysis of microarray and gene expression data, however, cluster analysis of sequences is still in its infancy. Existing (516) and original (46) full genome RABV sequences were used to demonstrate the application of AP for RABV clustering. On a global scale, AP proposed four clusters, i.e. New World cluster, Arctic/Arctic-like, Cosmopolitan, and Asian as previously assigned by phylogenetic studies. By combining AP with established phylogenetic analyses, it is possible to resolve phylogenetic relationships between verifiably determined clusters and sequences. This workflow will be useful in confirming cluster distributions in a uniform transparent manner, not only for RABV, but also for other comparative sequence analyses. Rabies is one of the oldest known zoonoses, caused by lyssaviruses. In recent years, more than 21,000 nucleotide sequences for rabies viruses (RABV) have been deposited in public databases. In this study, a novel mathematical approach called affinity propagation (AP) clustering, a highly powerful tool, to verifiably divide full genome RABV sequences into genetic clusters, was used. A panel of existing and novel RABV full genome sequences was used to demonstrate the application of AP for RABV clustering. Using a combination of AP with established phylogenetic analyses is useful in resolving phylogenetic relationships between more objectively determined clusters and sequences. This workflow will help to substantiate a transparent cluster distribution, not only for RABV, but also for other comparative sequence analyses.
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Affiliation(s)
- Susanne Fischer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Greifswald-Insel Riems, Germany
| | - Conrad M. Freuling
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology, OIE Reference Laboratory for Rabies, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany
| | - Thomas Müller
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology, OIE Reference Laboratory for Rabies, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany
- * E-mail:
| | - Florian Pfaff
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Ulrich Bodenhofer
- Institute of Bioinformatics, Johannes Kepler University Linz, Linz, Austria
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology, OIE Reference Laboratory for Rabies, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany
| | - Mareike Fischer
- Institute of Mathematics and Computer Science, University Greifswald, Greifswald, Germany
| | - Denise A. Marston
- Wildlife Zoonoses and Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), OIE Reference Laboratory for Rabies, WHO Collaborating Centre for Characterization of Lyssaviruses, Weybridge, United Kingdom
| | - Anthony R. Fooks
- Wildlife Zoonoses and Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), OIE Reference Laboratory for Rabies, WHO Collaborating Centre for Characterization of Lyssaviruses, Weybridge, United Kingdom
| | - Thomas C. Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology, OIE Reference Laboratory for Rabies, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany
| | - Franz J. Conraths
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Greifswald-Insel Riems, Germany
| | - Timo Homeier-Bachmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Greifswald-Insel Riems, Germany
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Sadeuh-Mba SA, Momo JB, Besong L, Loul S, Njouom R. Molecular characterization and phylogenetic relatedness of dog-derived Rabies Viruses circulating in Cameroon between 2010 and 2016. PLoS Negl Trop Dis 2017; 11:e0006041. [PMID: 29084223 PMCID: PMC5679643 DOI: 10.1371/journal.pntd.0006041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 11/09/2017] [Accepted: 10/15/2017] [Indexed: 12/25/2022] Open
Abstract
Rabies is enzootic among dog populations in some parts of Cameroon and the risk of human rabies is thought to be steadily high in these regions. However, the molecular epidemiology of circulating Rabies Virus (RABV) has been hardly considered in Cameroon as well as in most neighboring central African countries. To address this fundamental gap, 76 nucleoprotein (N) gene sequences of dog-derived RABV were obtained from 100 brain specimens sampled in Cameroon from 2010 to 2016. Studied sequences were subjected to molecular and phylogenetic analyses with reference strains retrieved from databases. The 71 studied Africa-1 isolates displayed 93.5–100% nucleotide (nt) and 98.3–100% amino-acid (aa) identities to each other while, the 5 studied Africa-2 isolates shared 99.4–99.7% sequence similarities at nt and aa levels. Maximum Likelihood based phylogenies inferred from nucleotide sequences confirmed all studied RABV isolates as members of the dog-related species 1 of the Lyssavirus genus. Individual isolates could be unambiguously assigned as either the Africa-1 subclade of the Cosmopolitan clade or the Africa 2 clade. The Africa-1 subclade appeared to be more prevalent and diversified. Indeed, 70 studied isolates segregated into 3 distinct circulating variants within Africa-1a lineage while a unique isolate was strikingly related to the Africa-1b lineage known to be prevalent in the neighboring Central African Republic and eastern Africa. Interestingly, all five Africa-2 isolates fell into the group-E lineage even though they appeared to be loosely related to databases available reference RABV; including those previously documented in Cameroon. This study uncovered the co-circulation of several Africa-1 and Africa-2 lineages in the southern regions of Cameroon. Striking phylogenetic outcasts to the geographic differentiation of RABV variants indicated that importation from close regions or neighboring countries apparently contributes to the sustainment of the enzootic cycle of domestic rabies in Cameroon. Rabies has been repeatedly reported among dog populations in Cameroon, especially in Yaounde, its capital city. However, the relative rates and genetic variability of Rabies Virus (RABV) variants circulating among dog populations in Cameroon are still to be documented. This study aimed to estimate the frequency and genetic diversity of RABV isolates originating from rabid dogs in the southern regions of Cameroon from 2010 to 2016. Overall, 76 of the 100 dog-derived RABV isolates sampled in Cameroon from 2010 to 2016 were successfully characterized. Our findings revealed that studied isolates belonged to the dog-related species 1 of the Lyssavirus genus, specifically 70 Africa-1a, 1 Africa-1b and 5 Africa-2 group-E lineages. The general phylogenetic pattern suggested an in-country geographic differentiation of the circulating RABV variants. This apparent geographic differentiation was contradicted by striking outcasts indicating importation from close or distant regions. Overall, this study uncovered the co-circulation of several Africa-1 and Africa-2 lineages in some southern regions of Cameroon, thus providing base-line molecular data that would be of interest for future stages of implementation of the rabies surveillance and control plan that is being setup in Cameroon.
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Affiliation(s)
- Serge Alain Sadeuh-Mba
- Virology Service, Centre Pasteur du Cameroun, Yaounde, Centre region, Cameroon
- * E-mail: ,
| | - Jean Blaise Momo
- Virology Service, Centre Pasteur du Cameroun, Yaounde, Centre region, Cameroon
| | - Laura Besong
- Ministry of Livestock, Fisheries and Animal Industries (MINEPIA), Yaounde, Centre region, Cameroon
| | - Sévérin Loul
- Ministry of Livestock, Fisheries and Animal Industries (MINEPIA), Yaounde, Centre region, Cameroon
| | - Richard Njouom
- Virology Service, Centre Pasteur du Cameroun, Yaounde, Centre region, Cameroon
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Velasco-Villa A, Mauldin MR, Shi M, Escobar LE, Gallardo-Romero NF, Damon I, Olson VA, Streicker DG, Emerson G. The history of rabies in the Western Hemisphere. Antiviral Res 2017. [PMID: 28365457 DOI: 10.1016/j.anti-viral.2017.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Before the introduction of control programs in the 20th century, rabies in domestic dogs occurred throughout the Western Hemisphere. However, historical records and phylogenetic analysis of multiple virus isolates indicate that, before the arrival of the first European colonizers, rabies virus was likely present only in bats and skunks. Canine rabies was either rare or absent among domestic dogs of Native Americans, and first arrived when many new dog breeds were imported during the period of European colonization. The introduction of the cosmopolitan dog rabies lyssavirus variant and the marked expansion of the dog population provided ideal conditions for the flourishing of enzootic canine rabies. The shift of dog-maintained viruses into gray foxes, coyotes, skunks and other wild mesocarnivores throughout the Americas and to mongooses in the Caribbean has augmented the risk of human rabies exposures and has complicated control efforts. At the same time, the continued presence of bat rabies poses novel challenges in the absolute elimination of canine and human rabies. This article compiles existing historical and phylogenetic evidence of the origins and subsequent dynamics of rabies in the Western Hemisphere, from the era preceding the arrival of the first European colonizers through the present day. A companion article reviews the current status of canine rabies control throughout the Western Hemisphere and steps that will be required to achieve and maintain its complete elimination (Velasco-Villa et al., 2017).
