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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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Condori RE, Kartskhia N, Avaliani L, Donduashvili M, Elbakidze T, Kapanadze A, Pieracci EG, Maghlakelidze G, Wadhwa A, Morgan CN, Reynolds M, Li Y, Ninidze L. Comparing the genetic typing methods for effective surveillance and rabies control in Georgia. Front Microbiol 2023; 14:1243510. [PMID: 38107855 PMCID: PMC10722154 DOI: 10.3389/fmicb.2023.1243510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/31/2023] [Indexed: 12/19/2023] Open
Abstract
A full nucleoprotein gene sequencing of 68 isolates collected from passive rabies surveillance system in Georgia between 2015 and 2016 identified two distinct dog rabies phylogroups, GEO_V1 and GEO_V2, which both belonged to the cosmopolitan dog clade. GEO_V1 was found throughout the country and was further divided into four sub-phylogroups that overlapped geographically; GEO_V2 was found in the southeast region and was closely related to dog rabies in Azerbaijan. A sequence analysis of the full N gene, partial nucleoprotein gene of N-terminal and C-terminal, and the amplicon sequences of pan-lyssavirus RT-qPCR LN34 showed that all four sequencing approaches provided clear genetic typing results of canine rabies and could further differentiate GEO_V1 and GEO_V2. The phylogenetic analysis results vary and were affected by the length of the sequences used. Amplicon sequencing of the LN34 assay positive samples provided a rapid and cost-effective method for rabies genetic typing, which is important for improving rabies surveillance and canine rabies eradication globally.
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Affiliation(s)
- Rene E. Condori
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Natia Kartskhia
- Veterinary Department, National Food Agency, Ministry of Environmental Protection and Agriculture, Tbilisi, Georgia
| | - Lasha Avaliani
- Veterinary Department, National Food Agency, Ministry of Environmental Protection and Agriculture, Tbilisi, Georgia
| | - Marina Donduashvili
- State Laboratory of Agriculture, Ministry of Environmental Protection and Agriculture, Tbilisi, Georgia
| | - Tinatin Elbakidze
- State Laboratory of Agriculture, Ministry of Environmental Protection and Agriculture, Tbilisi, Georgia
| | - Ana Kapanadze
- State Laboratory of Agriculture, Ministry of Environmental Protection and Agriculture, Tbilisi, Georgia
| | - Emily G. Pieracci
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Giorgi Maghlakelidze
- Center for Global Health, Centers for Disease Control and Prevention, Tbilisi, Georgia
| | - Ashutosh Wadhwa
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Clint N. Morgan
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Mary Reynolds
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Yu Li
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lena Ninidze
- Veterinary Department, National Food Agency, Ministry of Environmental Protection and Agriculture, Tbilisi, Georgia
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Huaman C, Paskey AC, Clouse C, Feasley A, Rader M, Rice GK, Luquette AE, Fitzpatrick MC, Drumm HM, Yan L, Cer RZ, Donduashvili M, Buchukuri T, Nanava A, Hulseberg CE, Washington MA, Laing ED, Malagon F, Broder CC, Bishop-Lilly KA, Schaefer BC. Genomic Surveillance of Rabies Virus in Georgian Canines. Viruses 2023; 15:1797. [PMID: 37766204 PMCID: PMC10537093 DOI: 10.3390/v15091797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/08/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Rabies is a fatal zoonosis that is considered a re-emerging infectious disease. Although rabies remains endemic in canines throughout much of the world, vaccination programs have essentially eliminated dog rabies in the Americas and much of Europe. However, despite the goal of eliminating dog rabies in the European Union by 2020, sporadic cases of dog rabies still occur in Eastern Europe, including Georgia. To assess the genetic diversity of the strains recently circulating in Georgia, we sequenced seventy-eight RABV-positive samples from the brain tissues of rabid dogs and jackals using Illumina short-read sequencing of total RNA shotgun libraries. Seventy-seven RABV genomes were successfully assembled and annotated, with seventy-four of them reaching the coding-complete status. Phylogenetic analyses of the nucleoprotein (N) and attachment glycoprotein (G) genes placed all the assembled genomes into the Cosmopolitan clade, consistent with the Georgian origin of the samples. An amino acid alignment of the G glycoprotein ectodomain identified twelve different sequences for this domain among the samples. Only one of the ectodomain groups contained a residue change in an antigenic site, an R264H change in the G5 antigenic site. Three isolates were cultured, and these were found to be efficiently neutralized by the human monoclonal antibody A6. Overall, our data show that recently circulating RABV isolates from Georgian canines are predominantly closely related phylogroup I viruses of the Cosmopolitan clade. Current human rabies vaccines should offer protection against infection by Georgian canine RABVs. The genomes have been deposited in GenBank (accessions: OQ603609-OQ603685).
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Affiliation(s)
- Celeste Huaman
- Department of Microbiology, Uniformed Services University, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Adrian C. Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Caitlyn Clouse
- Department of Microbiology, Uniformed Services University, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Austin Feasley
- Department of Microbiology, Uniformed Services University, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Madeline Rader
- Department of Microbiology, Uniformed Services University, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Gregory K. Rice
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Andrea E. Luquette
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Maren C. Fitzpatrick
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Hannah M. Drumm
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | - Lianying Yan
- Department of Microbiology, Uniformed Services University, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
| | | | - Tamar Buchukuri
- State Laboratory of Agriculture (SLA), Tbilisi 0159, Georgia
| | - Anna Nanava
- US Army Medical Research Directorate-Georgia (USAMRD-G), Tbilisi 0198, Georgia
| | | | | | - Eric D. Laing
- Department of Microbiology, Uniformed Services University, Bethesda, MD 20814, USA
| | - Francisco Malagon
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
- Leidos, Reston, VA 20190, USA
| | | | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Fort Detrick, Frederick, MD 21702, USA
| | - Brian C. Schaefer
- Department of Microbiology, Uniformed Services University, Bethesda, MD 20814, USA
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Wei Z, Shi A. The complete mitochondrial genomes of four lagriine species (Coleoptera, Tenebrionidae) and phylogenetic relationships within Tenebrionidae. PeerJ 2023; 11:e15483. [PMID: 37283890 PMCID: PMC10241167 DOI: 10.7717/peerj.15483] [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: 10/13/2022] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
It is common to use whole mitochondrial genomes to analyze phylogenetic relationships among insects. In this study, seven mitogenomes of Tenebrionidae are newly sequenced and annotated. Among them, four species (Cerogira janthinipennis (Fairmaire, 1886), Luprops yunnanus (Fairmaire, 1887), Anaedus unidentasus Wang & Ren, 2007, and Spinolyprops cribricollis Schawaller, 2012) represent the subfamily Lagriinae. In this subfamily, the mitogenomes of the tribes Goniaderini (A. unidentasus) and Lupropini (L. yunnanus and S. cribricollis) were first reported; they were found to be 15,328-16,437 bp in length and encode 37 typical mitochondrial genes (13 PCGs, 2 rRNAs, 22 tRNAs, and a single noncoding control region). Most protein-coding genes in these mitogenomes have typical ATN start codons and TAR or an incomplete stop codon T-. In these four lagriine species, F, L2, I, and N are the most frequently used amino acids. In the 13 PCGs, the gene atp8 (Pi = 0.978) was the most diverse nucleotide, while cox1 was the most conserved gene with the lowest value (Pi = 0.211). The phylogenetic results suggest that Pimelinae, Lagriinae, Blaptinae, Stenochiinae, and Alleculinae are monophyletic, Diaperinae is paraphyletic, and Tenebrioninae appears polyphyletic. In Lagriinae, the tribe Lupropini appears paraphyletic because Spinolyprops is clustered with Anaedus in Goniaderini. These mitogenomic data provide important molecular data for the phylogeny of Tenebrionidae.
