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Bucher A, Dimov A, Fink G, Chitnis N, Bonfoh B, Zinsstag J. Benefit-cost analysis of coordinated strategies for control of rabies in Africa. Nat Commun 2023; 14:5370. [PMID: 37679314 PMCID: PMC10484917 DOI: 10.1038/s41467-023-41110-2] [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: 05/20/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023] Open
Abstract
Previous research suggests that dog mass vaccination campaigns can eliminate rabies locally, resulting in large human and animal life gains. Despite these demonstrated benefits, dog vaccination programs remain scarce on the African continent. We conducted a benefit-cost analysis to demonstrate that engaging into vaccination campaigns is the dominant strategy for most countries even in the absence of coordinated action between them. And quantify how coordinated policy measures across countries in Africa could impact rabies incidence and associated costs. We show that coordinated dog mass vaccination between countries and PEP would lead to the elimination of dog rabies in Africa with total welfare gains of USD 9.5 billion (95% CI: 8.1 - 11.4 billion) between 2024 and 2054 (30 years). Coordinated disease control between African countries can lead to more socially and ecologically equitable outcomes by reducing the number of lost human lives to almost zero and possibly eliminating rabies.
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Affiliation(s)
- A Bucher
- Swiss Tropical and Public Health Institute, Kreuzstr. 2, 4123, Allschwil, Switzerland
- University of Basel, Petersplatz 1, 4003, Basel, Switzerland
| | - A Dimov
- Swiss Tropical and Public Health Institute, Kreuzstr. 2, 4123, Allschwil, Switzerland
- University of Basel, Petersplatz 1, 4003, Basel, Switzerland
- University of Zürich, Rämistrasse 71, 8006, Zürich, Switzerland
| | - G Fink
- Swiss Tropical and Public Health Institute, Kreuzstr. 2, 4123, Allschwil, Switzerland
- University of Basel, Petersplatz 1, 4003, Basel, Switzerland
| | - N Chitnis
- Swiss Tropical and Public Health Institute, Kreuzstr. 2, 4123, Allschwil, Switzerland
- University of Basel, Petersplatz 1, 4003, Basel, Switzerland
| | - B Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, 01 BP 1303, Abidjan 01, Côte d'Ivoire
| | - J Zinsstag
- Swiss Tropical and Public Health Institute, Kreuzstr. 2, 4123, Allschwil, Switzerland.
- University of Basel, Petersplatz 1, 4003, Basel, Switzerland.
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2
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Layan M, Dacheux L, Lemey P, Brunker K, Ma L, Troupin C, Dussart P, Chevalier V, Wood JLN, Ly S, Duong V, Bourhy H, Dellicour S. Uncovering the endemic circulation of rabies in Cambodia. Mol Ecol 2023; 32:5140-5155. [PMID: 37540190 DOI: 10.1111/mec.17087] [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: 11/22/2022] [Accepted: 07/18/2023] [Indexed: 08/05/2023]
Abstract
In epidemiology, endemicity characterizes sustained pathogen circulation in a geographical area, which involves a circulation that is not being maintained by external introductions. Because it could potentially shape the design of public health interventions, there is an interest in fully uncovering the endemic pattern of a disease. Here, we use a phylogeographic approach to investigate the endemic signature of rabies virus (RABV) circulation in Cambodia. Cambodia is located in one of the most affected regions by rabies in the world, but RABV circulation between and within Southeast Asian countries remains understudied. Our analyses are based on a new comprehensive data set of 199 RABV genomes collected between 2014 and 2017 as well as previously published Southeast Asian RABV sequences. We show that most Cambodian sequences belong to a distinct clade that has been circulating almost exclusively in Cambodia. Our results thus point towards rabies circulation in Cambodia that does not rely on external introductions. We further characterize within-Cambodia RABV circulation by estimating lineage dispersal metrics that appear to be similar to other settings, and by performing landscape phylogeographic analyses to investigate environmental factors impacting the dispersal dynamic of viral lineages. The latter analyses do not lead to the identification of environmental variables that would be associated with the heterogeneity of viral lineage dispersal velocities, which calls for a better understanding of local dog ecology and further investigations of the potential drivers of RABV spread in the region. Overall, our study illustrates how phylogeographic investigations can be performed to assess and characterize viral endemicity in a context of relatively limited data.
