1
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Rupprecht CE, Buchanan T, Cliquet F, King R, Müller T, Yakobson B, Yang DK. A Global Perspective on Oral Vaccination of Wildlife against Rabies. J Wildl Dis 2024; 60:241-284. [PMID: 38381612 DOI: 10.7589/jwd-d-23-00078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 01/03/2024] [Indexed: 02/23/2024]
Abstract
The long-term mitigation of human-domestic animal-wildlife conflicts is complex and difficult. Over the last 50 yr, the primary biomedical concepts and actualized collaborative global field applications of oral rabies vaccination to wildlife serve as one dramatic example that revolutionized the field of infectious disease management of free-ranging animals. Oral vaccination of wildlife occurred in diverse locales within Africa, Eurasia, the Middle East, and North America. Although rabies is not a candidate for eradication, over a billion doses of vaccine-laden baits distributed strategically by hand, at baiting stations, or via aircraft, resulted in widespread disease prevention, control, or local disease elimination among mesocarnivores. Pure, potent, safe, and efficacious vaccines consisted of either modified-live, highly attenuated, or recombinant viruses contained within attractive, edible baits. Since the late 1970s, major free-ranging target species have included coyotes (Canis latrans), foxes (Urocyon cinereoargenteus; Vulpes vulpes), jackals (Canis aureus; Lupulella mesomelas), raccoons (Procyon lotor), raccoon dogs (Nyctereutes procyonoides), and skunks (Mephitis mephitis). Operational progress has occurred in all but the latter species. Programmatic evaluations of oral rabies vaccination success have included: demonstration of biomarkers incorporated within vaccine-laden baits in target species as representative of bait contact; serological measurement of the induction of specific rabies virus neutralizing antibodies, indicative of an immune response to vaccine; and most importantly, the decreasing detection of rabies virus antigens in the brains of collected animals via enhanced laboratory-based surveillance, as evidence of management impact. Although often conceived mistakenly as a panacea, such cost-effective technology applied to free-ranging wildlife represents a real-world, One Health application benefiting agriculture, conservation biology, and public health. Based upon lessons learned with oral rabies vaccination of mesocarnivores, opportunities for future extension to other taxa and additional diseases will have far-reaching, transdisciplinary benefits.
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Affiliation(s)
- Charles E Rupprecht
- College of Forestry, Wildlife and Environment, College of Veterinary Medicine, Auburn University, 602 Duncan Drive, Auburn, Alabama 36849, USA
| | - Tore Buchanan
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Trent University, 2140 East Bank Drive, Peterborough, Ontario K9L1Z8, Canada
| | - Florence Cliquet
- ANSES, Nancy Laboratory for Rabies and Wildlife, European Union Reference Laboratory for Rabies Serology, European Union Reference Laboratory for Rabies, WHO Collaborating Centre for Research and Management in Zoonoses Control, WOAH Reference Laboratory for Rabies, Technopôle Agricole et Vétérinaire, Domaine de Pixérécourt, CS 40009 Malzeville, France
| | - Roni King
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Thomas Müller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, WHO Collaborating Centre for Rabies Surveillance and Research, WOAH Reference Laboratory for Rabies, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Boris Yakobson
- WOAH Reference Laboratory for Rabies, Kimron Veterinary Institute, Ministry of Agriculture, Derech HaMaccabim 62, Rishon Lezion, 50250, Israel
| | - Dong-Kun Yang
- Viral Disease Division, Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs, 177, Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea
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2
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Chupin SA, Sprygin AV, Zinyakov NG, Guseva NA, Shcherbinin SV, Korennoy FI, Adelshin RV, Mazloum A, Sukharkov AY, Nevzorova VV. Phylogenetic Characterization of Rabies Virus Field Isolates Collected from Animals in European Russian Regions in 2009-2022. Microorganisms 2023; 11:2526. [PMID: 37894184 PMCID: PMC10609256 DOI: 10.3390/microorganisms11102526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/01/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Rabies is a fatal disease of mammals that poses a high zoonotic risk to humans as well. The distribution of rabies is mainly driven by host animal migration and human-mediated dispersion. To contribute to the global understanding of the rabies virus (RABV) molecular epidemiology, 94 RABV field isolates collected from animals in 13 European Russian regions were phylogenetically characterized using the nearly full-size N gene nucleotide sequences. According to phylogenetic inferences, all isolates belonged to one of the two established phylogenetic groups, either group C (n = 54) or group D (n = 40), which are part of the clade Cosmopolitan of RABVs. Some representatives of group C collected from regions located far apart from each other had a remarkably high level of nucleotide identity. The possibility of the contribution of local bat species to the distribution of RABVs was discussed. Interestingly, over the years, the fraction of group D isolates has been constantly decreasing compared with that of group C isolates. The phylogenetic insights generated herein might have an important contribution to the control and surveillance of animal rabies epidemiology in the region.
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Affiliation(s)
- Sergei A. Chupin
- Reference Laboratory for Rabies and BSE, Federal Centre for Animal Health, 600901 Vladimir, Russia
| | - Alexandr V. Sprygin
- Laboratory of Molecular and Genetic Researches, Federal Centre for Animal Health, 600901 Vladimir, Russia; (A.V.S.); (A.M.)
| | - Nikolay G. Zinyakov
- Reference Laboratory for Viral Avian Diseases, Federal Centre for Animal Health, 600901 Vladimir, Russia
| | - Nelly A. Guseva
- Reference Laboratory for Viral Avian Diseases, Federal Centre for Animal Health, 600901 Vladimir, Russia
| | - Sergey V. Shcherbinin
- Information Analysis Centre under the Department for Veterinary Surveillance, Federal Centre for Animal Health, 600901 Vladimir, Russia (F.I.K.)
| | - Fedor I. Korennoy
- Information Analysis Centre under the Department for Veterinary Surveillance, Federal Centre for Animal Health, 600901 Vladimir, Russia (F.I.K.)
| | - Renat V. Adelshin
- Irkutsk Anti-Plague Research Institute of Siberia and the Far East, 664047 Irkutsk, Russia;
- Faculty of Biology and Soil Sciences, Irkutsk State University, 664033 Irkutsk, Russia
| | - Ali Mazloum
- Laboratory of Molecular and Genetic Researches, Federal Centre for Animal Health, 600901 Vladimir, Russia; (A.V.S.); (A.M.)
| | - Andrey Y. Sukharkov
- Reference Laboratory for Rabies and BSE, Federal Centre for Animal Health, 600901 Vladimir, Russia
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Podgoreanu P, Petre A, Tănasă RI, Dinu S, Oprea M, Marandiuc IM, Vlase E. Sequencing and Partial Molecular Characterization of BAB-TMP, the Babeș Strain of the Fixed Rabies Virus Adapted for Multiplication in Cell Lines. Viruses 2023; 15:1851. [PMID: 37766258 PMCID: PMC10536377 DOI: 10.3390/v15091851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/10/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
The rabies virus is a major zoonosis that causes severe nervous disease in humans, leading to paralysis and death. The world's second anti-rabies center was established in 1888 by Victor Babeș, in Bucharest, where an eponymous strain of rabies was isolated and used to develop a method for immunization. The Babeș strain of the rabies virus was used for over 100 years in Romania to produce a rabies vaccine for human use, based on animal nerve tissue, thus having a proven history of prophylactic use. The present study aimed to sequence the whole genome of the Babeș strain and to explore its genetic relationships with other vaccine strains as well as to characterize its relevant molecular traits. After being adapted for multiplication in cell lines and designated BAB-TMP, 99% of the viral genome was sequenced. The overall organization of the genome is similar to that of other rabies vaccine strains. Phylogenetic analysis indicated that the BAB-TMP strain is closely related to the Russian RV-97 vaccine strain, and both seem to have a common ancestor. The nucleoprotein gene of the investigated genome was the most conserved, and the glycoprotein showed several unique amino acid substitutions within the major antigenic sites and linear epitopes.
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Affiliation(s)
| | | | - Radu Iulian Tănasă
- Cantacuzino National Military Medical Institute for Research and Development, 050096 Bucharest, Romania; (P.P.); (A.P.)
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Holtz A, Baele G, Bourhy H, Zhukova A. Integrating full and partial genome sequences to decipher the global spread of canine rabies virus. Nat Commun 2023; 14:4247. [PMID: 37460566 DOI: 10.1038/s41467-023-39847-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/30/2023] [Indexed: 07/20/2023] Open
Abstract
Despite the rapid growth in viral genome sequencing, statistical methods face challenges in handling historical viral endemic diseases with large amounts of underutilized partial sequence data. We propose a phylogenetic pipeline that harnesses both full and partial viral genome sequences to investigate historical pathogen spread between countries. Its application to rabies virus (RABV) yields precise dating and confident estimates of its geographic dispersal. By using full genomes and partial sequences, we reduce both geographic and genetic biases that often hinder studies that focus on specific genes. Our pipeline reveals an emergence of the present canine-mediated RABV between years 1301 and 1403 and reveals regional introductions over a 700-year period. This geographic reconstruction enables us to locate episodes of human-mediated introductions of RABV and examine the role that European colonization played in its spread. Our approach enables phylogeographic analysis of large and genetically diverse data sets for many viral pathogens.
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Affiliation(s)
- Andrew Holtz
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015, Paris, France.
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Hervé Bourhy
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015, Paris, France
- World Health Organization Collaborating Center for Reference and Research on Rabies, Institut Pasteur, Paris, France
| | - Anna Zhukova
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015, Paris, France.