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Affiliation(s)
- Andres Velasco-Villa
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, 30329, GA, USA.
| | - Matthew R Mauldin
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, 30329, GA, USA; Oak Ridge Institute for Science and Education (ORISE), CDC Fellowship Program, Oak Ridge, TN, USA
| | - Mang Shi
- Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Luis E Escobar
- Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, Saint Paul, 55108, MN, USA
| | - Nadia F Gallardo-Romero
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, 30329, GA, USA
| | - Inger Damon
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, 30329, GA, USA
| | - Victoria A Olson
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, 30329, GA, USA
| | - Daniel G Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, Scotland, UK; MRC-University of Glasgow Centre for Virus Research, Sir Henry Wellcome Building, Glasgow, G61 1QH, Scotland, UK
| | - Ginny Emerson
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, 30329, GA, USA
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Nadin-Davis SA, Colville A, Trewby H, Biek R, Real L. Application of high-throughput sequencing to whole rabies viral genome characterisation and its use for phylogenetic re-evaluation of a raccoon strain incursion into the province of Ontario. Virus Res 2017; 232:123-133. [PMID: 28219746 PMCID: PMC5433798 DOI: 10.1016/j.virusres.2017.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/14/2017] [Accepted: 02/14/2017] [Indexed: 01/08/2023]
Abstract
Raccoon rabies remains a serious public health problem throughout much of the eastern seaboard of North America due to the urban nature of the reservoir host and the many challenges inherent in multi-jurisdictional efforts to administer co-ordinated and comprehensive wildlife rabies control programmes. Better understanding of the mechanisms of spread of rabies virus can play a significant role in guiding such control efforts. To facilitate a detailed molecular epidemiological study of raccoon rabies virus movements across eastern North America, we developed a methodology to efficiently determine whole genome sequences of hundreds of viral samples. The workflow combines the generation of a limited number of overlapping amplicons covering the complete viral genome and use of high throughput sequencing technology. The value of this approach is demonstrated through a retrospective phylogenetic analysis of an outbreak of raccoon rabies which occurred in the province of Ontario between 1999 and 2005. As demonstrated by the number of single nucleotide polymorphisms detected, whole genome sequence data were far more effective than single gene sequences in discriminating between samples and this facilitated the generation of more robust and informative phylogenies that yielded insights into the spatio-temporal pattern of viral spread. With minor modification this approach could be applied to other rabies virus variants thereby facilitating greatly improved phylogenetic inference and thus better understanding of the spread of this serious zoonotic disease. Such information will inform the most appropriate strategies for rabies control in wildlife reservoirs.
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Affiliation(s)
- Susan A Nadin-Davis
- Animal Health Microbiology Research, Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, Ontario, Canada.
| | - Adam Colville
- Animal Health Microbiology Research, Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, Ontario, Canada.
| | - Hannah Trewby
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK.
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK.
| | - Leslie Real
- Department of Biology, Emory University, Atlanta, GA 30322, United States.
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Traoré A, Picard-Meyer E, Mauti S, Biarnais M, Balmer O, Samaké K, Kamissoko B, Tembely S, Sery A, Traoré AK, Coulibaly AP, Robardet E, Zinsstag J, Cliquet F. Molecular Characterization of Canine Rabies Virus, Mali, 2006-2013. Emerg Infect Dis 2016; 22:866-70. [PMID: 27089307 PMCID: PMC4861505 DOI: 10.3201/eid2205.150470] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We genetically characterized 32 canine rabies viruses isolated in Mali during 2006–2013 and identified 3 subgroups that belonged to the Africa 2 lineage. We also detected subgroup F rabies virus. This information should be useful for development of mass vaccination campaigns for dogs and eventual large-scale control programs in this country.
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Hanke D, Freuling CM, Fischer S, Hueffer K, Hundertmark K, Nadin-Davis S, Marston D, Fooks AR, Bøtner A, Mettenleiter TC, Beer M, Rasmussen TB, Müller TF, Höper D. Spatio-temporal Analysis of the Genetic Diversity of Arctic Rabies Viruses and Their Reservoir Hosts in Greenland. PLoS Negl Trop Dis 2016; 10:e0004779. [PMID: 27459154 PMCID: PMC4961414 DOI: 10.1371/journal.pntd.0004779] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 05/24/2016] [Indexed: 12/05/2022] Open
Abstract
There has been limited knowledge on spatio-temporal epidemiology of zoonotic arctic fox rabies among countries bordering the Arctic, in particular Greenland. Previous molecular epidemiological studies have suggested the occurrence of one particular arctic rabies virus (RABV) lineage (arctic-3), but have been limited by a low number of available samples preventing in-depth high resolution phylogenetic analysis of RABVs at that time. However, an improved knowledge of the evolution, at a molecular level, of the circulating RABVs and a better understanding of the historical perspective of the disease in Greenland is necessary for better direct control measures on the island. These issues have been addressed by investigating the spatio-temporal genetic diversity of arctic RABVs and their reservoir host, the arctic fox, in Greenland using both full and partial genome sequences. Using a unique set of 79 arctic RABV full genome sequences from Greenland, Canada, USA (Alaska) and Russia obtained between 1977 and 2014, a description of the historic context in relation to the genetic diversity of currently circulating RABV in Greenland and neighboring Canadian Northern territories has been provided. The phylogenetic analysis confirmed delineation into four major arctic RABV lineages (arctic 1–4) with viruses from Greenland exclusively grouping into the circumpolar arctic-3 lineage. High resolution analysis enabled distinction of seven geographically distinct subclades (3.I – 3.VII) with two subclades containing viruses from both Greenland and Canada. By combining analysis of full length RABV genome sequences and host derived sequences encoding mitochondrial proteins obtained simultaneously from brain tissues of 49 arctic foxes, the interaction of viruses and their hosts was explored in detail. Such an approach can serve as a blueprint for analysis of infectious disease dynamics and virus-host interdependencies. The results showed a fine-scale spatial population structure in Greenland arctic foxes based on mitochondrial sequences, but provided no evidence for independent isolated evolutionary development of RABV in different arctic fox lineages. These data are invaluable to support future initiatives for arctic fox rabies control and elimination in Greenland. Next to dog-mediated rabies, wildlife rabies continues to pose a public health problem, particularly in the northern hemisphere. Control of this zoonosis at the animal source has been proven the most efficient route to reduction of human rabies burden. Successful elimination of red fox-mediated rabies in Western Europe and parts of North America has demonstrated the viability of wildlife rabies control strategies. In some regions, the epidemiology of wildlife rabies is well understood; this is not the case for arctic rabies, particularly in Greenland. Previous molecular epidemiological studies demonstrated the occurrence of one particular arctic rabies virus (RABV) lineage (arctic-3) but were limited by low sample numbers and limited sequence length so as to preclude generation of high resolution phylogenetic analysis. Here, a unique set comprised of 79 complete genome sequences of RABVs from Greenland, Canada, USA (Alaska) and Russia collected over the past four decades was analysed. The use of next generation sequencing (NGS) allowed simultaneous determination of host derived sequences encoding mitochondrial proteins from the same brain tissue of 49 arctic foxes. These sequence data combined with geographical and temporal information permit the study of the genetic diversity and evolution of circulating RABVs in Greenland against the background of reservoir host genetics. The results reveal the existence of a single arctic RABV lineage (arctic-3) in Greenland, which has evolved into multiple distinct variants. These analyses provide an improved knowledge of the evolution of the circulating viruses at the molecular level and a better understanding of the historical perspective of the disease in Greenland compared to other parts of the Arctic. This knowledge will support policy on rabies control in mammalian wildlife reservoirs.