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Kanankege KS, Errecaborde KM, Wiratsudakul A, Wongnak P, Yoopatthanawong C, Thanapongtharm W, Alvarez J, Perez A. Identifying high-risk areas for dog-mediated rabies using Bayesian spatial regression. One Health 2022; 15:100411. [PMID: 36277110 PMCID: PMC9582562 DOI: 10.1016/j.onehlt.2022.100411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/26/2022] Open
Abstract
Despite ongoing control efforts, rabies remains an endemic zoonotic disease in many countries. Determining high-risk areas and the space-time patterns of rabies spread, as it relates to epidemiologically important factors, can support policymakers and program managers alike to develop evidence-based targeted surveillance and control programs. In this One Health approach which selected Thailand as the example site, the location-based risk of contracting dog-mediated rabies by both human and animal populations was quantified using a Bayesian spatial regression model. Specifically, a conditional autoregressive (CAR) Bayesian zero-inflated Poisson (ZIP) regression was fitted to the reported human and animal rabies case counts of each district, from the 2012–2017 period. The human population was used as an offset. The epidemiologically important factors hypothesized as risk modifiers and therefore tested as predictors included: number of dog bites/attacks, the population of dogs and cats, number of Buddhist temples, garbage dumps, animal vaccination, post-exposure prophylaxis, poverty, and shared administrative borders. Disparate sources of data were used to improve the estimated associations and predictions. Model performance was assessed using cross-validation. Results suggested that accounting for the association between human and animal rabies with number of dog bites/attacks, number of owned and un-owned dogs; shared country borders, number of Buddhist temples, poverty levels, and accounting for spatial dependence between districts, may help to predict the risk districts for dog-mediated rabies in Thailand. The fitted values of the spatial regression were mapped to illustrate the risk of dog-mediated rabies. The cross-validation indicated an adequate performance of the spatial regression model (AUC = 0.81), suggesting that had this spatial regression approach been used to identify districts at risk in 2015, the cases reported in 2016/17 would have been predicted with model sensitivity and specificity of 0.71 and 0.80, respectively. While active surveillance is ideal, this approach of using multiple data sources to improve risk estimation may inform current rabies surveillance and control efforts including determining rabies-free zones, and the roll-out of human post-exposure prophylaxis and anti-rabies vaccines for animals in determining high-risk areas. Bayesian spatial regression was used to quantify location-based risk of dog-mediated rabies Available and publicly accessible data from disparate sources were gathered Risk was estimated using the association between Risk estimates were compared over time to determine the prediction ability Study suggests while active surveillance is ideal, using multiple data sources may improve risk estimation
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Mostafavi E, Ghasemian A, Abdinasir A, Nematollahi Mahani SA, Rawaf S, Salehi Vaziri M, Gouya MM, Minh Nhu Nguyen T, Al Awaidy S, Al Ariqi L, Islam MM, Abu Baker Abd Farag E, Obtel M, Omondi Mala P, Matar GM, Asghar RJ, Barakat A, Sahak MN, Abdulmonem Mansouri M, Swaka A. Emerging and Re-emerging Infectious Diseases in the WHO Eastern Mediterranean Region, 2001-2018. Int J Health Policy Manag 2022; 11:1286-1300. [PMID: 33904695 PMCID: PMC9808364 DOI: 10.34172/ijhpm.2021.13] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 02/08/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Countries in the World Health Organization (WHO) Eastern Mediterranean Region (EMR) are predisposed to highly contagious, severe and fatal, emerging infectious diseases (EIDs), and re-emerging infectious diseases (RIDs). This paper reviews the epidemiological situation of EIDs and RIDs of global concern in the EMR between 2001 and 2018. METHODS To do a narrative review, a complete list of studies in the field was we prepared following a systematic search approach. Studies that were purposively reviewed were identified to summarize the epidemiological situation of each targeted disease. A comprehensive search of all published studies on EIDs and RIDs between 2001 and 2018 was carried out through search engines including Medline, Web of Science, Scopus, Google Scholar, and ScienceDirect. RESULTS Leishmaniasis, hepatitis A virus (HAV) and hepatitis E virus (HEV) are reported from all countries in the region. Chikungunya, Crimean Congo hemorrhagic fever (CCHF), dengue fever, and H5N1 have been increasing in number, frequency, and expanding in their geographic distribution. Middle East respiratory syndrome (MERS), which was reported in this region in 2012 is still a public health concern. There are challenges to control cholera, diphtheria, leishmaniasis, measles, and poliomyelitis in some of the countries. Moreover, Alkhurma hemorrhagic fever (AHF), and Rift Valley fever (RVF) are limited to some countries in the region. Also, there is little information about the real situation of the plague, Q fever, and tularemia. CONCLUSION EIDs and RIDs are prevalent in most countries in the region and could further spread within the region. It is crucial to improve regional capacities and capabilities in preventing and responding to disease outbreaks with adequate resources and expertise.
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Affiliation(s)
- Ehsan Mostafavi
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Re-emerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Abdolmajid Ghasemian
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Re-emerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Abubakar Abdinasir
- Infectious Hazards Management, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt
| | - Seyed Alireza Nematollahi Mahani
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Re-emerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Salman Rawaf
- Department of Primary Care and Public Health, School of Public Health, Faculty of Medicine, Imperial College, London, UK
| | - Mostafa Salehi Vaziri
- Department of Arboviruses and Viral Hemorrhagic Fevers, Research Centre for Emerging and Re-emerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Mahdi Gouya
- Centre for Communicable Disease Control, Ministry of Health and Medical Education, Tehran, Iran
| | - Tran Minh Nhu Nguyen
- Infectious Hazards Management, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt
| | | | - Lubna Al Ariqi
- Infectious Hazards Management, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt
| | - Md. Mazharul Islam
- Department of Animal Resources, Ministry of Municipality and Environment, Doha, Qatar
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu Natal, Durban, South Africa
| | | | - Majdouline Obtel
- Laboratory of Community Medicine, Preventive Medicine and Hygiene, Public Health Department, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
- Laboratory of Epidemiology, Biostatistics and Clinical Research, Public Health Department, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Peter Omondi Mala
- Infectious Hazards Management, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt
| | - Ghassan M. Matar
- Department of Experimental Pathology, Immunology and Microbiology Center for Infectious Diseases Research, American University of Beirut & Medical Center, Beirut, Lebanon
| | - Rana Jawad Asghar
- University of Nebraska Medical Center, Omaha, NE, USA
- Global Health Strategists & Implementers (GHSI), Islamabad, Pakistan
| | - Amal Barakat
- Infectious Hazards Management, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt
| | - Mohammad Nadir Sahak
- Infectious Hazard Management Department, World Health Organization, Kabul, Afghanistan
| | - Mariam Abdulmonem Mansouri
- Communicable Diseases Control Department, Public Health Directorate Unit, Ministry of Health, Kuwait City, Kuwait
- Centre for Public Health, Queen’s University Belfast, Belfast, UK
| | - Alexandra Swaka
- Department of Primary Care and Public Health, School of Public Health, Faculty of Medicine, Imperial College, London, UK
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Huang X, Chen B, Wei Z, Shi A. First Report of Complete Mitochondrial Genome in the Tribes Coomaniellini and Dicercini (Coleoptera: Buprestidae) and Phylogenetic Implications. Genes (Basel) 2022; 13:genes13061074. [PMID: 35741836 PMCID: PMC9222259 DOI: 10.3390/genes13061074] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022] Open
Abstract
The complete mitochondrial genomes (mitogenomes) of the tribes Coomaniellini and Dicercini were sequenced and described in this study, including Coomaniella copipes (16,196 bp), Coomaniella dentata (16,179 bp), and Dicerca corrugata (16,276 bp). These complete mitogenomes are very similar in length and encoded 37 typical mitochondrial genes, including 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and 13 protein-coding genes (PCGs). Most of PCGs had typical ATN start codons and terminated with TAR. Among these mitogenomes, Leu2 (L2), Ile (I), Ser2 (S2), and Phe (F) were the four most frequently encoded amino acids. Moreover, phylogenetic analyses were performed based on three kinds of nucleotide matrixes (13 PCGs, 2 rRNAs, and 13 PCGs + 2 rRNAs) among the available sequenced species of the family Buprestidae using Bayesian inference and Maximum-likelihood methods. The results showed that a Chrysochroninae species interspersed in Buprestinae, and Coomaniellini is more closely related to Dicercini than Melanophilini. Moreover, the clade of Buprestidae was well separated from outgroups and the monophyly of Agrilinae is confirmed again. Our whole mitogenome phylogenetic results support that the genus Dicerca can be transferred from Chrysochroinae to Buprestinae; whether Dicercini can be completely transferred remains to be further verified after enriching samples. Our results have produced new complete mitogenomic data, which will provide information for future phylogenetic and taxonomic research.