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Dascalu MA, Picard-Meyer E, Robardet E, Servat A, Arseniev S, Groza O, Starciuc N, Vuta V, Barbuceanu F, Tanase OI, Daraban Bocaneti F, Quenault H, Hirchaud E, Blanchard Y, Velescu E, Cliquet F. Whole genome sequencing and phylogenetic characterisation of rabies virus strains from Moldova and north-eastern Romania. PLoS Negl Trop Dis 2023; 17:e0011446. [PMID: 37410714 DOI: 10.1371/journal.pntd.0011446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Rabies is the oldest fatal zoonotic disease recognised as a neglected tropical disease and is caused by an RNA virus belonging to the genus Lyssavirus, family Rhabdoviridae. METHODOLOGY/PRINCIPAL FINDINGS A deep molecular analysis was conducted on full-length nucleoprotein (N) gene and whole genome sequences of rabies virus from 37 animal brain samples collected between 2012 and 2017 to study the circulation of rabies virus (RABV) variants. The overall aim was to better understand their distribution in Moldova and north-eastern Romania. Both Sanger and high throughput sequencing on Ion Torrent and Illumina platforms were performed. Phylogenetic analysis of the RABV sequences from both Moldova and Romania revealed that all the samples (irrespective of the year of isolation and the species) belonged to a single phylogenetic group: north-eastern Europe (NEE), clustering into three assigned lineages: RO#5, RO#6 and RO#7. CONCLUSIONS/SIGNIFICANCE High throughput sequencing of RABV samples from domestic and wild animals was performed for the first time for both countries, providing new insights into virus evolution and epidemiology in this less studied region, expanding our understanding of the disease.
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Affiliation(s)
- Mihaela Anca Dascalu
- Department of Public Health, Faculty of Veterinary Medicine, Iasi University of Life Sciences "Ion Ionescu de la Brad", Mihail Sadoveanu Alley, Romania
| | - Evelyne Picard-Meyer
- 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 Laboratory for Rabies Serology, Technopôle Agricole et Vétérinaire, Malzéville, France
| | - Emmanuelle Robardet
- 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 Laboratory for Rabies Serology, Technopôle Agricole et Vétérinaire, Malzéville, France
| | - Alexandre Servat
- 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 Laboratory for Rabies Serology, Technopôle Agricole et Vétérinaire, Malzéville, France
| | | | - Oxana Groza
- Republican Center of Veterinary Diagnostic, Chisinau, Moldova
| | - Nicolae Starciuc
- Faculty of Veterinary Medicine, State Agrarian University, Chisinau, Moldova
| | - Vlad Vuta
- Institute for Diagnosis and Animal Health, OIE Reference Laboratory for Rabies, Bucharest, Romania; University of Agronomic Study and Veterinary Medicine, Faculty of Veterinary Medicine, Bucharest, Romania
| | - Florica Barbuceanu
- Institute for Diagnosis and Animal Health, OIE Reference Laboratory for Rabies, Bucharest, Romania; University of Agronomic Study and Veterinary Medicine, Faculty of Veterinary Medicine, Bucharest, Romania
| | - Oana Irina Tanase
- Department of Public Health, Faculty of Veterinary Medicine, Iasi University of Life Sciences "Ion Ionescu de la Brad", Mihail Sadoveanu Alley, Romania
| | - Florentina Daraban Bocaneti
- Department of Public Health, Faculty of Veterinary Medicine, Iasi University of Life Sciences "Ion Ionescu de la Brad", Mihail Sadoveanu Alley, Romania
| | - Helene Quenault
- ANSES, Nancy Ploufragan-Plouzané-Niort Laboratory, Viral Genetics and Biosafety Unit, Technopôle Agricole et Vétérinaire, Malzéville, France
| | - Edouard Hirchaud
- ANSES, Nancy Ploufragan-Plouzané-Niort Laboratory, Viral Genetics and Biosafety Unit, Technopôle Agricole et Vétérinaire, Malzéville, France
| | - Yannick Blanchard
- ANSES, Nancy Ploufragan-Plouzané-Niort Laboratory, Viral Genetics and Biosafety Unit, Technopôle Agricole et Vétérinaire, Malzéville, France
| | - Elena Velescu
- Department of Public Health, Faculty of Veterinary Medicine, Iasi University of Life Sciences "Ion Ionescu de la Brad", Mihail Sadoveanu Alley, Romania
| | - Florence Cliquet
- 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 Laboratory for Rabies Serology, Technopôle Agricole et Vétérinaire, Malzéville, France
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6
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Cai M, Liu H, Jiang F, Sun Y, Wang W, An Y, Zhang M, Li X, Liu D, Li Y, Yu Y, Huang W, Wang Y. Analysis of the evolution, infectivity and antigenicity of circulating rabies virus strains. Emerg Microbes Infect 2022; 11:1474-1487. [PMID: 35570580 PMCID: PMC9176641 DOI: 10.1080/22221751.2022.2078742] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Rabies virus has existed for thousands of years and is circulating in many species. In the present study, a total of 2896 rabies viruses isolated worldwide were phylogenetically classified into ten clusters based on the G gene sequence, and these clusters showed a close relationship with the hosts and regions that they were isolated from. Eighty-three representative G sequences were selected from ten clusters and were used to construct pseudoviruses using the VSV vector. The phylogenetic relationships, infectivity and antigenicity of the representative 83 pseudotyped rabies viruses were comprehensively analyzed. Eighty three pseudoviruses were divided into four antigentic clusters (GAgV), of which GAgV4 showed poor neutralization to all immunized sera. Further analysis showed that almost all strains in the GAgV4 were isolated from wild animals in the America, especially bats and skunks. No significant relationship in terms of phylogeny, infectivity and antigenicity was proved. Amino acid mutations at residues 231and 436 can affect the infectivity, while mutations at residues 113, 164 and 254 may affect the sensitivity to immunized animal sera, especially residue 254. We recommend close monitoring of infectivity and antigenicity, which should be more precise than simple genetic analysis.
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Affiliation(s)
- Meina Cai
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China.,Graduate School of Peking Union Medical College, Beijing, People's Republic of China
| | - Haizhou Liu
- National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China.,CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Fei Jiang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Yeqing Sun
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Wenbo Wang
- Division of Monoclonal Antibody Products, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Yimeng An
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Mengyi Zhang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Xueli Li
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Di Liu
- National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China.,CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Yuhua Li
- Department of Arboviral Vaccine, National Institutes for Food and Drug Control, (NIFDC), Beijing, People's Republic of China
| | - Yongxin Yu
- Department of Arboviral Vaccine, National Institutes for Food and Drug Control, (NIFDC), Beijing, People's Republic of China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China.,Graduate School of Peking Union Medical College, Beijing, People's Republic of China
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7
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Ogunjo S, Olusola A, Orimoloye I. Association Between Weather Parameters and SARS-CoV-2 Confirmed Cases in Two South African Cities. GEOHEALTH 2022; 6:e2021GH000520. [PMID: 36348988 PMCID: PMC9635841 DOI: 10.1029/2021gh000520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 04/10/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Several approaches have been used in the race against time to mitigate the spread and impact of COVID-19. In this study, we investigated the role of temperature, relative humidity, and particulate matter in the spread of COVID-19 cases within two densely populated cities of South Africa-Pretoria and Cape Town. The role of different levels of COVID-19 restrictions in the air pollution levels, obtained from the Purple Air Network, of the two cities were also considered. Our results suggest that 26.73% and 43.66% reduction in PM2.5 levels were observed in Cape Town and Pretoria respectively for no lockdown (Level 0) to the strictest lockdown level (Level 5). Furthermore, our results showed a significant relationship between particulate matter and COVID-19 in the two cities. Particulate matter was found to be a good predictor, based on the significance of causality test, of COVID-19 cases in Pretoria with a lag of 7 days and more. This suggests that the effect of particulate matter on the number of cases can be felt after 7 days and beyond in Pretoria.
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Affiliation(s)
- Samuel Ogunjo
- Department of PhysicsFederal University of TechnologyAkureNigeria
| | - Adeyemi Olusola
- Faculty of Environmental and Urban ChangeYork UniversityTorontoCanada
- Department of GeographyUniversity of the Free StateBloemfonteinSouth Africa
| | - Israel Orimoloye
- Department of Geography, Faculty of Food and AgricultureThe University of the West Indies, St. Augustine CampusSt. AugustineTrinidad and Tobago
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8
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Detection and molecular characterization of rabies virus isolates from humans in Cameroon. Diagn Microbiol Infect Dis 2022; 105:115834. [DOI: 10.1016/j.diagmicrobio.2022.115834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/06/2022] [Accepted: 10/09/2022] [Indexed: 11/20/2022]
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9
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Evolutionary analysis of rabies virus isolates from Georgia. Arch Virol 2022; 167:2293-2298. [DOI: 10.1007/s00705-022-05550-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/14/2022] [Indexed: 11/02/2022]
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10
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Miao F, Zhao J, Li N, Liu Y, Chen T, Mi L, Yang J, Chen Q, Zhang F, Feng J, Li S, Zhang S, Hu R. Genetic Diversity, Evolutionary Dynamics, and Pathogenicity of Ferret Badger Rabies Virus Variants in Mainland China, 2008–2018. Front Microbiol 2022; 13:929202. [PMID: 35910614 PMCID: PMC9330412 DOI: 10.3389/fmicb.2022.929202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/24/2022] [Indexed: 11/25/2022] Open
Abstract
In contrast to dog-associated human rabies cases decline year by year due to the rabies vaccination coverage rates increase in China, ferret badger (FB, Melogale moschata)-associated human rabies cases emerged in the 1990s, and are now an increasingly recognized problem in southeast China. To investigate epidemiology, temporal evolution dynamics, transmission characterization, and pathogenicity of FB-associated rabies viruses (RABVs), from 2008 to 2018, we collected 3,622 FB brain samples in Jiangxi and Zhejiang Province, and detected 112 RABV isolates. Four FB-related lineages were identified by phylogenetic analysis (lineages A–D), the estimated Times to Most Recent Common Ancestor were 1941, 1990, 1937, and 1997 for lineages A–D, respectively. Furthermore, although no FB-associated human rabies case has been reported there apart from Wuyuan area, FB-RABV isolates are mainly distributed in Jiangxi Province. Pathogenicity of FB-RABVs was assessed using peripheral inoculation in mice and in beagles with masseter muscles, mortality-rates ranging from 20 to 100% in mice and 0 to 20% in beagles in the groups infected with the various isolates. Screening of sera from humans with FB bites and no post-exposure prophylaxis to rabies revealed that five of nine were positive for neutralizing antibodies of RABV. All the results above indicated that FB-RABV variants caused a lesser pathogenicity in mice, beagles, and even humans. Vaccination in mice suggests that inactivated vaccine or recombinant subunit vaccine products can be used to control FB-associated rabies, however, oral vaccines for stray dogs and wildlife need to be developed and licensed in China urgently.