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Affiliation(s)
- Dennis Hanke
- Friedrich-Loeffler-Institut (FLI), Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Conrad M. Freuling
- FLI, Institute of Molecular Virology and Cell Biology, Greifswald-Insel Riems, Germany
| | - Susanne Fischer
- FLI, Institute of Epidemiology, Greifswald-Insel Riems, Germany
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska, Fairbanks, Alaska, United States of America
| | - Kris Hundertmark
- Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska, United States of America
| | - Susan Nadin-Davis
- Animal Health Microbiology Research, Canadian Food Inspection Agency (CFIA), Centre of Expertise for Rabies, Ottawa Laboratory, Ottawa, Ontario, Canada
| | - Denise Marston
- Animal and Plant Health Agency (APHA), Wildlife Zoonoses and Vector-borne Diseases Research Group, Addlestone, Surrey, United Kingdom
| | - Anthony R. Fooks
- Animal and Plant Health Agency (APHA), Wildlife Zoonoses and Vector-borne Diseases Research Group, Addlestone, Surrey, United Kingdom
- University of Liverpool, Department of Clinical Infection, Microbiology and Immunology, Liverpool, United Kingdom
| | - Anette Bøtner
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave, Denmark
| | | | - Martin Beer
- Friedrich-Loeffler-Institut (FLI), Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Thomas B. Rasmussen
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave, Denmark
| | - Thomas F. Müller
- FLI, Institute of Molecular Virology and Cell Biology, Greifswald-Insel Riems, Germany
- * E-mail:
| | - Dirk Höper
- Friedrich-Loeffler-Institut (FLI), Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
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Dato VM, Campagnolo ER, Long J, Rupprecht CE. A Systematic Review of Human Bat Rabies Virus Variant Cases: Evaluating Unprotected Physical Contact with Claws and Teeth in Support of Accurate Risk Assessments. PLoS One 2016; 11:e0159443. [PMID: 27459720 PMCID: PMC4961291 DOI: 10.1371/journal.pone.0159443] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/30/2016] [Indexed: 11/19/2022] Open
Abstract
In the United States and Canada, the most recent documented cases of rabies have been attributed to bat rabies viruses (RABV). We undertook this systematic review in an effort to summarize and enhance understanding of the risk of infection for individuals who have been potentially exposed to a suspect or confirmed rabid bat. United States rabies surveillance summaries documented a total of 41 human bat-rabies virus variant verified non-transplant cases between 1990 and 2015. All cases were fatal. Seven (17.1%) of 41 cases reported a bite from a bat. Ten (24.3%) cases had unprotected physical contact (UPC); these included seven cases that had a bat land or crawl on them (contact with claws) and one case that touched a bat's teeth. Seven (17.1%) cases had probable UPC. Insectivorous bat teeth are extremely sharp and highly efficient for predation upon arthropod prey. Bats also have sharp claws on the end of their thumbs and feet. One of the most common bat RABV variants has an ability to replicate in non-neural cells. Questioning individuals about unprotected contact with bat teeth and claws (including a bat landing or crawling on a person) may help identify additional exposures.
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Affiliation(s)
- Virginia M. Dato
- University of Pittsburgh, School of Medicine, Pittsburgh, PA, United States of America
| | - Enzo R. Campagnolo
- Pennsylvania Department of Health, Bureau of Epidemiology, Harrisburg, PA, United States of America
- Centers for Disease Control and Prevention, Office of Public Health Preparedness and Response, Division of State and Local Readiness, Field Services Branch, Atlanta, GA, United States of America
| | - Jonah Long
- Pennsylvania Department of Health, Bureau of Epidemiology, Harrisburg, PA, United States of America
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Tricou V, Bouscaillou J, Kamba Mebourou E, Koyanongo FD, Nakouné E, Kazanji M. Surveillance of Canine Rabies in the Central African Republic: Impact on Human Health and Molecular Epidemiology. PLoS Negl Trop Dis 2016; 10:e0004433. [PMID: 26859829 PMCID: PMC4747513 DOI: 10.1371/journal.pntd.0004433] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/13/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Although rabies represents an important public health threat, it is still a neglected disease in Asia and Africa where it causes tens of thousands of deaths annually despite available human and animal vaccines. In the Central African Republic (CAR), an endemic country for rabies, this disease remains poorly investigated. METHODS To evaluate the extent of the threat that rabies poses in the CAR, we analyzed data for 2012 from the National Reference Laboratory for Rabies, where laboratory confirmation was performed by immunofluorescence and PCR for both animal and human suspected cases, and data from the only anti-rabies dispensary of the country and only place where post-exposure prophylaxis (PEP) is available. Both are located in Bangui, the capital of the CAR. For positive samples, a portion of the N gene was amplified and sequenced to determine the molecular epidemiology of circulating strains. RESULTS In 2012, 966 exposed persons visited the anti-rabies dispensary and 632 received a post-exposure rabies vaccination. More than 90% of the exposed persons were from Bangui and its suburbs and almost 60% of them were under 15-years of age. No rabies-related human death was confirmed. Of the 82 samples from suspected rabid dogs tested, 69 were confirmed positive. Most of the rabid dogs were owned although unvaccinated. There was a strong spatiotemporal correlation within Bangui and within the country between reported human exposures and detection of rabid dogs (P<0.001). Phylogenetic analysis indicated that three variants belonging to Africa I and II lineages actively circulated in 2012. CONCLUSIONS These data indicate that canine rabies was endemic in the CAR in 2012 and had a detrimental impact on human health as shown by the hundreds of exposed persons who received PEP. Implementation of effective public health interventions including mass dog vaccination and improvement of the surveillance and the access to PEP are urgently needed in this country.
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Affiliation(s)
- Vianney Tricou
- Laboratoire de Virologie, Institut Pasteur de Bangui, Bangui, Central African Republic
- * E-mail:
| | | | | | - Fidèle Dieudonné Koyanongo
- Service de Santé Publique Vétérinaire, Agence Nationale du Développement de l'Elevage, Bangui, Central African Republic
| | - Emmanuel Nakouné
- Laboratoire de Virologie, Institut Pasteur de Bangui, Bangui, Central African Republic
- Laboratoire National de Référence pour la Rage, Institut Pasteur de Bangui, Bangui, Central African Republic
| | - Mirdad Kazanji
- Laboratoire de Virologie, Institut Pasteur de Bangui, Bangui, Central African Republic
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Robardet E, Picard-Meyer E, Dobroštana M, Jaceviciene I, Mähar K, Muižniece Z, Pridotkas G, Masiulis M, Niin E, Olševskis E, Cliquet F. Rabies in the Baltic States: Decoding a Process of Control and Elimination. PLoS Negl Trop Dis 2016; 10:e0004432. [PMID: 26849358 PMCID: PMC4743931 DOI: 10.1371/journal.pntd.0004432] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 01/13/2016] [Indexed: 11/19/2022] Open
Abstract
Rabies is a fatal zoonosis that still causes nearly 70, 000 human deaths every year. In Europe, the oral rabies vaccination (ORV) of red foxes (Vulpes vulpes) was developed in the late 1970s and has demonstrated its effectiveness in the eradication of the disease in Western and some Central European countries. Following the accession of the three Baltic countries--Estonia, Latvia and Lithuania--to the European Union in 2004, subsequent financial support has allowed the implementation of regular ORV campaigns since 2005-2006. This paper reviews ten years of surveillance efforts and ORV campaigns in these countries resulting in the near eradication of the disease. The various factors that may have influenced the results of vaccination monitoring were assessed using generalized linear models (GLMs) on bait uptake and on herd immunity. As shown in previous studies, juveniles had lower bait uptake level than adults. For the first time, raccoon dogs (Nyctereutes procyonoides) were shown to have significantly lower bait uptake proportion compared with red foxes. This result suggests potentially altered ORV effectiveness in this invasive species compared to the red foxes. An extensive phylogenetic analysis demonstrated that the North-East European (NEE) rabies phylogroup is endemic in all three Baltic countries. Although successive oral vaccination campaigns have substantially reduced the number of detected rabies cases, sporadic detection of the C lineage (European part of Russian phylogroup) underlines the risk of reintroduction via westward spread from bordering countries. Vaccine induced cases were also reported for the first time in non-target species (Martes martes and Meles meles).