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The Comparison of Full G and N Gene Sequences From Turkish Rabies Virus Field Strains. Virus Res 2022; 315:198790. [PMID: 35487366 DOI: 10.1016/j.virusres.2022.198790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/25/2022] [Accepted: 04/25/2022] [Indexed: 11/21/2022]
Abstract
The rabies infection is a zoonotic viral disease in humans and is spread by both wild and domestic carnivores. This study aimed to molecularly characterize the field strains of the rabies virus circulating in Turkey between 2013 and 2020. Brain samples obtained from 16 infected animals (8 cattle, one donkey, three foxes, three dogs, and one marten) were tested. Full nucleoprotein (N) and glycoprotein (G) gene sequences were used to determine the genetic and antigenic characteristics of the rabies virus field strains. The phylogenetic analyses revealed that the 16 field strains identified in Turkey belonged to the Cosmopolitan lineage.
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De Benedictis P, Leopardi S, Markotter W, Velasco-Villa A. The Importance of Accurate Host Species Identification in the Framework of Rabies Surveillance, Control and Elimination. Viruses 2022; 14:v14030492. [PMID: 35336899 PMCID: PMC8954416 DOI: 10.3390/v14030492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/31/2022] [Accepted: 02/23/2022] [Indexed: 02/03/2023] Open
Abstract
Accurate host identification is paramount to understand disease epidemiology and to apply appropriate control measures. This is especially important for multi-host pathogens such as the rabies virus, a major and almost invariably fatal zoonosis that has mobilized unanimous engagement at an international level towards the final goal of zero human deaths due to canine rabies. Currently, diagnostic laboratories implement a standardized identification using taxonomic keys. However, this method is challenged by high and undiscovered biodiversity, decomposition of carcasses and subjective misevaluation, as has been attested to by findings from a cohort of 242 archived specimens collected across Sub-Saharan Africa and submitted for rabies diagnosis. We applied two simple and cheap methods targeting the Cytochrome b and Cytochrome c oxidase subunit I to confirm the initial classification. We therefore suggest prioritizing a standardized protocol that includes, as a first step, the implementation of taxonomic keys at a family or subfamily level, followed by the molecular characterization of the host species.
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Affiliation(s)
- Paola De Benedictis
- FAO Reference Center for Rabies, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy;
- Correspondence:
| | - Stefania Leopardi
- FAO Reference Center for Rabies, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy;
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa;
| | - Andres Velasco-Villa
- Centers for Diseases Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30333, USA;
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Deviatkin AA, Vakulenko YA, Dashian MA, Lukashev AN. Evaluating the Impact of Anthropogenic Factors on the Dissemination of Contemporary Cosmopolitan, Arctic, and Arctic-like Rabies Viruses. Viruses 2021; 14:66. [PMID: 35062270 PMCID: PMC8777955 DOI: 10.3390/v14010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Rabies is a globally prevalent viral zoonosis that causes 59,000 deaths per year and has important economic consequences. Most virus spread is associated with the migration of its primary hosts. Anthropogenic dissemination, mainly via the transportation of rabid dogs, shaped virus ecology a few hundred years ago and is responsible for several current outbreaks. A systematic analysis of aberrant long-distance events in the steppe and Arctic-like groups of rabies virus was performed using statistical (Bayesian) phylogeography and plots of genetic vs. geographic distances. The two approaches produced similar results but had some significant differences and complemented each other. No phylogeographic analysis could be performed for the Arctic group because polar foxes transfer the virus across the whole circumpolar region at high velocity, and there was no correlation between genetic and geographic distances in this virus group. In the Arctic-like group and the steppe subgroup of the cosmopolitan group, a significant number of known sequences (15-20%) was associated with rapid long-distance transfers, which mainly occurred within Eurasia. Some of these events have been described previously, while others have not been documented. Most of the recent long-distance transfers apparently did not result in establishing the introduced virus, but a few had important implications for the phylogeographic history of rabies. Thus, human-mediated long-distance transmission of the rabies virus remains a significant threat that needs to be addressed.
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Affiliation(s)
- Andrei A. Deviatkin
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
- The National Medical Research Center for Endocrinology, 117036 Moscow, Russia
| | - Yulia A. Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (Y.A.V.); (A.N.L.)
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Mariia A. Dashian
- Faculty of Biomedicine, Pirogov Medical University, 117997 Moscow, Russia;
| | - Alexander N. Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (Y.A.V.); (A.N.L.)
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11
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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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12
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Nahata KD, Bollen N, Gill MS, Layan M, Bourhy H, Dellicour S, Baele G. On the Use of Phylogeographic Inference to Infer the Dispersal History of Rabies Virus: A Review Study. Viruses 2021; 13:v13081628. [PMID: 34452492 PMCID: PMC8402743 DOI: 10.3390/v13081628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/28/2022] Open
Abstract
Rabies is a neglected zoonotic disease which is caused by negative strand RNA-viruses belonging to the genus Lyssavirus. Within this genus, rabies viruses circulate in a diverse set of mammalian reservoir hosts, is present worldwide, and is almost always fatal in non-vaccinated humans. Approximately 59,000 people are still estimated to die from rabies each year, leading to a global initiative to work towards the goal of zero human deaths from dog-mediated rabies by 2030, requiring scientific efforts from different research fields. The past decade has seen a much increased use of phylogeographic and phylodynamic analyses to study the evolution and spread of rabies virus. We here review published studies in these research areas, making a distinction between the geographic resolution associated with the available sequence data. We pay special attention to environmental factors that these studies found to be relevant to the spread of rabies virus. Importantly, we highlight a knowledge gap in terms of applying these methods when all required data were available but not fully exploited. We conclude with an overview of recent methodological developments that have yet to be applied in phylogeographic and phylodynamic analyses of rabies virus.
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Affiliation(s)
- Kanika D. Nahata
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
- Correspondence:
| | - Nena Bollen
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
| | - Mandev S. Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
| | - Maylis Layan
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Sorbonne Université, UMR2000, CNRS, 75015 Paris, France;
| | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, 75015 Paris, France;
- WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, 75015 Paris, France
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
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Rabies in a Sand Cat (Felis margarita) in Saudi Arabia: One Health Implications. J Wildl Dis 2021; 57:977-979. [PMID: 34320648 DOI: 10.7589/jwd-d-20-00233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 04/15/2021] [Indexed: 11/20/2022]
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14
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Yu X, Zhu H, Bo Y, Li Y, Zhang J, Jiang L, Chen G, Zhang X, Wen Y. Molecular evolutionary analysis reveals Arctic-like rabies viruses evolved and dispersed independently in North and South Asia. J Vet Sci 2021; 22:e5. [PMID: 33522157 PMCID: PMC7850786 DOI: 10.4142/jvs.2021.22.e5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/06/2020] [Accepted: 10/28/2020] [Indexed: 02/05/2023] Open
Abstract
Background Arctic-like (AL) lineages of rabies viruses (RABVs) remains endemic in some Arctic and Asia countries. However, their evolutionary dynamics are largely unappreciated. Objectives We attempted to estimate the evolutionary history, geographic origin and spread of the Arctic-related RABVs. Methods Full length or partial sequences of the N and G genes were used to infer the evolutionary aspects of AL RABVs by Bayesian evolutionary analysis. Results The most recent common ancestor (tMRCA) of the current Arctic and AL RABVs emerged in the 1830s and evolved independently after diversification. Population demographic analysis indicated that the viruses experienced gradual growth followed by a sudden decrease in its population size from the mid-1980s to approximately 2000. Genetic flow patterns among the regions reveal a high geographic correlation in AL RABVs transmission. Discrete phylogeography suggests that the geographic origin of the AL RABVs was in east Russia in approximately the 1830s. The ancestral AL RABV then diversified and immigrated to the countries in Northeast Asia, while the viruses in South Asia were dispersed to the neighboring regions from India. The N and G genes of RABVs in both clades sustained high levels of purifying selection, and the positive selection sites were mainly found on the C-terminus of the G gene. Conclusions The current AL RABVs circulating in South and North Asia evolved and dispersed independently.