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Affiliation(s)
- Faming Miao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jinghui Zhao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Nan Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Ye Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Teng Chen
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Lijuan Mi
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jinjin Yang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Qi Chen
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Fei Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jie Feng
- Suzhou Shangfangshan Forest Zoo, Suzhou, China
| | - Shunfei Li
- Department of Innovative Medical Research, Chinese People’s Liberation Army General Hospital, Institute of Hospital Management, Beijing, China
- *Correspondence: Shunfei Li,
| | - Shoufeng Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- Shoufeng Zhang,
| | - Rongliang Hu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- Rongliang Hu,
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11
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Müller T, Hassel R, Jago M, Khaiseb S, van der Westhuizen J, Vos A, Calvelage S, Fischer S, Marston DA, Fooks AR, Höper D, Freuling CM. Rabies in kudu: Revisited. Adv Virus Res 2022; 112:115-173. [DOI: 10.1016/bs.aivir.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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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] [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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Yin C. Progress in the Development of Animal Rabies Vaccines in China. China CDC Wkly 2021; 3:825-830. [PMID: 34595001 PMCID: PMC8477054 DOI: 10.46234/ccdcw2021.204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/22/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Chunsheng Yin
- China Institute of Veterinary Drug Control, Beijing, China
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14
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Lojkić I, Šimić I, Bedeković T, Krešić N. Current Status of Rabies and Its Eradication in Eastern and Southeastern Europe. Pathogens 2021; 10:pathogens10060742. [PMID: 34204652 PMCID: PMC8231232 DOI: 10.3390/pathogens10060742] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/27/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022] Open
Abstract
The objective of this paper is to provide an overview of the current status of rabies in Europe, with special emphasis on Croatia and Southeast and East Europe. Due to the systematic implementation of a rabies eradication program by oral vaccination of wild animals, by the end of the 20th century, most West and Central European countries were rabies-free. The EU goal was to eradicate rabies in wildlife and domestic animals by 2020. No matter how achievable the goal seemed to be, the disease is still present in the eastern part of the EU, as was notified in 2020 by two member states—Poland and Romania. Croatia has been rabies-free for the last seven years but given that it borders a non-EU country in which a case of rabies was confirmed in 2020, it will continue to contribute to the maintenance of the rabies-free region. A rabies-free EU can only be achieved by continuous oral vaccination, coordination and a regional approach. The prevention of reintroductions from bordering countries in which rabies has not been eradicated yet, and the support for the eradication efforts made by these countries, are goals still pending.
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Affiliation(s)
- Ivana Lojkić
- Laboratory for Rabies and General Virology, Department of Virology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (T.B.); (N.K.)
- Correspondence:
| | - Ivana Šimić
- Laboratory for Molecular Virology, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia;
| | - Tomislav Bedeković
- Laboratory for Rabies and General Virology, Department of Virology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (T.B.); (N.K.)
| | - Nina Krešić
- Laboratory for Rabies and General Virology, Department of Virology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (T.B.); (N.K.)
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15
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Wierzbicki H, Zatoń-Dobrowolska M, Mucha A, Moska M. Insight into the Genetic Population Structure of Wild Red Foxes in Poland Reveals Low Risk of Genetic Introgression from Escaped Farm Red Foxes. Genes (Basel) 2021; 12:genes12050637. [PMID: 33922932 PMCID: PMC8146073 DOI: 10.3390/genes12050637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/28/2021] [Accepted: 04/23/2021] [Indexed: 11/21/2022] Open
Abstract
In this study we assessed the level of genetic introgression between red foxes bred on fur farms in Poland and the native wild population. We also evaluated the impact of a geographic barrier and isolation by distance on gene flow between two isolated subpopulations of the native red fox and their genetic differentiation. Nuclear and mitochondrial DNA was collected from a total of 308 individuals (200 farm and 108 wild red foxes) to study non-native allele flow from farm into wild red fox populations. Genetic structure analyses performed using 24 autosomal microsatellites showed two genetic clusters as being the most probable number of distinct populations. No strong admixture signals between farm and wild red foxes were detected, and significant genetic differentiation was identified between the two groups. This was also apparent from the mtDNA analysis. None of the concatenated haplotypes detected in farm foxes was found in wild animals. The consequence of this was that the haplotype network displayed two genetically distinct groups: farm foxes were completely separated from native ones. Neither the River Vistula nor isolation by distance had a significant impact on gene flow between the separated wild red fox subpopulations. The results of our research indicate a low probability of genetic introgression between farm and native red foxes, and no threat to the genetic integrity of this species.
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16
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Černe D, Hostnik P, Toplak I. The Successful Elimination of Sylvatic Rabies Using Oral Vaccination of Foxes in Slovenia. Viruses 2021; 13:405. [PMID: 33806582 PMCID: PMC8001208 DOI: 10.3390/v13030405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 01/21/2023] Open
Abstract
Sylvatic rabies was present in Slovenia between 1973 and 2013, with the red fox as the main reservoir of the rabies virus. The first oral rabies vaccination (ORV) control program in foxes started in 1988, using the manual distribution of baits. Significant improvement of fox vaccination was achieved with the aerial distribution of baits, starting in 1995 and successfully finished with the final, fifty-ninth vaccination campaign in 2019. Between 1979 and 2019, a total of 86,471 samples were tested, and 10,975 (12.69%) rabies-positive animals were identified. Within the ORV, two different vaccines were used, containing modified live virus strain Street Alabama Dufferin (SAD) B19 and SAD Bern, while the last ORV campaigns were completed in 2019, with a vaccine containing a genetically modified strain of SPBN GASGAS. Molecular epidemiological studies of 95 rabies-positive samples, originating from red foxes, badgers, cattle, dogs, martens, cats, and horses, revealed a low genetic diversity of circulating strains and high similarity to strains from neighboring countries. During the elimination program, few vaccine-induced rabies cases were detected: three in red foxes and one case in a marten, with no epidemiological relevance. Slovenia has been officially declared a country free of rabies since 2016.
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Affiliation(s)
- Danijela Černe
- Institute of Microbiology and Parasitology, Virology Unit, Veterinary Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (P.H.); (I.T.)
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17
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Pharande RR, Majee SB, Gaikwad SS, Moregoankar SD, Bannalikar A, Doiphode A, Gandge R, Dighe D, Ingle S, Mukherjee S. Evolutionary analysis of rabies virus using the partial Nucleoprotein and Glycoprotein gene in Mumbai region of India. J Gen Virol 2021; 102. [PMID: 33544071 DOI: 10.1099/jgv.0.001521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nearly 1.7 million cases of dog bites are reported every year in India and many cases of animal rabies are left unattended and undiagnosed. Therefore, a mere diagnosis of rabies is not sufficient to understand the epidemiology and the spread of the rabies virus (RV) in animals. There is a paucity of information about the evolutionary dynamics of RV in dogs and its biodiversity patterns in India. In total, 50 dog-brain samples suspected of rabies were screened by the nucleoprotein- (N) and glycoprotein- (G) gene PCR. The N and G genes were subsequently sequenced to understand the molecular evolution in these genes. The phylogenetic analysis of the N gene revealed that six isolates in the Mumbai region belonged to a single Arctic lineage. Time-scaled phylogeny by Bayesian coalescent analysis of the partial N gene revealed that the time to the most recent common ancestor (TMRCA) for the sequences belonged to the cluster from 2006.68 with a highest posterior density of 95 % betweeen 2005-2008, which is assigned to Indian lineage I. Migration pattern revealed a strong Bayes factor between Mumbai to Delhi, Panji to Hyderabad, Delhi to Chennai, and Chennai to Chandigarh. Phylogenetic analysis of the G gene revealed that the RVs circulating in the Mumbai region are divided into three lineages. Time-scaled phylogeny by the Bayesian coalescent analysis method estimated that the TMRCA for sequences under study was from 1993 and Indian clusters was from 1962. In conclusion, the phylogenetic analysis of the N gene revealed that six isolates belonged to single Arctic lineages along with other Indian isolates and they were clustered into a single lineage but divided into three clades based on the G-gene sequences. The present study highlights and enhances the current molecular epidemiology and evolution of RV and revealed strong location bias and geographical clustering within Indian isolates on the basis of N and G genes.
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Affiliation(s)
| | - Sharmila Badal Majee
- Department of Veterinary Microbiology, Mumbai Veterinary College, Parel, Mumbai-400012, India
| | - Satish S Gaikwad
- Animal Biotechnology Educational and Research Cell, COVAS, Parbhani, India
| | | | | | - Aakash Doiphode
- Department of Animal Genetics and Breeding, KNPCVS, Shirval, Pune, India
| | - Rajashri Gandge
- Department of Veterinary Microbiology, Mumbai Veterinary College, Mumbai, India
| | - Dhananjay Dighe
- Department of Preventive Medicine, Mumbai Veterinary College, Parel, Mumbai, India
| | - Sonal Ingle
- Animal Biotechnology, Mumbai Veterinary College, Mumbai
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18
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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] [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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19
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Colombi D, Poletto C, Nakouné E, Bourhy H, Colizza V. Long-range movements coupled with heterogeneous incubation period sustain dog rabies at the national scale in Africa. PLoS Negl Trop Dis 2020; 14:e0008317. [PMID: 32453756 PMCID: PMC7274467 DOI: 10.1371/journal.pntd.0008317] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 06/05/2020] [Accepted: 04/22/2020] [Indexed: 12/25/2022] Open
Abstract
Dog-transmitted rabies is responsible for more than 98% of human cases worldwide, remaining a persistent problem in developing countries. Mass vaccination targets predominantly major cities, often compromising disease control due to re-introductions. Previous work suggested that areas neighboring cities may behave as the source of these re-introductions. To evaluate this hypothesis, we introduce a spatially explicit metapopulation model for rabies diffusion in Central African Republic. Calibrated on epidemiological data for the capital city, Bangui, the model predicts that long-range movements are essential for continuous re-introductions of rabies-exposed dogs across settlements, eased by the large fluctuations of the incubation period. Bangui's neighborhood, instead, would not be enough to self-sustain the epidemic, contrary to previous expectations. Our findings suggest that restricting long-range travels may be very efficient in limiting rabies persistence in a large and fragmented dog population. Our framework can be applied to other geographical contexts where dog rabies is endemic.