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Affiliation(s)
- Emmanuelle Robardet
- ANSES, Nancy Laboratory for Rabies and Wildlife, Bâtiment H, Technopôle Agricole et Vétérinaire, CS 40 009, Malzéville, France
| | - Evelyne Picard-Meyer
- ANSES, Nancy Laboratory for Rabies and Wildlife, Bâtiment H, Technopôle Agricole et Vétérinaire, CS 40 009, Malzéville, France
| | - Marianna Dobroštana
- BIOR, Institute of Food Safety, Animal Health and Environment "BIOR", Riga, Latvia
| | - Ingrida Jaceviciene
- National Food and Veterinary Risk Assessment Institute of Lithuania, Vilnius, Lithuania
- Vilniaus Kolegija/University of Applied Sciences Faculty of Agrotechnologies, Buivydiškės, Vilnius district, Lithuania
| | - Katrin Mähar
- Estonian Veterinary and Food Laboratory, Tartu, Estonia
| | - Zita Muižniece
- BIOR, Institute of Food Safety, Animal Health and Environment "BIOR", Riga, Latvia
| | - Gediminas Pridotkas
- National Food and Veterinary Risk Assessment Institute of Lithuania, Vilnius, Lithuania
| | | | - Enel Niin
- Estonian Veterinary and Food Board, Tallin, Estonia
| | - Edvīns Olševskis
- BIOR, Institute of Food Safety, Animal Health and Environment "BIOR", Riga, Latvia
- Food and Veterinary Service, Riga, Latvia
| | - Florence Cliquet
- ANSES, Nancy Laboratory for Rabies and Wildlife, Bâtiment H, Technopôle Agricole et Vétérinaire, CS 40 009, Malzéville, France
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de Thoisy B, Bourhy H, Delaval M, Pontier D, Dacheux L, Darcissac E, Donato D, Guidez A, Larrous F, Lavenir R, Salmier A, Lacoste V, Lavergne A. Bioecological Drivers of Rabies Virus Circulation in a Neotropical Bat Community. PLoS Negl Trop Dis 2016; 10:e0004378. [PMID: 26808820 PMCID: PMC4726525 DOI: 10.1371/journal.pntd.0004378] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/18/2015] [Indexed: 12/26/2022] Open
Abstract
INTRODUCTION In addition to the commonly accepted importance of the vampire bat in the maintenance and transmission of the rabies virus (RABV) in South America, RABV infection of other species is widely evidenced, challenging their role in the viral cycle. METHODOLOGY / PRINCIPLES FINDINGS To identify the bioecological drivers of RABV circulation in neotropical bat communities, we conducted a molecular and serological survey on almost 1,000 bats from 30 species, and a 4-year longitudinal survey in two colonies of vampire bats in French Guiana. RABV was molecularly detected in a common vampire and in a frugivorous bat. The sequences corresponded to haematophagous bat-related strains and were close to viruses circulating in the Brazilian Amazon region. Species' seroprevalence ranged from 0 to 20%, and the risk of seropositivity was higher in bats with a haematophagous diet, living in monospecific colonies and in dense forests. The longitudinal survey showed substantial temporal fluctuations, with individual waves of seroconversions and waning immunity. The high prevalences observed in bat communities, in most habitats and in species that do not share the same microhabitats and bioecological patterns, the temporal variations, and a rather short period of detectable antibodies as observed in recaptured vampires suggest (i) frequent exposure of animals, (ii) an ability of the infected host to control and eliminate the virus, (iii) more relaxed modes of exposure between bats than the commonly assumed infection via direct contact with saliva of infected animals, all of which should be further investigated. CONCLUSIONS / SIGNIFICANCE We hypothesize that RABV circulation in French Guiana is mainly maintained in the pristine forest habitats that may provide sufficient food resources to allow vampire bats, the main prevalent species, to survive and RABV to be propagated. However, on the forest edge and in disturbed areas, human activities may induce more insidious effects such as defaunation. One of the ecological consequences is the disappearance of resources for tertiary or secondary consumers. Populations of vampires may then shift to alternative resources such as cattle, domestic animals and humans. Therefore, a good forest status, allowing both a dilution effect in highly rich bat communities and the maintenance of large populations of medium-sized and large mammals used as prey by vampires, should prevent their migration to anthropized areas.
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Affiliation(s)
- Benoit de Thoisy
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Hervé Bourhy
- Lyssavirus Dynamics and Host adaptation Unit, National Reference Centre for Rabies, Institut Pasteur, Paris, France
| | | | - Dominique Pontier
- Laboratoire de Biométrie et Biologie évolutive, UMR CNRS 5558, Université Lyon 1 / CNRS, Villeurbanne, France
| | - Laurent Dacheux
- Lyssavirus Dynamics and Host adaptation Unit, National Reference Centre for Rabies, Institut Pasteur, Paris, France
| | - Edith Darcissac
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Damien Donato
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Amandine Guidez
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Florence Larrous
- Lyssavirus Dynamics and Host adaptation Unit, National Reference Centre for Rabies, Institut Pasteur, Paris, France
| | - Rachel Lavenir
- Lyssavirus Dynamics and Host adaptation Unit, National Reference Centre for Rabies, Institut Pasteur, Paris, France
| | - Arielle Salmier
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Vincent Lacoste
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Anne Lavergne
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
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Tao XY, Guo ZY, Li H, Jiao WT, Shen XX, Zhu WY, Rayner S, Tang Q. Rabies Cases in the West of China Have Two Distinct Origins. PLoS Negl Trop Dis 2015; 9:e0004140. [PMID: 26484668 PMCID: PMC4618851 DOI: 10.1371/journal.pntd.0004140] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/15/2015] [Indexed: 12/03/2022] Open
Abstract
In China, rabies remains an ongoing threat to public health. Although control efforts have been effective in reducing the number of annual cases, the virus continues to spread into new areas. Tibet, Qinghai, Gansu and Ningxia in western China have, until recently, reported only a handful of events. However, since 2011, there have been increasing numbers of cases recorded in these areas. In this study, we report the collection and analysis of samples collected from these regions. We find that cases originate from two different sources. Strains collected from Gansu and Ningxia are closely related to the primary lineage associated with the current epizootic, whereas those from Tibet and Qinghai are related to the Arctic-like-2 lineage that is most commonly associated with wildlife cases in China. Thus, it appears that while the epizootic is beginning to encroach into Gansu and Ningxia, Tibet and Qinghai a significant number of rabies cases originate from wildlife. Overall, the number of annual cases of human rabies reported in China has been decreasing since 2007. However, some Western provinces, where few human cases have been reported in recent years, are beginning to see increasing incidence of rabies. Specifically, Ningxia, Qinghai and Gansu began to report human cases respectively from 2011, 2012 and 2013, while Tibet had its first laboratory confirmed dog rabies case in 2012. Consequently, as part of the national rabies surveillance program, we collected specimens from biting dogs or human saliva from suspected rabies cases in these areas, and after sequencing positive samples, performed a phylogenetic analysis based on the nucleoprotein gene complete sequences. Our results indicate that while Ningxia and Gansu rabies strains are very close to the lineage associated with most cases in mainland China, Tibet and Qinghai strains belong to the global Arctic-like-2 clade, which is typically associated with wild life in China and neighboring countries. Thus, it appears that, rabies reemergence in the west of China has two distinct origins, and Tibet and Qinghai rabies cases were isolated events rather than an indication of the ongoing epizootic in China.
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Affiliation(s)
- Xiao-Yan Tao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Zhen-Yang Guo
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hao Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Wen-Tao Jiao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin-Xin Shen
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Wu-Yang Zhu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Simon Rayner
- Department of Medical Genetics, University of Oslo, Oslo, Norway
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- * E-mail: (SR); (QT)
| | - Qing Tang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
- * E-mail: (SR); (QT)
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Zhang HL, Zhang YZ, Yang WH, Tao XY, Li H, Ding JC, Feng Y, Yang DJ, Zhang J, He J, Shen XX, Wang LH, Zhang YZ, Song M, Tang Q. Molecular epidemiology of reemergent rabies in Yunnan Province, southwestern China. Emerg Infect Dis 2015; 20:1433-42. [PMID: 25144604 PMCID: PMC4178403 DOI: 10.3201/eid2009.130440] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This province is a focal point for spread of rabies between Southeast Asia and China. Yunnan Province in China borders 3 countries (Vietnam, Laos, and Myanmar) in Southeast Asia. In the 1980s, a large-scale rabies epidemic occurred in this province, which subsided by the late 1990s. However, 3 human cases of rabies in 2000 indicated reemergence of the disease in 1 county. In 2012, rabies was detected in 77 counties; 663 persons died of rabies during this new epidemic. Fifty two rabies virus strains obtained during 2008–2012 were identified and analyzed phylogenetically by sequencing the nucleoprotein gene. Of the 4 clades identified, clades YN-A and YN-C were closely related to strains from neighboring provinces, and clade YN-B was closely related to strains from Southeast Asia, but formed a distinct branch. Rabies virus diversity might be attributed to dog movements among counties, provinces, and neighboring countries. These findings suggest that Yunnan Province is a focal point for spread of rabies between Southeast Asia and China.