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Affiliation(s)
- Xin Yu
- School of Life Sciences, Ludong University, Yantai 264025, China.,Shandong Provincial Key Laboratory of Quality Safety Monitoring and Risk Assessment for Animal Products, Ji?nan 250022, China
| | - Hongwei Zhu
- School of Life Sciences, Ludong University, Yantai 264025, China.,Shandong Provincial Key Laboratory of Quality Safety Monitoring and Risk Assessment for Animal Products, Ji?nan 250022, China
| | - Yongheng Bo
- Shandong Provincial Key Laboratory of Quality Safety Monitoring and Risk Assessment for Animal Products, Ji?nan 250022, China
| | - Youzhi Li
- Shandong Provincial Key Laboratory of Quality Safety Monitoring and Risk Assessment for Animal Products, Ji?nan 250022, China
| | - Jianlong Zhang
- School of Life Sciences, Ludong University, Yantai 264025, China.,Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264025, China
| | - Linlin Jiang
- School of Life Sciences, Ludong University, Yantai 264025, China.,Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264025, China
| | - Guozhong Chen
- School of Life Sciences, Ludong University, Yantai 264025, China.,Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264025, China
| | - Xingxiao Zhang
- School of Life Sciences, Ludong University, Yantai 264025, China.,Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264025, China.
| | - Yongjun Wen
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China.
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Mathematical modelling and phylodynamics for the study of dog rabies dynamics and control: A scoping review. PLoS Negl Trop Dis 2021; 15:e0009449. [PMID: 34043640 PMCID: PMC8189497 DOI: 10.1371/journal.pntd.0009449] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 06/09/2021] [Accepted: 05/05/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Rabies is a fatal yet vaccine-preventable disease. In the last two decades, domestic dog populations have been shown to constitute the predominant reservoir of rabies in developing countries, causing 99% of human rabies cases. Despite substantial control efforts, dog rabies is still widely endemic and is spreading across previously rabies-free areas. Developing a detailed understanding of dog rabies dynamics and the impact of vaccination is essential to optimize existing control strategies and developing new ones. In this scoping review, we aimed at disentangling the respective contributions of mathematical models and phylodynamic approaches to advancing the understanding of rabies dynamics and control in domestic dog populations. We also addressed the methodological limitations of both approaches and the remaining issues related to studying rabies spread and how this could be applied to rabies control. METHODOLOGY/PRINCIPAL FINDINGS We reviewed how mathematical modelling of disease dynamics and phylodynamics have been developed and used to characterize dog rabies dynamics and control. Through a detailed search of the PubMed, Web of Science, and Scopus databases, we identified a total of n = 59 relevant studies using mathematical models (n = 30), phylodynamic inference (n = 22) and interdisciplinary approaches (n = 7). We found that despite often relying on scarce rabies epidemiological data, mathematical models investigated multiple aspects of rabies dynamics and control. These models confirmed the overwhelming efficacy of massive dog vaccination campaigns in all settings and unraveled the role of dog population structure and frequent introductions in dog rabies maintenance. Phylodynamic approaches successfully disentangled the evolutionary and environmental determinants of rabies dispersal and consistently reported support for the role of reintroduction events and human-mediated transportation over long distances in the maintenance of rabies in endemic areas. Potential biases in data collection still need to be properly accounted for in most of these analyses. Finally, interdisciplinary studies were determined to provide the most comprehensive assessments through hypothesis generation and testing. They also represent new avenues, especially concerning the reconstruction of local transmission chains or clusters through data integration. CONCLUSIONS/SIGNIFICANCE Despite advances in rabies knowledge, substantial uncertainty remains regarding the mechanisms of local spread, the role of wildlife in dog rabies maintenance, and the impact of community behavior on the efficacy of control strategies including vaccination of dogs. Future integrative approaches that use phylodynamic analyses and mechanistic models within a single framework could take full advantage of not only viral sequences but also additional epidemiological information as well as dog ecology data to refine our understanding of rabies spread and control. This would represent a significant improvement on past studies and a promising opportunity for canine rabies research in the frame of the One Health concept that aims to achieve better public health outcomes through cross-sector collaboration.
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16
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AL-Eitan LN, Wu G, Golding M, Tang Y, Goharriz H, Marston DA, Fooks AR, McElhinney LM. Whole-genome sequencing and phylogenetic analysis of rabies viruses from Jordan. PLoS Negl Trop Dis 2021; 15:e0009431. [PMID: 34014930 PMCID: PMC8171950 DOI: 10.1371/journal.pntd.0009431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/02/2021] [Accepted: 04/30/2021] [Indexed: 12/21/2022] Open
Abstract
Human fatalities caused by rabies are rarely reported in Jordan; however, domestic animals are more likely to fall victim to rabies compared to wild animals, at least this is the case in Jordan due to the presence of canine rabies. In this study, twelve brain samples from domestic and wild animals suspected of being infected with rabies virus from different regions of Jordan were collected during 2019. Seven of them tested positive using the fluorescent antibody test and real-time SYBR RT-PCR assay. Five specimens were from stray dogs and two from foxes. The whole genome sequences were obtained from the positive samples. Sequence analysis showed that one dog virus from Al Quwaysimah city located in Amman governorate, was closely related to an Israeli strain belonging to a Cosmopolitan ME1a clade. The genomes of the remaining six viruses (four from dogs and two from foxes) collected from different areas of Jordan were genetically-related to each other and clustered together with sequences from Iran and Turkey; all belong to Cosmopolitan ME2 clade. These sequences were analyzed with six other Jordanian rabies virus nucleoprotein (N) gene sequences available in the public database, five of them belong to ME1a clade and one belongs to ME1b clade. Rabies virus whole genome data is scarce across the Middle East. This study provides a better understanding of the molecular epidemiology of rabies virus in the region. In this study, we performed whole genome sequencing (WGS) for rabies virus (RABV) isolates from seven samples, five of which were of stray dogs, and the other two were from foxes. Specimens were collected from animals across Jordan, including Balqa, Amman, Irbid, Tafilah, and Madaba governorates. Six out of the seven isolates were belonging to the Cosmopolitan ME2 clade, which related to the Iranian and Turkish sequences. This is not the case previously, where the majority of the Jordanian isolates belong to Cosmopolitan ME1a clade and closely related to the sequences from Israel. This shift might be due to the applied regulations across borders between Jordan and Israel. Besides the growth in travel and trade movement between Jordan and Turkey, where the latter is a border country with Iran. These collected data, where such studies are not common in the Middle East countries, will enhance our understanding of the RABV evolution and epidemiology in the region for rapid and effective response for rabies virus outbreaks.
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Affiliation(s)
- Laith N. AL-Eitan
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid, Jordan
- * E-mail:
| | - Guanghui Wu
- Animal and Plant Health Agency (APHA, Weybridge), Surrey, United Kingdom
| | - Megan Golding
- Animal and Plant Health Agency (APHA, Weybridge), Surrey, United Kingdom
| | - Yue Tang
- Animal and Plant Health Agency (APHA, Weybridge), Surrey, United Kingdom
| | - Hooman Goharriz
- Animal and Plant Health Agency (APHA, Weybridge), Surrey, United Kingdom
| | - Denise A. Marston
- Animal and Plant Health Agency (APHA, Weybridge), Surrey, United Kingdom
| | - Anthony R. Fooks
- Animal and Plant Health Agency (APHA, Weybridge), Surrey, United Kingdom
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Rabies in the Middle East, Eastern Europe, Central Asia and North Africa: Building evidence and delivering a regional approach to rabies elimination. J Infect Public Health 2021; 14:787-794. [PMID: 34022738 DOI: 10.1016/j.jiph.2021.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 02/07/2021] [Accepted: 02/18/2021] [Indexed: 12/25/2022] Open
Abstract
The Middle East, Eastern Europe, Central Asia and North Africa Rabies Control Network (MERACON), is built upon the achievements of the Middle East and Eastern Europe Rabies Expert Bureau (MEEREB). MERACON aims to foster collaboration among Member States (MS) and develop shared regional objectives, building momentum towards dog-mediated rabies control and elimination. Here we assess the epidemiology of rabies and preparedness in twelve participating MS, using case and rabies capacity data for 2017, and compare our findings with previous published reports and a predictive burden model. Across MS, the number of reported cases of dog rabies per 100,000 dog population and the number of reported human deaths per 100,000 population as a result of dog-mediated rabies appeared weakly associated. Compared to 2014 there has been a decrease in the number of reported human cases in five of the twelve MS, three MS reported an increase, two MS continued to report zero cases, and the remaining two MS were not listed in the 2014 study and therefore no comparison could be drawn. Vaccination coverage in dogs has increased since 2014 in half (4/8) of the MS where data are available. Most importantly, it is evident that there is a need for improved data collection, sharing and reporting at both the national and international levels. With the formation of the MERACON network, MS will be able to align with international best practices, while also fostering international support with other MS and international organisations.