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Affiliation(s)
- Davide Colombi
- INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP, Paris, France
- Computational Epidemiology Laboratory, Institute for Scientific Interchange (ISI), Turin, Italy
- Physics Department and INFN, University of Turin, Turin, Italy
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP, Paris, France
| | | | - Hervé Bourhy
- Institut Pasteur, Unit Lyssavirus Epidemiology and Neuropathology, WHO Collaborating Center for Reference and Research on Rabies, Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP, Paris, France
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20
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Orłowska A, Iwan E, Smreczak M, Rola J. Evaluation of Direct Metagenomics and Target Enriched Approaches for High-throughput Sequencing of Field Rabies Viruses. J Vet Res 2019; 63:471-479. [PMID: 31934655 PMCID: PMC6950431 DOI: 10.2478/jvetres-2019-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 11/04/2019] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION High-throughput sequencing (HTS) identifies random viral fragments in environmental samples metagenomically. High reliability gains it broad application in virus evolution, host-virus interaction, and pathogenicity studies. Deep sequencing of field samples with content of host genetic material and bacteria often produces insufficient data for metagenomics and must be preceded by target enrichment. The main goal of the study was the evaluation of HTS for complete genome sequencing of field-case rabies viruses (RABVs). MATERIAL AND METHODS The material was 23 RABVs isolated mainly from red foxes and one European bat lyssavirus-1 isolate propagated in neuroblastoma cells. Three methods of RNA isolation were tested for the direct metagenomics and RABV-enriched approaches. Deep sequencing was performed with a MiSeq sequencer (Illumina) and reagent v3 kit. Bioinformatics data were evaluated by Kraken and Centrifuge software and de novo assembly was done with metaSPAdes. RESULTS Testing RNA extraction procedures revealed the deep sequencing scope superiority of the combined TRIzol/column method. This HTS methodology made it possible to obtain complete genomes of all the RABV isolates collected in the field. Significantly greater rates of RABV genome coverages (over 5,900) were obtained with RABV enrichment. Direct metagenomic studies sequenced the full length of 6 out of 16 RABV isolates with a medium coverage between 1 and 71. CONCLUSION Direct metagenomics gives the most realistic illustration of the field sample microbiome, but with low coverage. For deep characterisation of viruses, e.g. for spatial and temporal phylogeography during outbreaks, target enrichment is recommended as it covers sequences much more completely.
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Affiliation(s)
- Anna Orłowska
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Ewelina Iwan
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Marcin Smreczak
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Jerzy Rola
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
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21
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Dellicour S, Troupin C, Jahanbakhsh F, Salama A, Massoudi S, Moghaddam MK, Baele G, Lemey P, Gholami A, Bourhy H. Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages - Application to rabies virus spread in Iran. Mol Ecol 2019; 28:4335-4350. [PMID: 31535448 DOI: 10.1111/mec.15222] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 08/04/2019] [Accepted: 08/05/2019] [Indexed: 12/26/2022]
Abstract
Recent years have seen the extensive use of phylogeographic approaches to unveil the dispersal history of virus epidemics. Spatially explicit reconstructions of viral spread represent valuable sources of lineage movement data that can be exploited to investigate the impact of underlying environmental layers on the dispersal of pathogens. Here, we performed phylogeographic inference and applied different post hoc approaches to analyse a new and comprehensive data set of viral genomes to elucidate the dispersal history and dynamics of rabies virus (RABV) in Iran, which have remained largely unknown. We first analysed the association between environmental factors and variations in dispersal velocity among lineages. Second, we present, test and apply a new approach to study the link between environmental conditions and the dispersal direction of lineages. The statistical performance (power of detection, false-positive rate) of this new method was assessed using simulations. We performed phylogeographic analyses of RABV genomes, allowing us to describe the large diversity of RABV in Iran and to confirm the cocirculation of several clades in the country. Overall, we estimate a relatively high lineage dispersal velocity, similar to previous estimates for dog rabies virus spread in northern Africa. Finally, we highlight a tendency for RABV lineages to spread in accessible areas associated with high human population density. Our analytical workflow illustrates how phylogeographic approaches can be used to investigate the impact of environmental factors on several aspects of viral dispersal dynamics.
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Affiliation(s)
- Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium.,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Cécile Troupin
- Unit Lyssavirus Epidemiology and Neuropathology, WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Paris, France
| | - Fatemeh Jahanbakhsh
- WHO Collaborating Centre for Reference and Research on Rabies, Pasteur Institute of Iran, Tehran, Iran
| | - Akram Salama
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Siamak Massoudi
- Department of Environment, Wildlife Diseases Group, Wildlife Bureau, Tehran, Iran
| | - Madjid K Moghaddam
- Department of Environment, Wildlife Diseases Group, Wildlife Bureau, Tehran, Iran
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Alireza Gholami
- WHO Collaborating Centre for Reference and Research on Rabies, Pasteur Institute of Iran, Tehran, Iran
| | - Hervé Bourhy
- Unit Lyssavirus Epidemiology and Neuropathology, WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Paris, France
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22
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Genetic diversity of rabies virus in different host species and geographic regions of Zambia and Zimbabwe. Virus Genes 2019; 55:713-719. [PMID: 31267444 DOI: 10.1007/s11262-019-01682-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/27/2019] [Indexed: 10/26/2022]
Abstract
Rabies is endemic in Zambia and Zimbabwe. The previously investigated strains of rabies virus in central Zambia belong to the Africa 1b lineage, with similar circulating virus strains found in the various tested hosts and regions. However, prior work assessed only limited regions and host species. Thus, this study aimed to more comprehensively determine the genetic diversity of rabies virus across regions of Zambia and Zimbabwe. RNA (n = 76) was extracted from positive direct fluorescent antibody test brain tissues from dog, cow, goat, cat, pig, human, and jackal collected from Zambia and Zimbabwe. The amplicons of the nucleoprotein and glycoprotein genes were obtained from all examined samples by nested RT-PCR and subsequently sequenced. A phylogenetic analysis of the N gene confirmed that all the endemic strains of rabies virus in Zambia and Zimbabwe belong to the Africa 1b lineage. The obtained viral gene sequences were phylogenetically divided into two clusters. Cluster II comprised only Zambian strains. In contrast, cluster I comprised both Zambia and Zimbabwe strains, with strains from Zimbabwe forming a distinct lineage from Zambian strains, implying viral genetic divergence due to geographical barriers. However, no evidence of clustering based on host or region was observed, implying the circulation of similar virus strains occurs in different hosts and regions of Zambia and Zimbabwe. The clustering of rabies virus strains from jackals with those from domestic animals provides evidence of similar virus strains circulating in both wildlife and domestic animals, and that the jackal might be one of the potential reservoirs of rabies virus infection. In this study, no strains circulating in Zimbabwe were detected in Zambia.
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Comparison of intra- and inter-host genetic diversity in rabies virus during experimental cross-species transmission. PLoS Pathog 2019; 15:e1007799. [PMID: 31220188 PMCID: PMC6615636 DOI: 10.1371/journal.ppat.1007799] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 07/09/2019] [Accepted: 04/29/2019] [Indexed: 12/25/2022] Open
Abstract
The development of high-throughput genome sequencing enables accurate measurements of levels of sub-consensus intra-host virus genetic diversity and analysis of the role played by natural selection during cross-species transmission. We analysed the natural and experimental evolution of rabies virus (RABV), an important example of a virus that is able to make multiple host jumps. In particular, we (i) analyzed RABV evolution during experimental host switching with the goal of identifying possible genetic markers of host adaptation, (ii) compared the mutational changes observed during passage with those observed in natura, and (iii) determined whether the colonization of new hosts or tissues requires adaptive evolution in the virus. To address these aims, animal infection models (dog and fox) and primary cell culture models (embryo brain cells of dog and fox) were developed and viral variation was studied in detail through deep genome sequencing. Our analysis revealed a strong unidirectional host evolutionary effect, as dog-adapted rabies virus was able to replicate in fox and fox cells relatively easily, while dogs or neuronal dog cells were not easily susceptible to fox adapted-RABV. This suggests that dog RABV may be able to adapt to some hosts more easily than other host variants, or that when RABV switched from dogs to red foxes it lost its ability to adapt easily to other species. Although no difference in patterns of mutation variation between different host organs was observed, mutations were common following both in vitro and in vivo passage. However, only a small number of these mutations also appeared in natura, suggesting that adaptation during successful cross-species virus transmission is a complex, multifactorial evolutionary process. Understanding the mechanisms that underpin the cross-species transmission and host adaptation of rabies virus (RABV) remains an important part of the ongoing goal to reduce and eliminate rabies. We utilized next-generation sequencing to perform a deep comparative analysis of the genomic evolution of RABV subpopulations during host adaptation in culture and in animals, with the aim of determining the molecular mechanisms involved in the host-species or tissue adaptation of rabies virus. In particular, we aimed to determine whether experimental evolution can recapitulate evolution in nature. Our results suggest that a limited number of mutations that appeared following both in vitro and in vivo passage were observed in natura. This study also suggests that dog RABV may be able to adapt to some hosts more easily than other host variants.
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Comprehensive Analysis of Codon Usage on Rabies Virus and Other Lyssaviruses. Int J Mol Sci 2018; 19:ijms19082397. [PMID: 30110957 PMCID: PMC6121662 DOI: 10.3390/ijms19082397] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 12/15/2022] Open
Abstract
Rabies virus (RABV) and other lyssaviruses can cause rabies and rabies-like diseases, which are a persistent public health threat to humans and other mammals. Lyssaviruses exhibit distinct characteristics in terms of geographical distribution and host specificity, indicative of a long-standing diversification to adapt to the environment. However, the evolutionary diversity of lyssaviruses, in terms of codon usage, is still unclear. We found that RABV has the lowest codon usage bias among lyssaviruses strains, evidenced by its high mean effective number of codons (ENC) (53.84 ± 0.35). Moreover, natural selection is the driving force in shaping the codon usage pattern of these strains. In summary, our study sheds light on the codon usage patterns of lyssaviruses, which can aid in the development of control strategies and experimental research.