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Orłowska A, Żmudziński JF. Genetic characterisation of the rabies virus vaccine strains used for oral immunization of foxes in Poland to estimate the effectiveness of vaccination. Arch Virol 2014; 160:509-15. [PMID: 25408374 PMCID: PMC4315525 DOI: 10.1007/s00705-014-2269-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/25/2014] [Indexed: 11/25/2022]
Abstract
The main reservoir of rabies virus in Poland has been the red fox. To control rabies in wildlife, oral immunization of foxes was introduced in 1993. The vaccine is effective when it confers immunity against the virus circulating in the environment. To assess the above issue, a study of the molecular characteristics of 570-bp fragments of the N and G genes of vaccine strains SAD B19 and SAD Bern against street virus strains was performed. The results confirmed the similarity of the vaccine strains and rabies virus strains circulating in the environment and also demonstrate the genetic stability of vaccine strains that have been distributed in Poland for 20 years.
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Affiliation(s)
- Anna Orłowska
- Department of Virology, National Veterinary Research Institute, Partyzantów 57 Avenue, 24-100, Puławy, Poland,
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Affiliation(s)
- Ye Liu
- Key Laboratory of Jinlin Provincial Zoonosis, Laboratory of Epidemiology, Veterinary Research Institute, Academy of Military Medical Sciences, Changchun, 130122 China
| | - Shoufeng Zhang
- Key Laboratory of Jinlin Provincial Zoonosis, Laboratory of Epidemiology, Veterinary Research Institute, Academy of Military Medical Sciences, Changchun, 130122 China
| | - Jinghui Zhao
- Key Laboratory of Jinlin Provincial Zoonosis, Laboratory of Epidemiology, Veterinary Research Institute, Academy of Military Medical Sciences, Changchun, 130122 China
| | - Fei Zhang
- Key Laboratory of Jinlin Provincial Zoonosis, Laboratory of Epidemiology, Veterinary Research Institute, Academy of Military Medical Sciences, Changchun, 130122 China
| | - Nan Li
- Key Laboratory of Jinlin Provincial Zoonosis, Laboratory of Epidemiology, Veterinary Research Institute, Academy of Military Medical Sciences, Changchun, 130122 China
| | - Hai Lian
- Key Laboratory of Jinlin Provincial Zoonosis, Laboratory of Epidemiology, Veterinary Research Institute, Academy of Military Medical Sciences, Changchun, 130122 China
| | - Wurengege
- Department of Physiology, Hetao College, Bayannur, 015000 Inner Mongolia, China
| | - Shiyu Guo
- Department of Physiology, School of Medicine, Showa University, Tokyo, 142 Japan
| | - Rongliang Hu
- Key Laboratory of Jinlin Provincial Zoonosis, Laboratory of Epidemiology, Veterinary Research Institute, Academy of Military Medical Sciences, Changchun, 130122 China
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Zieger U, Marston DA, Sharma R, Chikweto A, Tiwari K, Sayyid M, Louison B, Goharriz H, Voller K, Breed AC, Werling D, Fooks AR, Horton DL. The phylogeography of rabies in Grenada, West Indies, and implications for control. PLoS Negl Trop Dis 2014; 8:e3251. [PMID: 25330178 PMCID: PMC4199513 DOI: 10.1371/journal.pntd.0003251] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 09/08/2014] [Indexed: 12/25/2022] Open
Abstract
In Grenada, West Indies, rabies is endemic, and is thought to be maintained in a wildlife host, the small Indian mongoose (Herpestes auropunctatus) with occasional spillover into other hosts. Therefore, the present study was undertaken to improve understanding of rabies epidemiology in Grenada and to inform rabies control policy. Mongooses were trapped island-wide between April 2011 and March 2013 and examined for the presence of Rabies virus (RABV) antigen using the direct fluorescent antibody test (dFAT) and PCR, and for serum neutralizing antibodies (SNA) using the fluorescent antibody virus neutralization test (FAVN). An additional cohort of brain samples from clinical rabies suspects submitted between April 2011 and March 2014 were also investigated for the presence of virus. Two of the 171 (1.7%) live-trapped mongooses were RABV positive by FAT and PCR, and 20 (11.7%) had SNAs. Rabies was diagnosed in 31 of the submitted animals with suspicious clinical signs: 16 mongooses, 12 dogs, 2 cats and 1 goat. Our investigation has revealed that rabies infection spread from the northeast to the southwest of Grenada within the study period. Phylogenetic analysis revealed that the viruses from Grenada formed a monophyletic clade within the cosmopolitan lineage with a common ancestor predicted to have occurred recently (6-23 years ago), and are distinct from those found in Cuba and Puerto Rico, where mongoose rabies is also endemic. These data suggest that it is likely that this specific strain of RABV was imported from European regions rather than the Americas. These data contribute essential information for any potential rabies control program in Grenada and demonstrate the importance of a sound evidence base for planning interventions.
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Affiliation(s)
- Ulrike Zieger
- School of Veterinary Medicine, St. George's University, St. George's, Grenada
| | - Denise A. Marston
- Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Ravindra Sharma
- School of Veterinary Medicine, St. George's University, St. George's, Grenada
| | - Alfred Chikweto
- School of Veterinary Medicine, St. George's University, St. George's, Grenada
| | - Keshaw Tiwari
- School of Veterinary Medicine, St. George's University, St. George's, Grenada
| | - Muzzamil Sayyid
- School of Veterinary Medicine, St. George's University, St. George's, Grenada
| | | | - Hooman Goharriz
- Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Katja Voller
- Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Andrew C. Breed
- Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey, United Kingdom
- School of Veterinary Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Dirk Werling
- Royal Veterinary College, University of London, Hatfield, United Kingdom
| | - Anthony R. Fooks
- Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey, United Kingdom
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Daniel L. Horton
- Animal Health and Veterinary Laboratories Agency, New Haw, Addlestone, Surrey, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guilford, United Kingdom
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Tasioudi KE, Iliadou P, Agianniotaki EI, Robardet E, Liandris E, Doudounakis S, Tzani M, Tsaroucha P, Picard-Meyer E, Cliquet F, Mangana-Vougiouka O. Recurrence of animal rabies, Greece, 2012. Emerg Infect Dis 2014; 20:326-8. [PMID: 24447622 PMCID: PMC3901465 DOI: 10.3201/eid2002.130473] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Picard-Meyer E, Robardet E, Arthur L, Larcher G, Harbusch C, Servat A, Cliquet F. Bat rabies in France: a 24-year retrospective epidemiological study. PLoS One 2014; 9:e98622. [PMID: 24892287 PMCID: PMC4044004 DOI: 10.1371/journal.pone.0098622] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/05/2014] [Indexed: 11/18/2022] Open
Abstract
Since bat rabies surveillance was first implemented in France in 1989, 48 autochthonous rabies cases without human contamination have been reported using routine diagnosis methods. In this retrospective study, data on bats submitted for rabies testing were analysed in order to better understand the epidemiology of EBLV-1 in bats in France and to investigate some epidemiological trends. Of the 3176 bats submitted for rabies diagnosis from 1989 to 2013, 1.96% (48/2447 analysed) were diagnosed positive. Among the twelve recognised virus species within the Lyssavirus genus, two species were isolated in France. 47 positive bats were morphologically identified as Eptesicus serotinus and were shown to be infected by both the EBLV-1a and the EBLV-1b lineages. Isolation of BBLV in Myotis nattereri was reported once in the north-east of France in 2012. The phylogenetic characterisation of all 47 French EBLV-1 isolates sampled between 1989 and 2013 and the French BBLV sample against 21 referenced partial nucleoprotein sequences confirmed the low genetic diversity of EBLV-1 despite its extensive geographical range. Statistical analysis performed on the serotine bat data collected from 1989 to 2013 showed seasonal variation of rabies occurrence with a significantly higher proportion of positive samples detected during the autumn compared to the spring and the summer period (34% of positive bats detected in autumn, 15% in summer, 13% in spring and 12% in winter). In this study, we have provided the details of the geographical distribution of EBLV-1a in the south-west of France and the north-south division of EBLV-1b with its subdivisions into three phylogenetic groups: group B1 in the north-west, group B2 in the centre and group B3 in the north-east of France.