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Affiliation(s)
- Maylis Layan
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, UMR2000, CNRS, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Laurent Dacheux
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Université Paris Cité, Paris, France
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Laurence Ma
- Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Université Paris Cité, Paris, France
| | - Cécile Troupin
- Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Véronique Chevalier
- CIRAD, UMR ASTRE, Montpellier, France
- ASTRE, Univ. Montpellier CIRAD, INRAE, Montpellier, France
- Epidemiology and Clinical Research, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - James L N Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sowath Ly
- Epidemiology and Public Health, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Université Paris Cité, Paris, France
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
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3
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Capin JBG, Sanque AJC, Eng MNJ, Lagare A, Sepulveda MCB, Murao LAE. Emerging Genomic Trends on Rabies Virus in Davao Region, Philippines, 2018-2021. Viruses 2023; 15:1658. [PMID: 37632001 PMCID: PMC10459148 DOI: 10.3390/v15081658] [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: 06/26/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 08/27/2023] Open
Abstract
Rabies, caused by the rabies virus (RABV), remains a significant public health issue in the Philippines despite efforts to control it. To eliminate rabies by 2030, effective surveillance strategies are crucial. In this study, we examined RABV evolution and phylodynamics in the Davao Region using genome sequences from Davao City and nearby provinces. We adapted the RABV ARTIC Protocol for Oxford Nanopore High-Throughput Sequencing to optimize workflow efficiency under limited resources. Comparing new virus samples collected from June 2019 to June 2021 (n = 38) with baseline samples from June 2018 to May 2019 (n = 49), new sub-clades were observed in the phylogenetic tree, suggesting divergence from older variants that were previously undetected. Most of the new viruses belonged to the Asian SEA4_A1.1.1 lineage, but new (SEA4_B1 and SEA4_B1.1) and emerging (SEA4_B1.1_E1) lineages that have never been reported in the Philippines were also identified. The baseline study reported phylogeographic clustering of RABV isolates from the same areas. However, this pattern was disrupted in the current biosurveillance, with variants detected in areas outside the original cluster. Furthermore, our findings revealed significant transmission routes between Davao City and neighboring provinces, contrasting with the predominantly intra-city transmission observed in the baseline study. These results underscore the need for ongoing and timely genomic surveillance to monitor genetic diversity changes and the emergence of novel strains, as well as to track alterations in transmission pathways. Implementing cost-effective next-generation sequencing workflows will facilitate the integration of genomic surveillance into rabies control programs, particularly in resource-limited settings. Collaborations between different sectors can empower local laboratories and experts in genomic technologies and analysis.
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Affiliation(s)
- Jessel Babe G. Capin
- Department of Biological Science and Environmental Studies, College of Science and Mathematics, University of the Philippines Mindanao, Davao City 8000, Philippines; (J.B.G.C.); (A.J.C.S.)
| | - Angela Jahn C. Sanque
- Department of Biological Science and Environmental Studies, College of Science and Mathematics, University of the Philippines Mindanao, Davao City 8000, Philippines; (J.B.G.C.); (A.J.C.S.)
| | - Maria Noreen J. Eng
- Davao City Veterinarian’s Office, Davao City 8000, Philippines; (M.N.J.E.); (A.L.); (M.C.B.S.)
| | - Arlene Lagare
- Davao City Veterinarian’s Office, Davao City 8000, Philippines; (M.N.J.E.); (A.L.); (M.C.B.S.)
| | | | - Lyre Anni E. Murao
- Department of Biological Science and Environmental Studies, College of Science and Mathematics, University of the Philippines Mindanao, Davao City 8000, Philippines; (J.B.G.C.); (A.J.C.S.)
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4
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Update on laboratory data of animal rabies at the Centre Pasteur of Cameroon from 2014 to 2021. Res Vet Sci 2023; 157:6-12. [PMID: 36842248 DOI: 10.1016/j.rvsc.2023.02.008] [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: 10/29/2022] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
Rabies is a worldwide zoonotic disease mainly transmitted to humans by an infected dog bite. Despite the endemicity of rabies in dogs and few documented cases in Cameroon, there is still not enough data on frequency of rabies cases in animals. The present study aims to update data on the circulation of rabies in animals screened at the Centre Pasteur of Cameroon (CPC) between 2014 and 2021. The detection of rabies in animals was based on passive surveillance. Animal rabies cases were confirmed on brain biopsies using fluorescent antibody test and SYBR green based real-time RT-PCR for negative results confirmation. The total nucleoprotein (N) gene of animal-derived RABV isolated were amplified by hemi nested RT-PCR and subjected to phylogenetic analyses. From 2014 to 2021, a total of 92 animals including 86 dogs (93.5%), 3 cats, 2 pigs and 1 chiropteran were screened for rabies at the CPC. From the 86 dog sampled, 62.3% (54/86) were tested positive for rabies and 1 out of 3 cat samples was also tested positive. The PEP demand was very high (59,371) during the study period. Phylogenetic analyses assigned all 15 studied isolates successfully sequenced to the Africa-1a lineage belonging to the Cosmopolitan clade. The study highlights the frequent circulation of rabies in Cameroon and the role of dogs and cat as main reservoir and vector of rabies.