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Chen J, Liu G, Jin T, Zhang R, Ou X, Zhang H, Lin P, Yao D, Chen S, Luo M, Yang F, Huang D, Sun B, Zhang R. Epidemiological and Genetic Characteristics of Rabies Virus Transmitted Through Organ Transplantation. Front Cell Infect Microbiol 2018; 8:86. [PMID: 29637047 PMCID: PMC5880885 DOI: 10.3389/fcimb.2018.00086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/02/2018] [Indexed: 11/26/2022] Open
Abstract
In January 2016, two patients died of rabies after receiving kidney transplants from a common organ donor at a hospital in Changsha, Hunan, China. The medical records, epidemiological data of the organ donor, two kidney and a liver recipients were reviewed. Intravitam saliva samples of the two kidney recipients were tested for rabies virus (RABV) using real-time RT-PCR, and the nucleoprotein (N) gene was amplified and sequenced by Sanger sequencing. Whole genome sequences were analyzed using next-generation sequencing. The N genes of the two kidney recipients showed 100% nucleic acid identity. Phylogenetic analysis of the complete genome, N and glycoprotein (G) genes indicated that the RABV was homologous with dog isolates from the Hunan province and belong to the China I lineage, which is widespread in China. The organ donor was a 22-month-old boy who died from unknown acute progressive encephalitis. After undergoing sub-hypothermia hibernation therapy, rabies-associated symptoms were atypical, and rabies was neglected because serum RABV-specific antibodies were negative. An unknown wound on the forehead of the donor was found 2 months before the onset of symptoms. Based on the clinical, epidemiological, and molecular findings, we speculated that the RABV initially originated in the donor from a dog bite, and was then transmitted to the recipients by organ transplantation. An uncertain exposure history and misdiagnosis played important roles in the spread of the RABV. Rabies should be considered in patients with acute progressive encephalitis of unexplained etiology, especially in potential organ donors.
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Affiliation(s)
- Jingfang Chen
- Changsha Center for Disease Control and Prevention, Changsha, China.,Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Guang Liu
- China National Genebank-Shenzhen, Shenzhen, China.,Infection Omics Research Institute, BGI-Shenzhen, Shenzhen, China
| | - Tao Jin
- China National Genebank-Shenzhen, Shenzhen, China.,Infection Omics Research Institute, BGI-Shenzhen, Shenzhen, China
| | - Rusheng Zhang
- Changsha Center for Disease Control and Prevention, Changsha, China
| | - Xinhua Ou
- Changsha Center for Disease Control and Prevention, Changsha, China
| | - Heng Zhang
- Changsha Center for Disease Control and Prevention, Changsha, China
| | - Peng Lin
- China National Genebank-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Dong Yao
- Changsha Center for Disease Control and Prevention, Changsha, China
| | - Shuilian Chen
- Changsha Center for Disease Control and Prevention, Changsha, China
| | - Meiling Luo
- Changsha Center for Disease Control and Prevention, Changsha, China
| | - Fan Yang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Dana Huang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Biancheng Sun
- Changsha Center for Disease Control and Prevention, Changsha, China
| | - Renli Zhang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
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Brunker K, Lemey P, Marston DA, Fooks AR, Lugelo A, Ngeleja C, Hampson K, Biek R. Landscape attributes governing local transmission of an endemic zoonosis: Rabies virus in domestic dogs. Mol Ecol 2018; 27:773-788. [PMID: 29274171 PMCID: PMC5900915 DOI: 10.1111/mec.14470] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 12/24/2022]
Abstract
Landscape heterogeneity plays an important role in disease spread and persistence, but quantifying landscape influences and their scale dependence is challenging. Studies have focused on how environmental features or global transport networks influence pathogen invasion and spread, but their influence on local transmission dynamics that underpin the persistence of endemic diseases remains unexplored. Bayesian phylogeographic frameworks that incorporate spatial heterogeneities are promising tools for analysing linked epidemiological, environmental and genetic data. Here, we extend these methodological approaches to decipher the relative contribution and scale-dependent effects of landscape influences on the transmission of endemic rabies virus in Serengeti district, Tanzania (area ~4,900 km2 ). Utilizing detailed epidemiological data and 152 complete viral genomes collected between 2004 and 2013, we show that the localized presence of dogs but not their density is the most important determinant of diffusion, implying that culling will be ineffective for rabies control. Rivers and roads acted as barriers and facilitators to viral spread, respectively, and vaccination impeded diffusion despite variable annual coverage. Notably, we found that landscape effects were scale-dependent: rivers were barriers and roads facilitators on larger scales, whereas the distribution of dogs was important for rabies dispersal across multiple scales. This nuanced understanding of the spatial processes that underpin rabies transmission can be exploited for targeted control at the scale where it will have the greatest impact. Moreover, this research demonstrates how current phylogeographic frameworks can be adapted to improve our understanding of endemic disease dynamics at different spatial scales.
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Affiliation(s)
- Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- The Boyd Orr Centre for Population and Ecosystem HealthUniversity of GlasgowGlasgowUK
- Animal and Plant Health AgencyAddlestoneUK
| | - Philippe Lemey
- Department of Microbiology and ImmunologyKU Leuven – University of LeuvenLeuvenBelgium
| | | | | | - Ahmed Lugelo
- Department of Veterinary Medicine and Public HealthSokoine University of AgricultureMorogoroUnited Republic of Tanzania
| | - Chanasa Ngeleja
- Tanzania Veterinary Laboratory AgencyDar es SalaamUnited Republic of Tanzania
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- The Boyd Orr Centre for Population and Ecosystem HealthUniversity of GlasgowGlasgowUK
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- The Boyd Orr Centre for Population and Ecosystem HealthUniversity of GlasgowGlasgowUK
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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] [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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Singh R, Singh KP, Cherian S, Saminathan M, Kapoor S, Manjunatha Reddy GB, Panda S, Dhama K. Rabies - epidemiology, pathogenesis, public health concerns and advances in diagnosis and control: a comprehensive review. Vet Q 2017. [PMID: 28643547 DOI: 10.1080/01652176.2017.1343516] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rabies is a zoonotic, fatal and progressive neurological infection caused by rabies virus of the genus Lyssavirus and family Rhabdoviridae. It affects all warm-blooded animals and the disease is prevalent throughout the world and endemic in many countries except in Islands like Australia and Antarctica. Over 60,000 peoples die every year due to rabies, while approximately 15 million people receive rabies post-exposure prophylaxis (PEP) annually. Bite of rabid animals and saliva of infected host are mainly responsible for transmission and wildlife like raccoons, skunks, bats and foxes are main reservoirs for rabies. The incubation period is highly variable from 2 weeks to 6 years (avg. 2-3 months). Though severe neurologic signs and fatal outcome, neuropathological lesions are relatively mild. Rabies virus exploits various mechanisms to evade the host immune responses. Being a major zoonosis, precise and rapid diagnosis is important for early treatment and effective prevention and control measures. Traditional rapid Seller's staining and histopathological methods are still in use for diagnosis of rabies. Direct immunofluoroscent test (dFAT) is gold standard test and most commonly recommended for diagnosis of rabies in fresh brain tissues of dogs by both OIE and WHO. Mouse inoculation test (MIT) and polymerase chain reaction (PCR) are superior and used for routine diagnosis. Vaccination with live attenuated or inactivated viruses, DNA and recombinant vaccines can be done in endemic areas. This review describes in detail about epidemiology, transmission, pathogenesis, advances in diagnosis, vaccination and therapeutic approaches along with appropriate prevention and control strategies.
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Affiliation(s)
- Rajendra Singh
- a Division of Pathology , ICAR-Indian Veterinary Research Institute , Bareilly , Uttar Pradesh , India
| | - Karam Pal Singh
- b Centre for Animal Disease Research and Diagnosis (CADRAD) , ICAR-Indian Veterinary Research Institute , Bareilly , Uttar Pradesh , India
| | - Susan Cherian
- a Division of Pathology , ICAR-Indian Veterinary Research Institute , Bareilly , Uttar Pradesh , India
| | - Mani Saminathan
- a Division of Pathology , ICAR-Indian Veterinary Research Institute , Bareilly , Uttar Pradesh , India
| | - Sanjay Kapoor
- c Department of Veterinary Microbiology , LLR University of Veterinary and Animal Sciences , Hisar , Haryana , India
| | - G B Manjunatha Reddy
- d ICAR-National Institute of Veterinary Epidemiology and Disease Informatics , Bengaluru , Karnataka , India
| | - Shibani Panda
- a Division of Pathology , ICAR-Indian Veterinary Research Institute , Bareilly , Uttar Pradesh , India
| | - Kuldeep Dhama
- a Division of Pathology , ICAR-Indian Veterinary Research Institute , Bareilly , Uttar Pradesh , India
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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] [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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Efficacy of the oral rabies virus vaccine strain SPBN GASGAS in foxes and raccoon dogs. Vaccine 2017; 37:4750-4757. [PMID: 29042202 DOI: 10.1016/j.vaccine.2017.09.093] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 11/21/2022]
Abstract
To test the immunogenicity and efficacy of a new oral rabies virus vaccine strain SPBN GASGAS in wildlife target species, one group of foxes and two groups of raccoon dogs were offered a bait containing 1.7 ml of the vaccine (106.6 FFU/ml; 106.8 FFU/dose) and subsequently challenged approximately 180 days later with a fox rabies virus isolate. One group of raccoon dogs (n=30) received the same challenge dose (100.7 MICLD50/ml) as the red foxes (n=29). The other group with raccoon dogs (n=28) together with 8 animals that received the vaccine dose by direct instillation into the oral cavity (DIOC) were infected with a 40-fold higher dose of the challenge virus (102.3 MICLD50/ml). All but one of the 29 vaccinated foxes survived the challenge infection; meanwhile all 12 control foxes succumbed to rabies. Twenty-eight of 30 vaccinated raccoon dogs challenged with the same dose survived the infection, however only six of 12 control animals succumbed. When the higher challenge dose was administered, all 12 control animals died from rabies and all 36 vaccinated animals (28 baited plus 8 DIOC) survived. Blood samples were collected at different time points post vaccination and examined by both RFFIT and ELISA. The kinetics of the measured immune response was similar for both species, although in RFFIT slightly higher values were observed in foxes than in raccoon dogs. However, the immune response as measured in ELISA was identical for both species. The oral rabies virus vaccine SPBN GASGAS meets the efficacy requirements for live rabies virus vaccines as laid down by the European Pharmacopoeia.