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Affiliation(s)
- Evelyne Picard-Meyer
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Nancy Laboratory for Rabies and Wildlife, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies Serology, Malzeville, France
- * E-mail:
| | - Emmanuelle Robardet
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Nancy Laboratory for Rabies and Wildlife, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies Serology, Malzeville, France
| | | | - Gérald Larcher
- SFEPM Chiroptera Group, Museum d'Histoire Naturelle de Bourges, Bourges, France
| | | | - Alexandre Servat
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Nancy Laboratory for Rabies and Wildlife, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies Serology, Malzeville, France
| | - Florence Cliquet
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Nancy Laboratory for Rabies and Wildlife, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies Serology, Malzeville, France
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Chiou HY, Hsieh CH, Jeng CR, Chan FT, Wang HY, Pang VF. Molecular characterization of cryptically circulating rabies virus from ferret badgers, Taiwan. Emerg Infect Dis 2014; 20:790-8. [PMID: 24751120 PMCID: PMC4012806 DOI: 10.3201/eid2005.131389] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
After the last reported cases of rabies in a human in 1959 and a nonhuman animal in 1961, Taiwan was considered free from rabies. However, during 2012-2013, an outbreak occurred among ferret badgers in Taiwan. To examine the origin of this virus strain, we sequenced 3 complete genomes and acquired multiple rabies virus (RABV) nucleoprotein and glycoprotein sequences. Phylogeographic analyses demonstrated that the RABV affecting the Taiwan ferret badgers (RABV-TWFB) is a distinct lineage within the group of lineages from Asia and that it has been differentiated from its closest lineages, China I (including isolates from Chinese ferret badgers) and the Philippines, 158-210 years ago. The most recent common ancestor of RABV-TWFB originated 91-113 years ago. Our findings indicate that RABV could be cryptically circulating in the environment. An understanding of the underlying mechanism might shed light on the complex interaction between RABV and its host.
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ROBARDET E, ILIEVA D, ILIEV E, GAGNEV E, PICARD-MEYER E, CLIQUET F. Epidemiology and molecular diversity of rabies viruses in Bulgaria. Epidemiol Infect 2014; 142:871-7. [PMID: 23830231 PMCID: PMC9167666 DOI: 10.1017/s0950268813001556] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 05/21/2013] [Accepted: 06/01/2013] [Indexed: 11/06/2022] Open
Abstract
A health emergency situation occurred in Bulgaria in 2007 when positive rabies cases were notified in Sofia district in the central-western part of the country, suggesting a southward spread of the disease for the first time in the last 10 years. Phylogenetic analysis on 49 isolates sampled between 2009 and 2011 showed, for the first time, evidence of the existence of NEE and D clustered lineages in Bulgaria. Their geographical distribution clearly reveals the permeability of natural barriers, as already suggested by the disease spread that occurred across the Balkan mountain range in 2007. The monitoring and passive surveillance programmes conducted since the first 2009 oral vaccination campaign, the spatio-temporal evolution of the disease in the country since 2007, and the need for further investigation of the role of jackals in virus dispersion are discussed.
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Affiliation(s)
- E. ROBARDET
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Nancy; Laboratory for Rabies and Wildlife, WHO Collaborating Centre for Research and Management in Zoonoses Control, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Institute for Rabies Serology, Technopôle Agricole et Vétérinaire, Malzéville, France
| | - D. ILIEVA
- National Diagnostic Research Veterinary Medical Institute, National Reference Laboratory of Rabies and monitoring the effectiveness of the vaccination, Sofia, Bulgaria
| | - E. ILIEV
- Bulgarian Food Safety Agency, Sofia, Bulgaria
| | - E. GAGNEV
- Regional Food Safety Directorate, Kyustendil, Bulgaria
| | - E. PICARD-MEYER
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Nancy; Laboratory for Rabies and Wildlife, WHO Collaborating Centre for Research and Management in Zoonoses Control, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Institute for Rabies Serology, Technopôle Agricole et Vétérinaire, Malzéville, France
| | - F. CLIQUET
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Nancy; Laboratory for Rabies and Wildlife, WHO Collaborating Centre for Research and Management in Zoonoses Control, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Institute for Rabies Serology, Technopôle Agricole et Vétérinaire, Malzéville, France
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Zhao J, Liu Y, Zhang S, Zhang F, Wang Y, Mi L, Wang S, Hu R. Molecular characterization of three ferret badger (Melogale moschata) rabies virus isolates from Jiangxi province, China. Arch Virol 2014; 159:2059-67. [PMID: 24643334 DOI: 10.1007/s00705-014-2044-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 02/28/2014] [Indexed: 12/25/2022]
Abstract
Ferret badger (FB) rabies viruses JX09-17(fb), JX09-18 and JX10-37 were isolated from three different regions in Jiangxi province, China, in 2009 and 2010. The complete nucleotide sequence identity between these three isolates was 87-93 %. Compared with the other Chinese rabies virus isolates and vaccine strains, 101 substitutions (53 in JX10-37, 23 in JX09-17(fb) and 25 in JX09-18) in the five structural proteins were observed, and 47 of these substitutions (27 in JX10-37, 14 in JX09-17(fb) and 6 in JX09-18) were unique among lyssaviruses. Amino acid substitutions of S231 and Q333 were noted respectively in the G protein antigenic site I of JX10-37 and site III in JX09-17(fb). Phylogenetic analysis showed that JX09-17(fb) is rooted within the China I lineage, JX09-18 is in China II, and JX10-37 is independent. Evolutionary analysis and comparative sequence data indicate that isolate JX10-37 is a variant virus that diverged from canine rabies viruses around 1933 (range 1886-1963).
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Affiliation(s)
- Jinghui Zhao
- Laboratory of Epidemiology and Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute, Academy of Military Medical Sciences, 666 Liuying West Road, Changchun, 130122, People's Republic of China
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Abstract
The paper describes a phylogenetic study of 58 Polish isolates of rabies virus collected between 1992 and 2010. Sequences of the nucleoprotein (N) and glycoprotein (G) genes approximately 600 bp long were compared with reference sequences (GenBank) of European rabies viruses from neighbouring countries. The study confirmed a very high level of homology (94.4–100 %) of the Polish rabies virus strains irrespective of the date of isolation. Two variants of rabies virus: NEE (Northeastern Europe variant) and CE (Central Europe variant), depending on the geographical place of isolation, were circulating in Poland from 1992 to 2010. The Polish rabies virus isolates showed high similarity to European RABV strains, especially those collected in Ukraine and Romania. They were clearly different from vaccine strains SAD B19 and SAD Bern, which have been used for oral vaccination of foxes against rabies in Poland since 1993.