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Al-Mustapha A, Abubakar AT, Oyewo M, Bamidele FO, Ibrahim A, Shuaib MO, Olugasa B, Balogun MS, Kia G, Mazeri S, Heikinheimo A. Baseline epidemiology and associated dog ecology study towards stepwise elimination of rabies in Kwara state, Nigeria. Prev Vet Med 2021; 189:105295. [PMID: 33611031 DOI: 10.1016/j.prevetmed.2021.105295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 01/22/2021] [Accepted: 02/08/2021] [Indexed: 12/20/2022]
Abstract
Understanding domestic dog population dynamics and ecology is crucial to any effective rabies control program. This study was conducted as part of the baseline epidemiological studies necessary for the establishment of the Kwara Rabies Rapid Alert System "KRRAS". This study aimed to determine the dog population structure of Kwara State by assessing the dog ownership, vaccination status, and prevalence of dog bites. A total of 1460 questionnaires were administered to respondents in the three senatorial zones of the state using Open Data Kit (ODK) between June 2019 to January 2020. Of the 1460 households surveyed, 293 (20.1 %) owned at least one dog with an average of 2.25 dogs per household. The male to female ratio was 1.9:1 and 79.3 % (n = 523/659) of the owned dogs were local breeds. A total of 785 dogs was enumerated (659 dogs from 293 households and 126 free-roaming dogs) and 7811 persons which resulted in a dog-human ratio of 1:9.95. The estimated dog population is 376,789 (95 % CI: 343,700 - 379,878). Only 31 % (n = 204/659) of households vaccinated their dogs against rabies. The prevalence of dog-bite was 13 % (n = 193/1460) of which only 27 % of the victims (n = 61/225) received post-exposure prophylaxis (PEP). Dog ownership was significantly impacted by the ethnicity of respondents. Hausa (OR: 3.76; 95 % CI: 1.15-12.4; p < 0.001) and Nupe (OR: 4.48; 95 % CI: 1.77-11.33; p < 0.001) respondents owned dogs than Yoruba respondents. The rabies vaccination status of owned dogs was significantly impacted by the level of education (OR: 5.03; 95 % CI: 1.50-16.83; p < 0.001); history of previous dog bite incidents (OR: 1.74; 95 % CI: 0.95-3.17; p < 0.001); the breed of the dog with exotic dogs being more vaccinated (OR: 2.79: 95 % 0.64-12.05; p < 0.001). Similarly, Male dogs (OR: 1.49, 95 % 1.03-2.86; p < 0.001) and partially confined dogs (OR: 1.09, 95 % 0.45-2.11, p < 0.001) were found to be vaccinated against rabies. The results of the study showed low dog vaccination coverage, and high number of free roaming dogs. Hence, a threat to public health. The low dog vaccination coverage is below the 70-80 % target recommended for herd immunity by the World Health Organization.
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Affiliation(s)
- Ahmad Al-Mustapha
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland; Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Ibadan, Oyo State, Nigeria; Department of Veterinary Services, Kwara State Ministry of Agriculture and Rural Development, Ilorin, Nigeria.
| | - Ahmed Tijani Abubakar
- Department of Veterinary Services, Kwara State Ministry of Agriculture and Rural Development, Ilorin, Nigeria; Nigerian Field Epidemiology and Laboratory Training Program, Asokoro, Abuja, Nigeria
| | - Muftau Oyewo
- Department of Veterinary Services, Kwara State Ministry of Agriculture and Rural Development, Ilorin, Nigeria; Nigerian Field Epidemiology and Laboratory Training Program, Asokoro, Abuja, Nigeria
| | - Folashade O Bamidele
- Department of Veterinary Services, Kwara State Ministry of Agriculture and Rural Development, Ilorin, Nigeria; Nigerian Field Epidemiology and Laboratory Training Program, Asokoro, Abuja, Nigeria
| | - Ahmed Ibrahim
- Department of Veterinary Services, Kwara State Ministry of Agriculture and Rural Development, Ilorin, Nigeria
| | - Muhammad Osu Shuaib
- Federal Department of Veterinary and Pest Control Services, Federal Ministry of Agriculture and Rural Development, Abuja, Nigeria
| | - Babasola Olugasa
- Department of Veterinary Public Health and Preventive Medicine, Centre for Control and Prevention of Zoonoses (CCPZ), Faculty of Veterinary Medicine, University of Ibadan, Nigeria
| | | | - Grace Kia
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria, Kaduna State, Nigeria; War Against Rabies Foundation, Abuja, Nigeria
| | - Stella Mazeri
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, The University of Edinburgh, Edinburgh, UK
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland
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Mitochondrial genomes of four American characins and phylogenetic relationships within the family Characidae (Teleostei: Characiformes). Gene 2020; 762:145041. [DOI: 10.1016/j.gene.2020.145041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/11/2020] [Accepted: 08/04/2020] [Indexed: 01/08/2023]
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20
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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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21
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Ismail MZ, AL- Hamdi NK, AL- Amery AN, Marston DA, McElhinney L, Taylor E, del Rio Vilas V, Dadan TM, Fooks AR, Horton DL. Quantifying and mapping the burden of human and animal rabies in Iraq. PLoS Negl Trop Dis 2020; 14:e0008622. [PMID: 33090993 PMCID: PMC7580899 DOI: 10.1371/journal.pntd.0008622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 07/21/2020] [Indexed: 11/19/2022] Open
Abstract
Rabies was first reported in ancient Iraqi civilizations, yet it remains a poorly quantified and important public health threat in the region. Efforts to control rabies in Iraq including dog population control, and vaccination of livestock and dogs, have increased since 2010. Officially reported data on human rabies, dog bites, and animal rabies cases between 2012 and 2017 are analysed here to assess the effect of existing control efforts, to inform future strategies, and to highlight gaps in surveillance and reporting. The results of molecular characterization of 32 viruses from animal cases from throughout Iraq are presented, to improve the understanding of rabies dynamics in the animal reservoir. Although annual numbers of reported human cases were lower in the period between 2012 and 2017 than prior to 2010, human cases continue. There was a distinct gender and age bias among human cases with nine cases in males for every one female and twice as many cases in children than adults. Spatial clustering analysis and phylogenetic evidence suggests rabies is endemic throughout the country, with no regional variation in risk, but better surveillance and reporting is required to underpin control strategies.