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Glycoprotein-G-gene-based molecular and phylogenetic analysis of rabies viruses associated with a large outbreak of bovine rabies in southern Brazil. Arch Virol 2017; 162:3697-3704. [PMID: 28856449 DOI: 10.1007/s00705-017-3533-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/31/2017] [Indexed: 10/19/2022]
Abstract
A large outbreak of hematophagous-bat-associated bovine rabies has been occurring in Rio Grande do Sul (RS), the southernmost Brazilian state, since 2011, with official estimates exceeding 50,000 cattle deaths. The present article describes a genetic characterization of rabies virus (RABV) recovered from 59 affected cattle and two sheep, from 56 herds in 16 municipalities (2012-2016). Molecular analysis was performed using the nucleotide (nt) and predicted amino acid (aa) sequences of RABV glycoprotein G (G). A high level of nt and aa sequence identity was observed among the examined G sequences, ranging from 98.4 to 100%, and from 97.3 to 100%, respectively. Likewise, high levels of nt and aa sequence identity were observed with bovine (nt, 99.8%; aa, 99.8%) and hematophagous bat (nt, 99.5%; aa, 99.4%) RABV sequences from GenBank, and lower levels were observed with carnivore RABV sequences (nt, 92.8%; aa, 88.1%). Some random mutations were observed in the analyzed sequences, and a few consistent mutations were observed in some sequences belonging to cluster 2, subcluster 2b. The clustering of the sequences was observed in a phylogenetic tree, where two distinct clusters were evident. Cluster 1 comprised RABV sequences covering the entire study period (2012 to 2016), but subclusters corresponding to different years could be identified, indicating virus evolution and/or introduction of new viruses into the population. In some cases, viruses from the same location obtained within a short period grouped into different subclusters, suggesting co-circulation of viruses of different origins. Subcluster segregation was also observed in sequences obtained in the same region during different periods, indicating the involvement of different viruses in the cases at different times. In summary, our results indicate that the outbreaks occurring in RS (2012 to 2016) probably involved RABV of different origins, in addition to a possible evolution of RABV isolates within this period.
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He W, Zhang H, Zhang Y, Wang R, Lu S, Ji Y, Liu C, Yuan P, Su S. Codon usage bias in the N gene of rabies virus. INFECTION GENETICS AND EVOLUTION 2017; 54:458-465. [PMID: 28818621 DOI: 10.1016/j.meegid.2017.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 08/11/2017] [Accepted: 08/12/2017] [Indexed: 12/17/2022]
Abstract
Since its emergence, rabies virus (RABV) has been a major worldwide concern especially in developing countries. The nucleoprotein (N) of RABV is highly conserved and key for genetic typing, thus a better understanding of the N gene evolutionary trajectory can assist the development of control measures. We found that the N gene of RABV has a low codon usage bias with a mean effective number of codons (ENC) value of 56.33 influenced by both mutation pressure and natural selection. However, neutrality analysis indicated that natural selection dominates over mutation pressure. Additionally, we found that dinucleotide bias partly contributed to RABV codon usage bias. On the other hand, based on the clades of phylogenetic tree, we found that the evolutionary rate of the Africa 2 clade was the highest with a mean value of 3.75×10-3 substitutions per site per year. Above all, our results regarding N gene of RABV codon usage will serve future RABV evolution research.
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Affiliation(s)
- Wanting He
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Hongyu Zhang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yuchen Zhang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ruyi Wang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Sijia Lu
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yanjie Ji
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Chang Liu
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Pengkun Yuan
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
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Castillo-Neyra R, Zegarra E, Monroy Y, Bernedo RF, Cornejo-Rosello I, Paz-Soldan VA, Levy MZ. Spatial Association of Canine Rabies Outbreak and Ecological Urban Corridors, Arequipa, Peru. Trop Med Infect Dis 2017; 2:tropicalmed2030038. [PMID: 30270895 PMCID: PMC6082090 DOI: 10.3390/tropicalmed2030038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 11/16/2022] Open
Abstract
In the city of Arequipa, Peru, a rabid dog was detected in March 2015, marking the reintroduction of the rabies virus in the area; more rabid dogs have been detected since then. The presence of free-roaming dogs in Arequipa seems to be higher in dry water channels, which are widespread in the city. We created a geographic information system (GIS) with surveillance data on the location of rabid dogs detected during the first year of the outbreak, as well as the water channels. We conducted a spatial analysis using Monte Carlo simulations to determine if detected rabid dogs were closer to the water channels than expected. Thirty rabid dogs were detected during the first year of the outbreak, and they were statistically associated with the water channels (average distance to closest water channel = 334 m; p-value = 0.027). Water channels might play a role in the ecology of free-roaming dog populations, functioning as ecological corridors. Landscape ecology could assist in understanding the impact of these urban structures on control activities and the persistence of transmission.
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Affiliation(s)
- Ricardo Castillo-Neyra
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Zoonotic Disease Research Lab, One Health Unit, School of Public Health, Universidad Peruana Cayetano Heredia, Lima 15102, Peru.
| | - Edith Zegarra
- Gerencia Regional de Salud de Arequipa, Ministerio de Salud, Arequipa 04002, Peru.
| | - Ynes Monroy
- Gerencia Regional de Salud de Arequipa, Ministerio de Salud, Arequipa 04002, Peru.
| | - Reyno F Bernedo
- Gerencia Regional de Salud de Arequipa, Ministerio de Salud, Arequipa 04002, Peru.
| | | | - Valerie A Paz-Soldan
- Zoonotic Disease Research Lab, One Health Unit, School of Public Health, Universidad Peruana Cayetano Heredia, Lima 15102, Peru.
- Department of Global Community Health and Behavioral Sciences, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA.
| | - Michael Z Levy
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Zoonotic Disease Research Lab, One Health Unit, School of Public Health, Universidad Peruana Cayetano Heredia, Lima 15102, Peru.
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Hornyák Á, Juhász T, Forró B, Kecskeméti S, Bányai K. Resurgence of rabies in Hungary during 2013-2014: An attempt to track the origin of identified strains. Transbound Emerg Dis 2017; 65:e14-e24. [PMID: 28497505 DOI: 10.1111/tbed.12658] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Indexed: 01/01/2023]
Abstract
In 2013-2014, accumulation of rabies episodes raised concerns regarding ongoing elimination programme in Hungary. Nearly four dozen cases were identified over a 13-month period in the central region of the country far behind the immunization zones. Although the outbreak was successfully controlled, the origin of disease remained unknown. In this study, we sequenced the partial N and G genes from 47 Hungarian rabies virus (RV) strains isolated from the 2013-2014 outbreak. Sequencing and phylogenetic analysis of the N and G genes showed that the Hungarian RV isolates share high nucleotide similarity among each other (up to 100%). When analysing the N gene, comparable sequence similarity was seen between the outbreak strains and some historic Romanian RV strains. Unfortunately, in the lack of available sequence data from the Romanian RV strains, the genetic relationship within the G gene could not be determined. Phylogenetic analysis of Hungarian RV isolates detected in the past revealed that multiple independent RV lineages circulated in our country over the past 25 years. The parental strain of the 2013-2014 outbreak may have been imported independently perhaps from east through transborder movement of a reservoir animal. Next to the introduction, this imported RV strain seems to have spread clonally in the affected area. Our findings indicate that despite effective control measures that, overall, minimized the incidence of rabies over the past decade, field and laboratory monitoring needs to be continued to make rabies elimination programme in Hungary successful.
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Affiliation(s)
- Á Hornyák
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, Hungary
| | - T Juhász
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, Hungary
| | - B Forró
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - S Kecskeméti
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Debrecen, Hungary
| | - K Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
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Deviatkin AA, Lukashev AN, Poleshchuk EM, Dedkov VG, Tkachev SE, Sidorov GN, Karganova GG, Galkina IV, Shchelkanov MY, Shipulin GA. The phylodynamics of the rabies virus in the Russian Federation. PLoS One 2017; 12:e0171855. [PMID: 28225771 PMCID: PMC5321407 DOI: 10.1371/journal.pone.0171855] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/26/2017] [Indexed: 12/25/2022] Open
Abstract
Near complete rabies virus N gene sequences (1,110 nt) were determined for 82 isolates obtained from different regions of Russia between 2008 and 2016. These sequences were analyzed together with 108 representative GenBank sequences from 1977-2016 using the Bayesian coalescent approach. The timing of the major evolutionary events was estimated. Most of the isolates represented the steppe rabies virus group C, which was found over a vast geographic region from Central Russia to Mongolia and split into three groups (C0-C2) with discrete geographic prevalence. A single strain of the steppe rabies virus lineage was isolated in the far eastern part of Russia (Primorsky Krai), likely as a result of a recent anthropogenic introduction. For the first time the polar rabies virus group A2, previously reported in Alaska, was described in the northern part of European Russia and at the Franz Josef Land. Phylogenetic analysis suggested that all currently circulating rabies virus groups in the Russian Federation were introduced within the few last centuries, with most of the groups spreading in the 20th century. The dating of evolutionary events was highly concordant with the historical epidemiological data.