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Affiliation(s)
- Anna Orłowska
- Department of Virology, National Veterinary Research Institute, Partyzantów 57 Avenue, 24-100, Puławy, Poland,
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Escobar LE, Peterson AT, Favi M, Yung V, Pons DJ, Medina-Vogel G. Ecology and geography of transmission of two bat-borne rabies lineages in Chile. PLoS Negl Trop Dis 2013; 7:e2577. [PMID: 24349592 PMCID: PMC3861194 DOI: 10.1371/journal.pntd.0002577] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/25/2013] [Indexed: 11/12/2022] Open
Abstract
Rabies was known to humans as a disease thousands of years ago. In America, insectivorous bats are natural reservoirs of rabies virus. The bat species Tadarida brasiliensis and Lasiurus cinereus, with their respective, host-specific rabies virus variants AgV4 and AgV6, are the principal rabies reservoirs in Chile. However, little is known about the roles of bat species in the ecology and geographic distribution of the virus. This contribution aims to address a series of questions regarding the ecology of rabies transmission in Chile. Analyzing records from 1985–2011 at the Instituto de Salud Pública de Chile (ISP) and using ecological niche modeling, we address these questions to help in understanding rabies-bat ecological dynamics in South America. We found ecological niche identity between both hosts and both viral variants, indicating that niches of all actors in the system are undifferentiated, although the viruses do not necessarily occupy the full geographic distributions of their hosts. Bat species and rabies viruses share similar niches, and our models had significant predictive power even across unsampled regions; results thus suggest that outbreaks may occur under consistent, stable, and predictable circumstances. The situation of rabies in America has been changing: rabies in dogs has decreased considerably, but bats are increasingly documented as natural reservoirs of other rabies variants. A significant gap exists in understanding of bat-borne rabies in Latin America. We identified bat species known to be connected with enzootic rabies with different antigenic variants in Chile, and compiled large-scale data sets by which to test for ecological niche differences among virus lineages and bat hosts. Our results begin to characterize important ecological factors affecting rabies distribution; modeling rabies in Chile allows comparisons across different latitudes and diverse landscapes. We found that rabies virus strains are found in similar environments, regardless of the bat host involved. This research improves understanding of bat-borne rabies dynamics, and important step towards preventing and controlling this and other emergent diseases linked to bats.
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Affiliation(s)
- Luis E. Escobar
- Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Santiago, Chile
| | - A. Townsend Peterson
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Myriam Favi
- Sección Rabia, Subdepartamento Virología, Instituto de Salud Pública de Chile, Ñuñoa, Santiago, Chile
| | - Verónica Yung
- Sección Rabia, Subdepartamento Virología, Instituto de Salud Pública de Chile, Ñuñoa, Santiago, Chile
| | - Daniel J. Pons
- Departamento de Matemática, Universidad Andres Bello, Santiago, Chile
| | - Gonzalo Medina-Vogel
- Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Santiago, Chile
- * E-mail:
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Kuzmina NA, Lemey P, Kuzmin IV, Mayes BC, Ellison JA, Orciari LA, Hightower D, Taylor ST, Rupprecht CE. The phylogeography and spatiotemporal spread of south-central skunk rabies virus. PLoS One 2013; 8:e82348. [PMID: 24312657 PMCID: PMC3849458 DOI: 10.1371/journal.pone.0082348] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 10/25/2013] [Indexed: 12/25/2022] Open
Abstract
The south-central skunk rabies virus (SCSK) is the most broadly distributed terrestrial viral lineage in North America. Skunk rabies has not been efficiently targeted by oral vaccination campaigns and represents a natural system of pathogen invasion, yielding insights to rabies emergence. In the present study we reconstructed spatiotemporal spread of SCSK in the whole territory of its circulation using a combination of Bayesian methods. The analysis based on 241 glycoprotein gene sequences demonstrated that SCSK is much more divergent phylogenetically than was appreciated previously. According to our analyses the SCSK originated in the territory of Texas ~170 years ago, and spread geographically during the following decades. The wavefront velocity in the northward direction was significantly greater than in the eastward and westward directions. Rivers (except the Mississippi River and Rio Grande River) did not constitute significant barriers for epizootic spread, in contrast to deserts and mountains. The mean dispersal rate of skunk rabies was lower than that of the raccoon and fox rabies. Viral lineages circulate in their areas with limited evidence of geographic spread during decades. However, spatiotemporal reconstruction shows that after a long period of stability the dispersal rate and wavefront velocity of SCSK are increasing. Our results indicate that there is a need to develop control measures for SCSK, and suggest how such measure can be implemented most efficiently. Our approach can be extrapolated to other rabies reservoirs and used as a tool for investigation of epizootic patterns and planning interventions towards disease elimination.
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Affiliation(s)
- Natalia A. Kuzmina
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Philippe Lemey
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Ivan V. Kuzmin
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Bonny C. Mayes
- Zoonosis Control Branch, Texas Department of State Health Services, Austin, Texas, United States of America
| | - James A. Ellison
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Lillian A. Orciari
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Dillon Hightower
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Steven T. Taylor
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Charles E. Rupprecht
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Department of Epidemiology and Public Health, Ross University School of Veterinary Medicine, Basseterre, St. Kitts, West Indies
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Pant GR, Lavenir R, Wong FYK, Certoma A, Larrous F, Bhatta DR, Bourhy H, Stevens V, Dacheux L. Recent emergence and spread of an Arctic-related phylogenetic lineage of rabies virus in Nepal. PLoS Negl Trop Dis 2013; 7:e2560. [PMID: 24278494 PMCID: PMC3836727 DOI: 10.1371/journal.pntd.0002560] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 10/14/2013] [Indexed: 12/25/2022] Open
Abstract
Rabies is a zoonotic disease that is endemic in many parts of the developing world, especially in Africa and Asia. However its epidemiology remains largely unappreciated in much of these regions, such as in Nepal, where limited information is available about the spatiotemporal dynamics of the main etiological agent, the rabies virus (RABV). In this study, we describe for the first time the phylogenetic diversity and evolution of RABV circulating in Nepal, as well as their geographical relationships within the broader region. A total of 24 new isolates obtained from Nepal and collected from 2003 to 2011 were full-length sequenced for both the nucleoprotein and the glycoprotein genes, and analysed using neighbour-joining and maximum-likelihood phylogenetic methods with representative viruses from all over the world, including new related RABV strains from neighbouring or more distant countries (Afghanistan, Greenland, Iran, Russia and USA). Despite Nepal's limited land surface and its particular geographical position within the Indian subcontinent, our study revealed the presence of a surprising wide genetic diversity of RABV, with the co-existence of three different phylogenetic groups: an Indian subcontinent clade and two different Arctic-like sub-clades within the Arctic-related clade. This observation suggests at least two independent episodes of rabies introduction from neighbouring countries. In addition, specific phylogenetic and temporal evolution analysis of viruses within the Arctic-related clade has identified a new recently emerged RABV lineage we named as the Arctic-like 3 (AL-3) sub-clade that is already widely spread in Nepal. Rabies is endemic in most Asian countries and represents a serious public health issue, with an estimated 31,000 people dying each year of this disease. The majority of human cases are transmitted by domestic dogs, which act as the principal reservoir host and vector. However, molecular epidemiology and evolutionary dynamics of the main etiological agent, the rabies virus (RABV), remains largely unappreciated in some regions such as in Nepal. Based on a subset of 24 new Nepalese isolates collected from 2003 to 2011 and representative RABV strains at a global scale, phylogenetic analysis based on the complete nucleoprotein and glycoprotein genes sequences revealed the presence of a surprising wide genetic diversity of RABV circulating in this country. The presence of three different co-existing phylogenetic groups was identified: an Indian subcontinent clade and two different Arctic-like sub-clades within the Arctic-related clade, namely Arctic-like (AL)-1, lineage a (AL-1a), and AL-3. Among these clusters, the AL-3 sub-clade appears as the major Nepalese phylogroup which emerged relatively recently in this country, within the last 30 years. These data has raised some concerns about the exchange of RABV between different countries, and provided key elements for implementation of effective control measures of rabies in Nepal.