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Affiliation(s)
- Mashair Z. Ismail
- Central Veterinary Laboratory, Veterinary Directorate, Baghdad, Iraq
| | | | - Ali N. AL- Amery
- Central Veterinary Laboratory, Veterinary Directorate, Baghdad, Iraq
| | - Denise A. Marston
- Animal and Plant Health Agency (APHA), Rabies and Viral Zoonoses Group, (WHO Collaborating Centre for the Characterisation of Rabies and Rabies-Related Viruses, OIE Reference Laboratory for Rabies), Weybridge, New Haw, Surrey, United Kingdom
| | - Lorraine McElhinney
- Animal and Plant Health Agency (APHA), Rabies and Viral Zoonoses Group, (WHO Collaborating Centre for the Characterisation of Rabies and Rabies-Related Viruses, OIE Reference Laboratory for Rabies), Weybridge, New Haw, Surrey, United Kingdom
- University of Liverpool, Institute of Infection & Global Health, Liverpool, United Kingdom
| | - Emma Taylor
- University of Surrey, School of Veterinary Medicine, Guildford, United Kingdom
| | | | - Thani M. Dadan
- Center for Disease Control, Zoonosis Section, Ministry of Health, Baghdad, Iraq
| | - Anthony R. Fooks
- Animal and Plant Health Agency (APHA), Rabies and Viral Zoonoses Group, (WHO Collaborating Centre for the Characterisation of Rabies and Rabies-Related Viruses, OIE Reference Laboratory for Rabies), Weybridge, New Haw, Surrey, United Kingdom
- University of Liverpool, Institute of Infection & Global Health, Liverpool, United Kingdom
- University of London, St George's Hospital Medical School, Institute for Infection and Immunity, London, United Kingdom
| | - Daniel L. Horton
- University of Surrey, School of Veterinary Medicine, Guildford, United Kingdom
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22
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Oude Munnink BB, Farag EABA, GeurtsvanKessel C, Schapendonk C, van der Linden A, Kohl R, Arron G, Ziglam H, Goravey WGM, Coyle PV, Ibrahim I, Mohran KA, Alrajhi MMS, Islam MM, Abdeen R, Al-Zeyara AAMAH, Younis NM, Al-Romaihi HE, Thani MHJA, Molenkamp R, Sikkema RS, Koopmans M. First molecular analysis of rabies virus in Qatar and clinical cases imported into Qatar, a case report. Int J Infect Dis 2020; 96:323-326. [PMID: 32376305 DOI: 10.1016/j.ijid.2020.04.070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 04/23/2020] [Accepted: 04/25/2020] [Indexed: 11/27/2022] Open
Abstract
Identifying the origin of the rabies virus (RABV) infection may have significant implications for control measures. Here, we identified the source of a RABV infection of two Nepalese migrants in Qatar by comparing their RABV genomes with RABV genomes isolated from the brains of a RABV infected camel and fox from Qatar.
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Affiliation(s)
- Bas B Oude Munnink
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | | | - Corine GeurtsvanKessel
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | - Claudia Schapendonk
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | - Anne van der Linden
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | - Robert Kohl
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | - Georgina Arron
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | | | | | | | | | - Khaled A Mohran
- Department of Animal Resources, Ministry of Municipals and Environment, Doha, Qatar; Animal Health Research Institute, Biotechnology Departments ERC, Dokki, Egypt
| | | | - Md Mazharul Islam
- Department of Animal Resources, Ministry of Municipals and Environment, Doha, Qatar
| | - Randa Abdeen
- Department of Animal Resources, Ministry of Municipals and Environment, Doha, Qatar
| | | | - Nidal Mahmoud Younis
- Department of Animal Resources, Ministry of Municipals and Environment, Doha, Qatar
| | | | | | - Richard Molenkamp
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | - Reina S Sikkema
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
| | - Marion Koopmans
- Erasmus MC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
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23
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A phylogenetic study of new rabies virus strains in different regions of Iran. Virus Genes 2020; 56:361-368. [PMID: 32236772 DOI: 10.1007/s11262-020-01752-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 03/16/2020] [Indexed: 10/24/2022]
Abstract
Rabies is the most critical zoonotic disease in Iran, which imposes many extra costs on health care system in each country. The present study aimed to determine the molecular characteristics of the wild circulating strains of the rabies virus (RABV) collected in Iran during 2015-2017. Rabies-suspected samples were collected from different regions of Iran and identified for RABV antigen confirmation using fluorescent antibody tests. Polymerase chain reaction (PCR) was performed on positive samples and gene sequencing was done on rabies nucleoprotein and glycoprotein genes to determine the rabies molecular characteristics. Accordingly, nine street RABVes were isolated. Then, N (802 bp) and G (735 bp) genes were amplified with specific primers using PCR. The sequence of nine strains was determined and compared with another 50 close to them, and the phylogenetic tree was plotted using neighbor-joining method by Mega 7 software. The molecular characteristic results indicated that all new strains belong to RABV wild species. As a result, the most prevalent strains of RABV in northwest, west, center, and south of Iran were identified. The present study may provide a better insight into the identification of all RABV strains, and understanding the evolutionary nature of RABV and how its hosts change in the world over the centuries.
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24
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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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25
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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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26
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Abstract
The status of rabies as a neglected disease has made its eradication rather challenging in different parts of the world despite the availability of a successful vaccine. Lebanon, in particular, is a country endemic to the disease with several cases of rabies deaths reported over the past 30 years. The risk of rabies, however, has taken a new turn over the past few years in Lebanon with two emerging situations that have made the control of the disease rather challenging: the neighbouring Syrian war and the local garbage crisis. Both of these milestone events might have contributed to an increase in the number of disease vectors as well as individuals at risk, thus nourishing the cycle of disease transmission. In this observational study, the effect of these two events are investigated, with an update on the status of this preventable, yet often neglected, disease in the country. Both events were found to be concomitant with a notable increase in the number of dog bites and thus possible rabies exposure. Current regulations are explored through interviews with veterinarians, and custom recommendations, ranging from policies to control dog populations to awareness campaigns in high-risk individuals, are then proposed to help control the disease.
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27
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Abstract
Many infectious diseases originating from, or carried by, wildlife affect wildlife conservation and biodiversity, livestock health, or human health. We provide an update on changes in the epidemiology of 25 selected infectious, wildlife-related diseases in Europe (from 2010-16) that had an impact, or may have a future impact, on the health of wildlife, livestock, and humans. These pathogens were selected based on their: 1) identification in recent Europe-wide projects as important surveillance targets, 2) inclusion in European Union legislation as pathogens requiring obligatory surveillance, 3) presence in recent literature on wildlife-related diseases in Europe since 2010, 4) inclusion in key pathogen lists released by the Office International des Epizooties, 5) identification in conference presentations and informal discussions on a group email list by a European network of wildlife disease scientists from the European Wildlife Disease Association, or 6) identification as pathogens with changes in their epidemiology during 2010-16. The wildlife pathogens or diseases included in this review are: avian influenza virus, seal influenza virus, lagoviruses, rabies virus, bat lyssaviruses, filoviruses, canine distemper virus, morbilliviruses in aquatic mammals, bluetongue virus, West Nile virus, hantaviruses, Schmallenberg virus, Crimean-Congo hemorrhagic fever virus, African swine fever virus, amphibian ranavirus, hepatitis E virus, bovine tuberculosis ( Mycobacterium bovis), tularemia ( Francisella tularensis), brucellosis ( Brucella spp.), salmonellosis ( Salmonella spp.), Coxiella burnetii, chytridiomycosis, Echinococcus multilocularis, Leishmania infantum, and chronic wasting disease. Further work is needed to identify all of the key drivers of disease change and emergence, as they appear to be influencing the incidence and spread of these pathogens in Europe. We present a summary of these recent changes during 2010-16 to discuss possible commonalities and drivers of disease change and to identify directions for future work on wildlife-related diseases in Europe. Many of the pathogens are entering Europe from other continents while others are expanding their ranges inside and beyond Europe. Surveillance for these wildlife-related diseases at a continental scale is therefore important for planet-wide assessment, awareness of, and preparedness for the risks they may pose to wildlife, domestic animal, and human health.
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28
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Bannazadeh Baghi H, Alinezhad F, Kuzmin I, Rupprecht CE. A Perspective on Rabies in the Middle East-Beyond Neglect. Vet Sci 2018; 5:E67. [PMID: 30018199 PMCID: PMC6165288 DOI: 10.3390/vetsci5030067] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/09/2018] [Accepted: 07/13/2018] [Indexed: 12/25/2022] Open
Abstract
Rabies is a neglected but preventable viral zoonosis that poses a substantial threat to public health. In this regard, a global program has been initiated for the elimination of human rabies caused by rabid dogs through the mass vaccination of canine populations. Geographic areas vary greatly towards attainment of this objective. For example, while dog-mediated and wildlife rabies have been largely controlled in major parts of the Americas and Western Europe, the Middle East still grapples with human rabies transmitted by unvaccinated dogs and cats. Rabies prevention and control in the Middle East is quite difficult because the region is transcontinental, encompassing portions of Africa, Asia, and Europe, while consisting of politically, culturally, and economically diverse countries that are often subject to war and unrest. Consequently, one over-riding dilemma is the misinformation or complete lack of rabies surveillance data from this area. This communication is an attempt to provide an overview of rabies in the Middle East, as a cohesive approach for the honing of disease management in each area, based on data compiled from multiple sources. In addition, the related regional transboundary movement of rabies was investigated through phylogenetic studies of available viral gene sequences. Thereafter, the epidemiological status of rabies was assessed for the region. Finally, localities were classified first by the Stepwise Approach towards Rabies Elimination framework and then categorized into four different groups based on management theme: "rabies free"; owned dog and domestic animal vaccination; community dog vaccination; and wildlife vaccination. The classification system proposed herein may serve as a baseline for future efforts. This is especially important due to the severe lack of rabies information available for the Middle East as a whole and a need for a comprehensive program focusing on the entirety of the region in light of renewed international commitment towards canine rabies elimination.