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Affiliation(s)
- Andrei A. Deviatkin
- Federal Budget Institute of Science Central Research Institute for Epidemiology, Moscow, Russian Federation
- Federal Budget Institute Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russian Federation
- Research Institute of Occupational Health, Moscow, Russian Federation
| | - Alexander N. Lukashev
- Federal Budget Institute Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russian Federation
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
- RUDN University, Moscow, Russia
| | | | - Vladimir G. Dedkov
- Federal Budget Institute of Science Central Research Institute for Epidemiology, Moscow, Russian Federation
- Research Institute of Occupational Health, Moscow, Russian Federation
| | - Sergey E. Tkachev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), Novosibirsk, Russian Federation
| | - Gennadiy N. Sidorov
- Institute for Natural Foci Infections, Omsk, Russian Federation
- Omsk State Pedagogical University, Omsk, Russian Federation
| | - Galina G. Karganova
- Federal Budget Institute Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russian Federation
| | | | - Mikhail Yu. Shchelkanov
- Far Eastern Federal University, Vladivostok, Russian Federation
- Institute of Biology and Soil Science, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, Russian Federation
| | - German A. Shipulin
- Federal Budget Institute of Science Central Research Institute for Epidemiology, Moscow, Russian Federation
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Krzowska-Firych J, Tomasiewicz K, Kozøowska A. Post-exposure rabies prophylaxis in humans exposed to animals in Lublin province (Eastern Poland) in 2012-2015 - A retrospective study. Hum Vaccin Immunother 2017; 13:1-6. [PMID: 28166482 DOI: 10.1080/21645515.2017.1285474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Rabies continues to be one of the most important viral diseases and remains a significant threat to public health across the globe. The post-exposure prophylaxis in humans can effectively prevent death after exposure to a potentially infected animal. In Poland, recommendations for rabies PEP followed the national guidelines which recommend that people should receive PEP when bitten by an animal suspected to be infected by rabies. PEP in humans includes cleansing and disinfecting the wound or point of contact, and administering anti-rabies immunization. Rabies vaccine should be given for contacts of category II and category III exposures. RIG should be given for category III contact. The vaccination schedule includes 5 doses given within a 30 day period (the Essen regimen). THE AIM The aim of our study was to determine the frequency of post-exposure prophylaxis among patients exposed to animals and also to assess the animal species suspected as a source of rabies exposure. METHODS We have retrospectively analyzed medical records from the years 2012-2015 of all adult patients who were exposed to animals and consulted at the Dispensary of Rabies Prophylaxis in the Department of Infectious Diseases at the Medical University in Lublin, Poland. All consulted patients were asked to give an informed consent in case of decision to use collected data for future research work. Ethical approval was obtained from the Ethics Committee of the Medical University of Lublin, Poland, and all patients included in this study gave an informed consent during consultation after the exposure to animals. RESULTS During the studied 4-year period, 511 persons exposed to animals were consulted and prophylactic procedure consisting of active immunization were applied in 54.2% of the total consulted. Dogs and cats were the most common animal species suspected as the source of the rabies exposure. Anti-rabies prophylaxis was applied in 45.8% of all vaccinated patients exposed to dogs, and in 24.2% exposed to cats. All patients with bite wounds were consulted at the Department of Surgery and wound care followed surgical recommendations. In the study group, 45 patients had category III contact. There were 38 patients exposed to dogs, and 7 exposed to cats. There were no people exposed to wildlife in this group. All animals were available for veterinary observation. During and after exposure, none of the animals that serve as a potential source of infection presented with symptoms of rabies. The local epidemiological data indicated that during exposures of our patients, there were no confirmed cases of rabies among animals in Lublin province. Based on the data mentioned above, RIG was not applied. During the studied period in Lublin province, rabies was confirmed mainly in wildlife, and only in 2 dogs. CONCLUSIONS In Lublin province, people are still at risk of exposure to rabid animals. The majority of our patients were vaccinated after domestic animals exposure, but rabies was confirmed mainly in wildlife, and since 2013, there were no cases of rabies among domestic animals.
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Troupin C, Dacheux L, Tanguy M, Sabeta C, Blanc H, Bouchier C, Vignuzzi M, Duchene S, Holmes EC, Bourhy H. Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts. PLoS Pathog 2016; 12:e1006041. [PMID: 27977811 PMCID: PMC5158080 DOI: 10.1371/journal.ppat.1006041] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 11/03/2016] [Indexed: 12/25/2022] Open
Abstract
The natural evolution of rabies virus (RABV) provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics. Zoonoses account for most recently emerged infectious diseases of humans, although little is known about the evolutionary mechanisms involved in cross-species virus transmission. Understanding the evolutionary patterns and processes that underpin such cross-species transmission is of importance for predicting the spread of zoonotic infections, and hence to their ultimate control. We present a large-scale and detailed reconstruction of the evolutionary history of rabies virus (RABV) in domestic and wildlife animal species. RABV is of particular interest as it is capable of infecting many mammals but, paradoxically, is only maintained in distinct epidemiological cycles associated with animal species from the orders Carnivora and Chiroptera. We show that bat-related RABV and dog-related RABV have experienced very different evolutionary dynamics, and that host jumps are sometimes characterized by significant increases in evolutionary rate. Among Carnivora, the association between RABV and particular host species most likely arose from a combination of the historical human-mediated spread of the virus and jumps into new primary host species. In addition, we show that changes in host species are associated with multiple evolutionary pathways including the occurrence of host-specific parallel evolution. Overall, our data indicate that the establishment of dog-related RABV in new carnivore hosts may only require subtle adaptive evolution.
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Affiliation(s)
- Cécile Troupin
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Laurent Dacheux
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Marion Tanguy
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
- Institut Pasteur, Genomics Platform, Paris, France
| | - Claude Sabeta
- Agricultural Research Council, Onderstepoort Veterinary Institute, OIE Rabies Reference Laboratory, Pretoria, South Africa
| | - Hervé Blanc
- Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, Viral Populations and Pathogenesis Unit, Paris, France
| | | | - Marco Vignuzzi
- Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, Viral Populations and Pathogenesis Unit, Paris, France
| | - Sebastián Duchene
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
- Centre for Systems Genomics, University of Melbourne, Parkville, Victoria, Australia
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Hervé Bourhy
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
- * E-mail:
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Phylogenetic analysis of rabies virus isolated from canids in North and Northeast Brazil. Arch Virol 2016; 162:71-77. [DOI: 10.1007/s00705-016-3079-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/19/2016] [Indexed: 10/20/2022]
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Vaccine-induced rabies case in a cow (Bos taurus): Molecular characterisation of vaccine strain in brain tissue. Vaccine 2016; 34:5021-5025. [PMID: 27576075 DOI: 10.1016/j.vaccine.2016.08.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/28/2016] [Accepted: 08/02/2016] [Indexed: 12/25/2022]
Abstract
Rabies is a fatal neuropathogenic zoonosis caused by the rabies virus of the Lyssavirus genus, Rhabdoviridae family. The oral vaccination of foxes - the main reservoir of rabies in Europe - using a live attenuated rabies virus vaccine was successfully conducted in many Western European countries. In July 2015, a rabies vaccine strain was isolated from the brain tissues of a clinically suspect cow (Bos taurus) in Romania. The nucleotide analysis of both N and G gene sequences showed 100% identity between the rabid animal, the GenBank reference SAD B19 strain and five rabies vaccine batches used for the national oral vaccination campaign targeting foxes.
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Rabies outbreak in Greece during 2012–2014: use of Geographical Information System for analysis, risk assessment and control. Epidemiol Infect 2016; 144:3068-3079. [DOI: 10.1017/s0950268816001527] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SUMMARYThe objectives of this work were (i) geographical analysis of the 2012–2014 outbreak of rabies in Greece using GIS and (ii) comparative analysis of animal cases with data of potential human exposure to rabies together with environmental data, in order to provide information for risk assessment, effective monitoring and control. Most animal cases (40/48) involved red foxes, while domestic animals were also diagnosed with rabies. Overall, 80% of the cases were diagnosed in central northern Greece; 75% of the cases were diagnosed in low altitudes (<343·5 m), within a distance of 1 km from human settlements. Median distance from livestock farms was 201·25 m. Most people potentially exposed to rabies (889/1060) presented with dog bite injuries. Maximum entropy analysis revealed that distance from farms contributed the highest percentage in defining environmental niche profiles for rabid foxes. Oral vaccination programmes were implemented in 24 administrative units of the country during 2013 and 2014, covering a total surface area of ~60 000 km2. Rabies re-occurrence in Greece emphasizes the need for ongoing surveillance in cross-border areas and in areas with intense human activity.
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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] [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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Phylogenetic analysis of Indian rabies virus isolates targeting the complete glycoprotein gene. INFECTION GENETICS AND EVOLUTION 2015; 36:333-338. [DOI: 10.1016/j.meegid.2015.09.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 08/19/2015] [Accepted: 09/25/2015] [Indexed: 11/19/2022]
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Tsai KJ, Hsu WC, Chuang WC, Chang JC, Tu YC, Tsai HJ, Liu HF, Wang FI, Lee SH. Emergence of a sylvatic enzootic formosan ferret badger-associated rabies in Taiwan and the geographical separation of two phylogenetic groups of rabies viruses. Vet Microbiol 2015; 182:28-34. [PMID: 26711025 DOI: 10.1016/j.vetmic.2015.10.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 09/17/2015] [Accepted: 10/28/2015] [Indexed: 11/16/2022]
Abstract
Taiwan had been declared rabies-free in humans and domestic animals for five decades until July 2013, when surprisingly, three Formosan ferret badgers (FB) were diagnosed with rabies. Since then, a variety of wild carnivores and other wildlife species have been found dead, neurologically ill, or exhibiting aggressive behaviors around the island. To determine the affected animal species, geographic areas, and environments, animal bodies were examined for rabies by direct fluorescent antibody test (FAT). The viral genomes from the brains of selected rabid animals were sequenced for the phylogeny of rabies viruses (RABV). Out of a total of 1016 wild carnivores, 276/831 (33.2%) Formosan FBs were FAT positive, with occasional biting incidents in 1 dog and suspected spillover in 1 house shrew. All other animals tested, including dogs, cats, bats, mice, house shrews, and squirrels, were rabies-negative. The rabies was badger-associated and confined to nine counties/cities in sylvatic environments. Phylogeny of nucleoprotein and glycoprotein genes from 59 Formosan FB-associated RABV revealed them to be clustered in two distinct groups, TWI and TWII, consistent with the geographic segregation into western and eastern Taiwan provided by the Central Mountain Range and into northern rabies-free and central-southern rabies-affected regions by a river bisecting western Taiwan. The unique features of geographic and genetic segregation, sylvatic enzooticity, and FB-association of RABV suggest a logical strategy for the control of rabies in this nation.