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Affiliation(s)
- Ganesh R. Pant
- Rabies Vaccine Production Laboratory, Tripureshwor, Kathmandu, Nepal
| | - Rachel Lavenir
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, National Reference Centre for Rabies, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Frank Y. K. Wong
- Australian Animal Health Laboratory, CSIRO Animal Food and Health Sciences, Geelong, Victoria, Australia
| | - Andrea Certoma
- Australian Animal Health Laboratory, CSIRO Animal Food and Health Sciences, Geelong, Victoria, Australia
| | - Florence Larrous
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, National Reference Centre for Rabies, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Dwij R. Bhatta
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Hervé Bourhy
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, National Reference Centre for Rabies, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Vittoria Stevens
- Australian Animal Health Laboratory, CSIRO Animal Food and Health Sciences, Geelong, Victoria, Australia
- * E-mail: (VS); (LD)
| | - Laurent Dacheux
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, National Reference Centre for Rabies, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
- * E-mail: (VS); (LD)
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Abstract
The present study was done to determine the molecular epidemiology of rabies virus (RV) in Vietnam. The nucleoprotein (N) and glycoprotein (G) genes of RVs were amplified from the brains of ten rabid dogs of Ho Chi Minh City, Vietnam. The nucleotide sequences of these genes were compared with those of other Asian strains to find the possible relationship among them. Phylogenetic analysis revealed that the Asian N gene segregated into three main branches, namely South-East Asia 1 (SEA 1), South-East Asia 2 (SEA 2) and Indian subcontinent (ISC) genotypes. The SEA 1 genotype comprised RVs from Malaysia, Vietnam and Thailand. The SEA 2 genotype contained strains from the Philippines, and the ISC genotype comprised strains from Sri Lanka and India. Phylogenetically G genes of RVs from Vietnam and Thailand were clustered together. Our study suggests that Vietnamese and Thai RVs are closely related and might have originated from a common ancestor.
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Affiliation(s)
- Junpei Yamagata
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, Oita University, Yufu, Oita, Japan
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Kasempimolporn S, Saengseesom W, Tirawatnapong T, Puempumpanich S, Sitprija V. Genetic Typing of Feline Rabies Virus Isolated in Greater Bangkok, Thailand. Microbiol Immunol 2013; 48:307-11. [PMID: 15107541 DOI: 10.1111/j.1348-0421.2004.tb03511.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
To study the molecular epidemiology of rabies virus that is prevalent among cats in greater Bangkok, Thailand, a total of 17 rabies virus isolates from cats were characterized and compared with 120 rabies virus isolates from dogs. Analyses were performed on the genetic polymorphism in the rabies virus nucleoprotein (N) gene. Rabies virus N gene of isolates was amplified by reverse transcriptionpolymerase chain reaction. The diversity of N gene was revealed by the restriction fragment length polymorphism (RFLP) method. The rabies virus isolates from cats could be classified into 5 types, designated as Dd I-Hf I, Dd II-Hf II, Dd III-Hf I, Dd IV-Hf I, and Dd IV-Hf III. Type Dd I-Hf I was encountered more frequently than the others. It was apparent that no less than five rabies virus types presented in the areas of Bangkok. Moreover, all five RFLP patterns were typical of those which had been observed in dogs. Our findings suggest that there had been viral transmission between the dogs and the cats.
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Affiliation(s)
- Songsri Kasempimolporn
- The Queen Saovabha Memorial Institute (WHO Collaborating Center for Research on Rabies), Thai Red Cross Society, Bangkok, Thailand.
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Seetahal JFR, Velasco-Villa A, Allicock OM, Adesiyun AA, Bissessar J, Amour K, Phillip-Hosein A, Marston DA, McElhinney LM, Shi M, Wharwood CA, Fooks AR, Carrington CVF. Evolutionary history and phylogeography of rabies viruses associated with outbreaks in Trinidad. PLoS Negl Trop Dis 2013; 7:e2365. [PMID: 23991230 PMCID: PMC3749974 DOI: 10.1371/journal.pntd.0002365] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 07/01/2013] [Indexed: 11/19/2022] Open
Abstract
Bat rabies is an emerging disease of public health significance in the Americas. The Caribbean island of Trinidad experiences periodic outbreaks within the livestock population. We performed molecular characterisation of Trinidad rabies virus (RABV) and used a Bayesian phylogeographic approach to investigate the extent to which outbreaks are a result of in situ evolution versus importation of virus from the nearby South American mainland. Trinidadian RABV sequences were confirmed as bat variant and clustered with Desmodus rotundus (vampire bat) related sequences. They fell into two largely temporally defined lineages designated Trinidad I and II. The Trinidad I lineage which included sequences from 1997-2000 (all but two of which were from the northeast of the island) was most closely related to RABV from Ecuador (2005, 2007), French Guiana (1990) and Venezuela (1993, 1994). Trinidad II comprised sequences from the southwest of the island, which clustered into two groups: Trinidad IIa, which included one sequence each from 2000 and 2007, and Trinidad IIb including all 2010 sequences. The Trinidad II sequences were most closely related to sequences from Brazil (1999, 2004) and Uruguay (2007, 2008). Phylogeographic analyses support three separate RABV introductions from the mainland from which each of the three Trinidadian lineages arose. The estimated dates for the introductions and subsequent lineage expansions suggest periods of in situ evolution within Trinidad following each introduction. These data also indicate co-circulation of Trinidad lineage I and IIa during 2000. In light of these findings and the likely vampire bat origin of Trinidadian RABV, further studies should be conducted to investigate the relationship between RABV spatiotemporal dynamics and vampire bat population ecology, in particular any movement between the mainland and Trinidad.
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Affiliation(s)
- Janine F. R. Seetahal
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
- Veterinary Diagnostic Laboratory, Ministry of Food Production, Champs Fleurs, Trinidad and Tobago
| | - Andres Velasco-Villa
- Rabies Program, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Orchid M. Allicock
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Abiodun A. Adesiyun
- School of Veterinary Medicine, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Joseph Bissessar
- Veterinary Diagnostic Laboratory, Ministry of Food Production, Champs Fleurs, Trinidad and Tobago
| | - Kirk Amour
- National Animal Disease Centre, Centeno, Trinidad and Tobago
| | | | - Denise A. Marston
- Wildlife Zoonoses and Vector-Borne Diseases Research Group, Animal Health and Veterinary Laboratories Agency (AHVLA), Addlestone, Surrey, United Kingdom
| | - Lorraine M. McElhinney
- Wildlife Zoonoses and Vector-Borne Diseases Research Group, Animal Health and Veterinary Laboratories Agency (AHVLA), Addlestone, Surrey, United Kingdom
| | - Mang Shi
- Rabies Program, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Anthony R. Fooks
- Wildlife Zoonoses and Vector-Borne Diseases Research Group, Animal Health and Veterinary Laboratories Agency (AHVLA), Addlestone, Surrey, United Kingdom
| | - Christine V. F. Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
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Cliquet F, Robardet E, Picard Meyer E. Genetic strain modification of a live rabies virus vaccine widely used in Europe for wildlife oral vaccination. Antiviral Res 2013; 100:84-9. [PMID: 23899697 DOI: 10.1016/j.antiviral.2013.07.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/16/2013] [Accepted: 07/18/2013] [Indexed: 11/18/2022]
Abstract
In Europe, the main reservoir and vector of rabies has been the red fox (Vulpes vulpes). Oral immunization of foxes with live vaccines, using attenuated rabies strains (SAD B19, SAD Bern), apathogenic mutants of an attenuated strain (SAG2) and the vaccinia-rabies glycoprotein recombinant virus vaccine (V-RG), has been shown to be the most effective method for the control and elimination of rabies. Among all vaccines currently used for wildlife oral vaccination, one vaccine (marketed as SAD Bern strain) has been widely used in Europe since 1992 with the distribution of 17million of baits in 2011. Because of the potential environmental safety risk of a live virus which could revert to virulence, the full genome sequencing of this vaccine was undertaken and the sequence was characterized and compared with those of referenced rabies viruses. The vaccine showed higher similarity to the strains belonging to the SAD B19 vaccine virus strains than to the SAD Bern vaccines. This study is the first one reporting on virus strain identity changes in this attenuated vaccine.
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Affiliation(s)
- Florence Cliquet
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Nancy Laboratory for Rabies and Wildlife, European Union Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies Serology, WHO Collaborating Centre for Research & Management in Zoonoses Control, OIE Reference Laboratory for Rabies, Technopôle agricole et vétérinaire, BP 40 009, 54 220 Malzéville Cedex, France.
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