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Affiliation(s)
- Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, 5166/15731 Tabriz, Iran.
- Immunology Research Center, Tabriz University of Medical Sciences, 5166/15731 Tabriz, Iran.
- Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, 5166/15731 Tabriz, Iran.
| | - Farbod Alinezhad
- Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, 5166/15731 Tabriz, Iran.
- Drug Applied Research Center, Tabriz University of Medical Sciences, 5166/15731 Tabriz, Iran.
| | - Ivan Kuzmin
- Medical Branch, University of Texas, Galveston, TX 77555, USA.
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29
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Fisher CR, Streicker DG, Schnell MJ. The spread and evolution of rabies virus: conquering new frontiers. Nat Rev Microbiol 2018; 16:241-255. [PMID: 29479072 PMCID: PMC6899062 DOI: 10.1038/nrmicro.2018.11] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Rabies is a lethal zoonotic disease that is caused by lyssaviruses, most often rabies virus. Despite control efforts, sporadic outbreaks in wildlife populations are largely unpredictable, underscoring our incomplete knowledge of what governs viral transmission and spread in reservoir hosts. Furthermore, the evolutionary history of rabies virus and related lyssaviruses remains largely unclear. Robust surveillance efforts combined with diagnostics and disease modelling are now providing insights into the epidemiology and evolution of rabies virus. The immune status of the host, the nature of exposure and strain differences all clearly influence infection and transmission dynamics. In this Review, we focus on rabies virus infections in the wildlife and synthesize current knowledge in the rapidly advancing fields of rabies virus epidemiology and evolution, and advocate for multidisciplinary approaches to advance our understanding of this disease.
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Affiliation(s)
- Christine R. Fisher
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Daniel G. Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Matthias J. Schnell
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Vaccine Center at Thomas Jefferson University, Philadelphia, PA, USA
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30
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Abstract
Effective methods to increase awareness of preventable infectious diseases are key components of successful control programmes. Rabies is an example of a disease with significant impact, where public awareness is variable. A recent awareness campaign in a rabies endemic region of Azerbaijan provided a unique opportunity to assess the efficacy of such campaigns. A cluster cross-sectional survey concerning rabies was undertaken following the awareness campaign in 600 households in 38 randomly selected towns, in districts covered by the campaign and matched control regions. This survey demonstrated that the relatively simple awareness campaign was effective at improving knowledge of rabies symptoms and vaccination schedules. Crucially, those in the awareness campaign group were also 1·4 times more likely to report that they had vaccinated their pets, an essential component of human rabies prevention. In addition, low knowledge of appropriate post-exposure treatment and animal sources of rabies provide information useful for future public awareness campaigns in the region and other similar areas.
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31
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Fooks AR, Cliquet F, Finke S, Freuling C, Hemachudha T, Mani RS, Müller T, Nadin-Davis S, Picard-Meyer E, Wilde H, Banyard AC. Rabies. Nat Rev Dis Primers 2017; 3:17091. [PMID: 29188797 DOI: 10.1038/nrdp.2017.91] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Rabies is a life-threatening neglected tropical disease: tens of thousands of cases are reported annually in endemic countries (mainly in Africa and Asia), although the actual numbers are most likely underestimated. Rabies is a zoonotic disease that is caused by infection with viruses of the Lyssavirus genus, which are transmitted via the saliva of an infected animal. Dogs are the most important reservoir for rabies viruses, and dog bites account for >99% of human cases. The virus first infects peripheral motor neurons, and symptoms occur after the virus reaches the central nervous system. Once clinical disease develops, it is almost certainly fatal. Primary prevention involves dog vaccination campaigns to reduce the virus reservoir. If exposure occurs, timely post-exposure prophylaxis can prevent the progression to clinical disease and involves appropriate wound care, the administration of rabies immunoglobulin and vaccination. A multifaceted approach for human rabies eradication that involves government support, disease awareness, vaccination of at-risk human populations and, most importantly, dog rabies control is necessary to achieve the WHO goal of reducing the number of cases of dog-mediated human rabies to zero by 2030.
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Affiliation(s)
- Anthony R Fooks
- Animal and Plant Health Agency (APHA), Wildlife Zoonoses and Vector Borne Diseases Research Group, (WHO Collaborating Centre for the Characterisation of Rabies and Rabies-Related Viruses, World Organisation for Animal Health (OIE) Reference Laboratory for Rabies), Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK.,Institute of Infection &Global Health, University of Liverpool, Liverpool, UK.,Institute for Infection and Immunity, St. George's Hospital Medical School, University of London, London, UK
| | - Florence Cliquet
- French Agency for Food, Environmental and Occupational Health &Safety (ANSES)-Nancy Laboratory for Rabies and Wildlife (European Union Reference Laboratory for Rabies, WHO Collaborating Centre for Research and Management in Zoonoses Control, OIE Reference Laboratory for Rabies, European Union Reference Institute for Rabies Serology), Technopôle Agricole et Vétérinaire de Pixérécourt, Malzéville, France
| | - Stefan Finke
- Institute of Molecular Virology and Cell Biology (WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Conrad Freuling
- Institute of Molecular Virology and Cell Biology (WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Thiravat Hemachudha
- Department of Medicine (Neurology) and (WHO Collaborating Centre for Research and Training on Viral Zoonoses), Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Thai Red Cross Emerging Infectious Disease-Health Science Centre, Thai Red Cross Society, Bangkok, Thailand
| | - Reeta S Mani
- Department of Neurovirology (WHO Collaborating Centre for Reference and Research in Rabies), National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Thomas Müller
- Institute of Molecular Virology and Cell Biology (WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Susan Nadin-Davis
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency (WHO Collaborating Centre for Control, Pathogenesis and Epidemiology of Rabies in Carnivores), Ottawa, Ontario, Canada
| | - Evelyne Picard-Meyer
- French Agency for Food, Environmental and Occupational Health &Safety (ANSES)-Nancy Laboratory for Rabies and Wildlife (European Union Reference Laboratory for Rabies, WHO Collaborating Centre for Research and Management in Zoonoses Control, OIE Reference Laboratory for Rabies, European Union Reference Institute for Rabies Serology), Technopôle Agricole et Vétérinaire de Pixérécourt, Malzéville, France
| | - Henry Wilde
- Department of Medicine (Neurology) and (WHO Collaborating Centre for Research and Training on Viral Zoonoses), Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ashley C Banyard
- Animal and Plant Health Agency (APHA), Wildlife Zoonoses and Vector Borne Diseases Research Group, (WHO Collaborating Centre for the Characterisation of Rabies and Rabies-Related Viruses, World Organisation for Animal Health (OIE) Reference Laboratory for Rabies), Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
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Dellicour S, Rose R, Faria NR, Vieira LFP, Bourhy H, Gilbert M, Lemey P, Pybus OG. Using Viral Gene Sequences to Compare and Explain the Heterogeneous Spatial Dynamics of Virus Epidemics. Mol Biol Evol 2017. [PMID: 28651357 DOI: 10.1093/molbev/msx176] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rabies is an important zoonotic disease distributed worldwide. A key question in rabies epidemiology is the identification of factors that impact virus dispersion. Here we apply new analytical methods, based on phylogeographic reconstructions of viral lineage movement, to undertake a comparative evolutionary-epidemiological study of the spatial dynamics of rabies virus (RABV) epidemics in different hosts and habitats. We compiled RABV data sets from skunk, raccoon, bat and domestic dog populations in order to investigate the viral diffusivity of different RABV epidemics, and to detect and compare the environmental factors that impact the velocity of viral spread in continuous spatial landscapes. We build on a recently developed statistical framework that uses spatially- and temporally-referenced phylogenies. We estimate several spatial statistics of virus spread, which reveal a higher diffusivity of RABV in domestic dogs compared with RABV in other mammals. This finding is explained by subsequent analyses of environmental heterogeneity, which indicate that factors relating to human geography play a significant role in RABV dispersion in domestic dogs. More generally, our results suggest that human-related factors are important worldwide in explaining RABV dispersion in terrestrial host species. Our study shows that phylogenetically informed viral movements can be used to elucidate the factors that impact virus dispersal, opening new opportunities for a better understanding of the impact of host species and environmental conditions on the spatial dynamics of rapidly evolving populations.