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Affiliation(s)
- K J Tsai
- Animal Health Research Institute, No.376, Chung-Cheng Rd., Tamsui District, New Taipei City 25158, Taiwan
| | - W C Hsu
- Animal Health Research Institute, No.376, Chung-Cheng Rd., Tamsui District, New Taipei City 25158, Taiwan
| | - W C Chuang
- Animal Health Research Institute, No.376, Chung-Cheng Rd., Tamsui District, New Taipei City 25158, Taiwan
| | - J C Chang
- Animal Health Research Institute, No.376, Chung-Cheng Rd., Tamsui District, New Taipei City 25158, Taiwan
| | - Y C Tu
- Animal Health Research Institute, No.376, Chung-Cheng Rd., Tamsui District, New Taipei City 25158, Taiwan
| | - H J Tsai
- Animal Health Research Institute, No.376, Chung-Cheng Rd., Tamsui District, New Taipei City 25158, Taiwan; School of Veterinary Medicine, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei City, 10617, Taiwan
| | - H F Liu
- Department of Medical Research, Mackay Memorial Hospital, No.45, Minsheng Rd., Tamsui District, New Taipei City 25160, Taiwan
| | - F I Wang
- School of Veterinary Medicine, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei City, 10617, Taiwan
| | - S H Lee
- Animal Drugs Inspection Branch, Animal Health Research Institute, No.21, Qiding, Zhunan Township, Miaoli County 35054, Taiwan.
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Lupulovic D, Maksimovic Zoric J, Vaskovic N, Bugarski D, Plavsic B, Ivanovic N, Petrovic T, Pusic I, Marcic D, Grgic Z, Lazic S. First Report on the Efficiency of Oral Vaccination of Foxes against Rabies in Serbia. Zoonoses Public Health 2015; 62:625-36. [DOI: 10.1111/zph.12196] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Indexed: 12/29/2022]
Affiliation(s)
- D. Lupulovic
- Scientific Veterinary Institute ‘Novi Sad’; Novi Sad Serbia
| | | | - N. Vaskovic
- Veterinary Institute ‘Kraljevo’; Kraljevo Serbia
| | - D. Bugarski
- Veterinary Directorate, Ministry of Agriculture and Environmental Protection; Belgrade Serbia
| | - B. Plavsic
- Veterinary Directorate, Ministry of Agriculture and Environmental Protection; Belgrade Serbia
| | | | - T. Petrovic
- Scientific Veterinary Institute ‘Novi Sad’; Novi Sad Serbia
| | - I. Pusic
- Scientific Veterinary Institute ‘Novi Sad’; Novi Sad Serbia
| | - D. Marcic
- Scientific Veterinary Institute ‘Novi Sad’; Novi Sad Serbia
| | - Z. Grgic
- Scientific Veterinary Institute ‘Novi Sad’; Novi Sad Serbia
| | - S. Lazic
- Scientific Veterinary Institute ‘Novi Sad’; Novi Sad Serbia
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Horton DL, McElhinney LM, Freuling CM, Marston DA, Banyard AC, Goharrriz H, Wise E, Breed AC, Saturday G, Kolodziejek J, Zilahi E, Al-Kobaisi MF, Nowotny N, Mueller T, Fooks AR. Complex epidemiology of a zoonotic disease in a culturally diverse region: phylogeography of rabies virus in the Middle East. PLoS Negl Trop Dis 2015; 9:e0003569. [PMID: 25811659 PMCID: PMC4374968 DOI: 10.1371/journal.pntd.0003569] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 01/27/2015] [Indexed: 12/15/2022] Open
Abstract
The Middle East is a culturally and politically diverse region at the gateway between Europe, Africa and Asia. Spatial dynamics of the fatal zoonotic disease rabies among countries of the Middle East and surrounding regions is poorly understood. An improved understanding of virus distribution is necessary to direct control methods. Previous studies have suggested regular trans-boundary movement, but have been unable to infer direction. Here we address these issues, by investigating the evolution of 183 rabies virus isolates collected from over 20 countries between 1972 and 2014. We have undertaken a discrete phylogeographic analysis on a subset of 139 samples to infer where and when movements of rabies have occurred. We provide evidence for four genetically distinct clades with separate origins currently circulating in the Middle East and surrounding countries. Introductions of these viruses have been followed by regular and multidirectional trans-boundary movements in some parts of the region, but relative isolation in others. There is evidence for minimal regular incursion of rabies from Central and Eastern Asia. These data support current initiatives for regional collaboration that are essential for rabies elimination.
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Affiliation(s)
- Daniel L Horton
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom; School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Lorraine M McElhinney
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom; Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Conrad M Freuling
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Denise A Marston
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Ashley C Banyard
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Hooman Goharrriz
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Emma Wise
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Andrew C Breed
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom
| | - Greg Saturday
- Rocky Mountain Laboratories (NIAID, NIH), Hamilton, Montana, United States of America; Formerly USAPHCR-Europe Laboratory Sciences, Veterinary Pathology, Landstuhl, Germany
| | - Jolanta Kolodziejek
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Erika Zilahi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Muhannad F Al-Kobaisi
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria; Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Thomas Mueller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Anthony R Fooks
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey, United Kingdom; Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
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Voloch CM, Capellão RT, Mello B, Schrago CG. Analysis of adaptive evolution in Lyssavirus genomes reveals pervasive diversifying selection during species diversification. Viruses 2014; 6:4465-78. [PMID: 25415197 PMCID: PMC4246234 DOI: 10.3390/v6114465] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 10/24/2014] [Accepted: 11/11/2014] [Indexed: 12/25/2022] Open
Abstract
Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G), RNA-dependent RNA polymerase (L) and polymerase (P) genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups.
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Affiliation(s)
- Carolina M Voloch
- Department of Genetics, Federal University of Rio de Janeiro, CEP: 21941-617, Brazil.
| | - Renata T Capellão
- Department of Genetics, Federal University of Rio de Janeiro, CEP: 21941-617, Brazil.
| | - Beatriz Mello
- Department of Genetics, Federal University of Rio de Janeiro, CEP: 21941-617, Brazil.
| | - Carlos G Schrago
- Department of Genetics, Federal University of Rio de Janeiro, CEP: 21941-617, Brazil.
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Severe fever with thrombocytopenia syndrome, an emerging tick-borne zoonosis. THE LANCET. INFECTIOUS DISEASES 2014; 14:763-772. [DOI: 10.1016/s1473-3099(14)70718-2] [Citation(s) in RCA: 310] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Johnson N, Aréchiga-Ceballos N, Aguilar-Setien A. Vampire bat rabies: ecology, epidemiology and control. Viruses 2014; 6:1911-28. [PMID: 24784570 PMCID: PMC4036541 DOI: 10.3390/v6051911] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/04/2014] [Accepted: 04/09/2014] [Indexed: 11/18/2022] Open
Abstract
Extensive surveillance in bat populations in response to recent emerging diseases has revealed that this group of mammals acts as a reservoir for a large range of viruses. However, the oldest known association between a zoonotic virus and a bat is that between rabies virus and the vampire bat. Vampire bats are only found in Latin America and their unique method of obtaining nutrition, blood-feeding or haematophagy, has only evolved in the New World. The adaptations that enable blood-feeding also make the vampire bat highly effective at transmitting rabies virus. Whether the virus was present in pre-Columbian America or was introduced is much disputed, however, the introduction of Old World livestock and associated landscape modification, which continues to the present day, has enabled vampire bat populations to increase. This in turn has provided the conditions for rabies re-emergence to threaten both livestock and human populations as vampire bats target large mammals. This review considers the ecology of the vampire bat that make it such an efficient vector for rabies, the current status of vampire-transmitted rabies and the future prospects for spread by this virus and its control.
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Affiliation(s)
- Nicholas Johnson
- Animal Health and Veterinary Laboratories Agency, Woodham Lane, Surrey, KT15 3NB, UK.
| | - Nidia Aréchiga-Ceballos
- Rabies Laboratory, Virology Department, Institute of Epidemiology Diagnostic and Reference (InDRE), Francisco de P. Miranda #177Bis. Colonia Unidad Lomas de Plateros. 01480 D.F., Mexico.
| | - Alvaro Aguilar-Setien
- Medical Immunology Research Unit, Paediatric Hospital, Naional Medical Center "Siglo XXL", Mexican Social Security Institute (IMSS), Av. Cuauhtémoc 330, Col. Doctores, 06720, D.F., Mexico.
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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] [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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Mullins J, McDevitt AD, Kowalczyk R, Ruczyńska I, Górny M, Wójcik JM. The influence of habitat structure on genetic differentiation in red fox populations in north-eastern Poland. ACTA ACUST UNITED AC 2014; 59:367-376. [PMID: 24954926 PMCID: PMC4058057 DOI: 10.1007/s13364-014-0180-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 03/05/2014] [Indexed: 02/02/2023]
Abstract
The red fox (Vulpes vulpes) has the widest global distribution among terrestrial carnivore species, occupying most of the Northern Hemisphere in its native range. Because it carries diseases that can be transmitted to humans and domestic animals, it is important to gather information about their movements and dispersal in their natural habitat but it is difficult to do so at a broad scale with trapping and telemetry. In this study, we have described the genetic diversity and structure of red fox populations in six areas of north-eastern Poland, based on samples collected from 2002–2003. We tested 22 microsatellite loci isolated from the dog and the red fox genome to select a panel of nine polymorphic loci suitable for this study. Genetic differentiation between the six studied populations was low to moderate and analysis in Structure revealed a panmictic population in the region. Spatial autocorrelation among all individuals showed a pattern of decreasing relatedness with increasing distance and this was not significantly negative until 93 km, indicating a pattern of isolation-by-distance over a large area. However, there was no correlation between genetic distance and either Euclidean distance or least-cost path distance at the population level. There was a significant relationship between genetic distance and the proportion of large forests and water along the Euclidean distances. These types of habitats may influence dispersal paths taken by red foxes, which is useful information in terms of wildlife disease management.
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Affiliation(s)
- Jacinta Mullins
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
| | - Allan D McDevitt
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland ; School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
| | - Iwona Ruczyńska
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
| | - Marcin Górny
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
| | - Jan M Wójcik
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
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