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Kozakiewicz CP, Burridge CP, Lee JS, Kraberger SJ, Fountain-Jones NM, Fisher RN, Lyren LM, Jennings MK, Riley SPD, Serieys LEK, Craft ME, Funk WC, Crooks KR, VandeWoude S, Carver S. Habitat connectivity and host relatedness influence virus spread across an urbanising landscape in a fragmentation-sensitive carnivore. Virus Evol 2022; 9:veac122. [PMID: 36694819 PMCID: PMC9865512 DOI: 10.1093/ve/veac122] [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: 08/04/2022] [Revised: 10/22/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Spatially heterogeneous landscape factors such as urbanisation can have substantial effects on the severity and spread of wildlife diseases. However, research linking patterns of pathogen transmission to landscape features remains rare. Using a combination of phylogeographic and machine learning approaches, we tested the influence of landscape and host factors on feline immunodeficiency virus (FIVLru) genetic variation and spread among bobcats (Lynx rufus) sampled from coastal southern California. We found evidence for increased rates of FIVLru lineage spread through areas of higher vegetation density. Furthermore, single-nucleotide polymorphism (SNP) variation among FIVLru sequences was associated with host genetic distances and geographic location, with FIVLru genetic discontinuities precisely correlating with known urban barriers to host dispersal. An effect of forest land cover on FIVLru SNP variation was likely attributable to host population structure and differences in forest land cover between different populations. Taken together, these results suggest that the spread of FIVLru is constrained by large-scale urban barriers to host movement. Although urbanisation at fine spatial scales did not appear to directly influence virus transmission or spread, we found evidence that viruses transmit and spread more quickly through areas containing higher proportions of natural habitat. These multiple lines of evidence demonstrate how urbanisation can change patterns of contact-dependent pathogen transmission and provide insights into how continued urban development may influence the incidence and management of wildlife disease.
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Affiliation(s)
| | | | - Justin S Lee
- Genomic Sequencing Laboratory, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | | | | | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA 92101, USA
| | - Lisa M Lyren
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA 92101, USA
| | - Megan K Jennings
- Biology Department, San Diego State University, San Diego, CA 92182, USA
| | - Seth P D Riley
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, CA 91360, USA
| | | | - Meggan E Craft
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN 55108, USA
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kevin R Crooks
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA,Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
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Chen S. Spatial and temporal dynamic analysis of rabies: A review of current methodologies. GEOSPATIAL HEALTH 2022; 17. [PMID: 36468590 DOI: 10.4081/gh.2022.1139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Rabies continues to be one of the deadliest, high risk diseases worldwide, posing a severe threat to public health. The lack of human-to-human transmission means that the spread of rabies is not significantly affected by the distribution of humans or migra- tion. Thus, the spatiotemporal dynamic of cases in both wild and domestic animals is an important issue that can result in human cases. This paper gives an overview of the methodologies for the spatial and temporal dynamic analysis of this disease. It introduces the most representative research progress of spatial aggregation, dynamic transmission, spatiotemporal distribution, epidemiologi- cal analysis and application of modelling in the study of rabies transmission in recent years. This overview should be useful for investigating the spatial and temporal dynamics of rabies, as it could help understanding the spread of cases as well as contribute to the development of better prevention and control strategies in ecology and epidemiology.
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Affiliation(s)
- Shuaicheng Chen
- College of Animal Science and Technology, Shandong Agricultural University.
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7
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Detection and molecular characterization of rabies virus isolates from humans in Cameroon. Diagn Microbiol Infect Dis 2022; 105:115834. [DOI: 10.1016/j.diagmicrobio.2022.115834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/06/2022] [Accepted: 10/09/2022] [Indexed: 11/20/2022]
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8
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Parag KV, Donnelly CA, Zarebski AE. Quantifying the information in noisy epidemic curves. NATURE COMPUTATIONAL SCIENCE 2022; 2:584-594. [PMID: 38177483 DOI: 10.1038/s43588-022-00313-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/08/2022] [Indexed: 01/06/2024]
Abstract
Reliably estimating the dynamics of transmissible diseases from noisy surveillance data is an enduring problem in modern epidemiology. Key parameters are often inferred from incident time series, with the aim of informing policy-makers on the growth rate of outbreaks or testing hypotheses about the effectiveness of public health interventions. However, the reliability of these inferences depends critically on reporting errors and latencies innate to the time series. Here, we develop an analytical framework to quantify the uncertainty induced by under-reporting and delays in reporting infections, as well as a metric for ranking surveillance data informativeness. We apply this metric to two primary data sources for inferring the instantaneous reproduction number: epidemic case and death curves. We find that the assumption of death curves as more reliable, commonly made for acute infectious diseases such as COVID-19 and influenza, is not obvious and possibly untrue in many settings. Our framework clarifies and quantifies how actionable information about pathogen transmissibility is lost due to surveillance limitations.