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Affiliation(s)
- Simon Dellicour
- Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
| | | | | | - Luiz Fernando Pereira Vieira
- Department of Laboratorial Diagnosis, Institute of Agricultural and Forest Defense of Espírito Santo (IDAF), Vitoria, Brazil
| | - Hervé Bourhy
- Institut Pasteur, Lyssavirus Dynamics and Host Adaptation Unit, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Marius Gilbert
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Philippe Lemey
- Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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33
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Marston DA, Horton DL, Nunez J, Ellis RJ, Orton RJ, Johnson N, Banyard AC, McElhinney LM, Freuling CM, Fırat M, Ünal N, Müller T, de Lamballerie X, Fooks AR. Genetic analysis of a rabies virus host shift event reveals within-host viral dynamics in a new host. Virus Evol 2017; 3:vex038. [PMID: 29255631 PMCID: PMC5729694 DOI: 10.1093/ve/vex038] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Host shift events play an important role in epizootics as adaptation to new hosts can profoundly affect the spread of the disease and the measures needed to control it. During the late 1990s, an epizootic in Turkey resulted in a sustained maintenance of rabies virus (RABV) within the fox population. We used Bayesian inferences to investigate whole genome sequences from fox and dog brain tissues from Turkey to demonstrate that the epizootic occurred in 1997 (±1 year). Furthermore, these data indicated that the epizootic was most likely due to a host shift from locally infected domestic dogs, rather than an incursion of a novel fox or dog RABV. No evidence was observed for genetic adaptation to foxes at consensus sequence level and dN/dS analysis suggested purifying selection. Therefore, the deep sequence data were analysed to investigate the sub-viral population during a host shift event. Viral heterogeneity was measured in all RABV samples; viruses from the early period after the host shift exhibited greater sequence variation in comparison to those from the later stage, and to those not involved in the host shift event, possibly indicating a role in establishing transmission within a new host. The transient increase in variation observed in the new host species may represent virus replication within a new environment, perhaps due to increased replication within the CNS, resulting in a larger population of viruses, or due to the lack of host constraints present in the new host reservoir.
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Affiliation(s)
- Denise A Marston
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
- UMR “Émergence des Pathologies Virales” (EPV: Aix-Marseille Univ—IRD 190—Inserm 1207 – EHESP – IHU Méditerranée Infection), Faculté de Médecine de Marseille, 27, Bd Jean Moulin,13005 Marseille, cedex 05 France
| | - Daniel L Horton
- School of Veterinary Medicine, University of Surrey, Guildford, GU2 7AL UK
| | - Javier Nunez
- Surveillance and Laboratory Services Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB UK
| | - Richard J Ellis
- Surveillance and Laboratory Services Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB UK
| | - Richard J Orton
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
- Centre for Virus Research, MRC-University of Glasgow, University of Glasgow, Glasgow, G61 1QH UK
| | - Nicholas Johnson
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
- Faculty of Health and Medical Science, University of Surrey, Guildford, GU2 7XH, UK
| | - Ashley C Banyard
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Lorraine M McElhinney
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
- Institute of Infection and Global Health, University of Liverpool, UK
| | - Conrad M Freuling
- Friedrich-Loeffler-Institute, (FLI), Institute of Molecular Virology and Cell Biology, Greifswald-Insel Riems, D-17493, Germany
| | - Müge Fırat
- Etlik Veterinary Control Central Research Institute A.S.Kolayli Street. No.21-21/A, 06020, Etlik, Ankara, Turkey
| | - Nil Ünal
- Etlik Veterinary Control Central Research Institute A.S.Kolayli Street. No.21-21/A, 06020, Etlik, Ankara, Turkey
| | - Thomas Müller
- Friedrich-Loeffler-Institute, (FLI), Institute of Molecular Virology and Cell Biology, Greifswald-Insel Riems, D-17493, Germany
| | - Xavier de Lamballerie
- UMR “Émergence des Pathologies Virales” (EPV: Aix-Marseille Univ—IRD 190—Inserm 1207 – EHESP – IHU Méditerranée Infection), Faculté de Médecine de Marseille, 27, Bd Jean Moulin,13005 Marseille, cedex 05 France
| | - Anthony R Fooks
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
- Institute of Infection and Global Health, University of Liverpool, UK
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34
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Brunker K, Marston DA, Horton DL, Cleaveland S, Fooks AR, Kazwala R, Ngeleja C, Lembo T, Sambo M, Mtema ZJ, Sikana L, Wilkie G, Biek R, Hampson K. Elucidating the phylodynamics of endemic rabies virus in eastern Africa using whole-genome sequencing. Virus Evol 2015; 1:vev011. [PMID: 27774283 PMCID: PMC5014479 DOI: 10.1093/ve/vev011] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Many of the pathogens perceived to pose the greatest risk to humans are viral zoonoses, responsible for a range of emerging and endemic infectious diseases. Phylogeography is a useful tool to understand the processes that give rise to spatial patterns and drive dynamics in virus populations. Increasingly, whole-genome information is being used to uncover these patterns, but the limits of phylogenetic resolution that can be achieved with this are unclear. Here, whole-genome variation was used to uncover fine-scale population structure in endemic canine rabies virus circulating in Tanzania. This is the first whole-genome population study of rabies virus and the first comprehensive phylogenetic analysis of rabies virus in East Africa, providing important insights into rabies transmission in an endemic system. In addition, sub-continental scale patterns of population structure were identified using partial gene data and used to determine population structure at larger spatial scales in Africa. While rabies virus has a defined spatial structure at large scales, increasingly frequent levels of admixture were observed at regional and local levels. Discrete phylogeographic analysis revealed long-distance dispersal within Tanzania, which could be attributed to human-mediated movement, and we found evidence of multiple persistent, co-circulating lineages at a very local scale in a single district, despite on-going mass dog vaccination campaigns. This may reflect the wider endemic circulation of these lineages over several decades alongside increased admixture due to human-mediated introductions. These data indicate that successful rabies control in Tanzania could be established at a national level, since most dispersal appears to be restricted within the confines of country borders but some coordination with neighbouring countries may be required to limit transboundary movements. Evidence of complex patterns of rabies circulation within Tanzania necessitates the use of whole-genome sequencing to delineate finer scale population structure that can that can guide interventions, such as the spatial scale and design of dog vaccination campaigns and dog movement controls to achieve and maintain freedom from disease.
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Affiliation(s)
- Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow G12 8QQ, UK; Animal and Plant Health Agency, Weybridge, Woodham Lane, KT15 3NB, UK
| | - Denise A Marston
- Animal and Plant Health Agency, Weybridge, Woodham Lane, KT15 3NB, UK
| | - Daniel L Horton
- Animal and Plant Health Agency, Weybridge, Woodham Lane, KT15 3NB, UK; School of Veterinary Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Sarah Cleaveland
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow G12 8QQ, UK
| | - Anthony R Fooks
- Animal and Plant Health Agency, Weybridge, Woodham Lane, KT15 3NB, UK
| | - Rudovick Kazwala
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, United Republic of Tanzania
| | - Chanasa Ngeleja
- Tanzania Veterinary Laboratory Agency, Dar es Salaam, United Republic of Tanzania, Temeke Veterinary, Mandela Road, P.O. BOX 9254
| | - Tiziana Lembo
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow G12 8QQ, UK
| | - Maganga Sambo
- Ifakara Health Institute, Ifakara, United Republic of Tanzania, P.O. Box 53
| | - Zacharia J Mtema
- Ifakara Health Institute, Ifakara, United Republic of Tanzania, P.O. Box 53
| | - Lwitiko Sikana
- Ifakara Health Institute, Ifakara, United Republic of Tanzania, P.O. Box 53
| | - Gavin Wilkie
- MRC Centre for Virus Research, University of Glasgow, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow G12 8QQ, UK
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow G12 8QQ, UK
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