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Affiliation(s)
- Kris V Parag
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK.
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK.
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
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9
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Nash RK, Nouvellet P, Cori A. Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges. PLOS DIGITAL HEALTH 2022; 1:e0000052. [PMID: 36812522 PMCID: PMC9931334 DOI: 10.1371/journal.pdig.0000052] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/27/2022] [Indexed: 12/24/2022]
Abstract
The time-varying reproduction number (Rt) is an important measure of transmissibility during outbreaks. Estimating whether and how rapidly an outbreak is growing (Rt > 1) or declining (Rt < 1) can inform the design, monitoring and adjustment of control measures in real-time. We use a popular R package for Rt estimation, EpiEstim, as a case study to evaluate the contexts in which Rt estimation methods have been used and identify unmet needs which would enable broader applicability of these methods in real-time. A scoping review, complemented by a small EpiEstim user survey, highlight issues with the current approaches, including the quality of input incidence data, the inability to account for geographical factors, and other methodological issues. We summarise the methods and software developed to tackle the problems identified, but conclude that significant gaps remain which should be addressed to enable easier, more robust and applicable estimation of Rt during epidemics.
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Affiliation(s)
- Rebecca K. Nash
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London
| | - Pierre Nouvellet
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London
- School of Life Sciences, University of Sussex
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London
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10
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Elimination of human rabies in Goa, India through an integrated One Health approach. Nat Commun 2022; 13:2788. [PMID: 35589709 PMCID: PMC9120018 DOI: 10.1038/s41467-022-30371-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 04/27/2022] [Indexed: 01/13/2023] Open
Abstract
Dog-mediated rabies kills tens of thousands of people each year in India, representing one third of the estimated global rabies burden. Whilst the World Health Organization (WHO), World Organization for Animal Health (OIE) and the Food and Agriculture Organization of the United Nations (FAO) have set a target for global dog-mediated human rabies elimination by 2030, examples of large-scale dog vaccination programs demonstrating elimination remain limited in Africa and Asia. We describe the development of a data-driven rabies elimination program from 2013 to 2019 in Goa State, India, culminating in human rabies elimination and a 92% reduction in monthly canine rabies cases. Smartphone technology enabled systematic spatial direction of remote teams to vaccinate over 95,000 dogs at 70% vaccination coverage, and rabies education teams to reach 150,000 children annually. An estimated 2249 disability-adjusted life years (DALYs) were averted over the program period at 526 USD per DALY, making the intervention 'very cost-effective' by WHO definitions. This One Health program demonstrates that human rabies elimination is achievable at the state level in India.
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Campbell K, Gifford RJ, Singer J, Hill V, O’Toole A, Rambaut A, Hampson K, Brunker K. Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination. PLoS Pathog 2022; 18:e1010023. [PMID: 35500026 PMCID: PMC9162366 DOI: 10.1371/journal.ppat.1010023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/02/2022] [Accepted: 03/30/2022] [Indexed: 12/17/2022] Open
Abstract
The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus, however the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 96 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, as well as areas of persistence and routes of virus movement, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as countries work towards eliminating dog-mediated rabies, as well as having potential for broader application to the surveillance of other viruses.
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Affiliation(s)
- Kathryn Campbell
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Robert J. Gifford
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Joshua Singer
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Aine O’Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
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12
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Antolin MF. From outbreaks to endemic disease. Science 2022; 376:453-454. [PMID: 35482884 DOI: 10.1126/science.abo7428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Relief from the effects of epidemics may signal the start of low-level disease persistence.
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Affiliation(s)
- Michael F Antolin
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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13
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Mancy R, Rajeev M, Lugelo A, Brunker K, Cleaveland S, Ferguson EA, Hotopp K, Kazwala R, Magoto M, Rysava K, Haydon DT, Hampson K. Rabies shows how scale of transmission can enable acute infections to persist at low prevalence. Science 2022; 376:512-516. [PMID: 35482879 PMCID: PMC7613728 DOI: 10.1126/science.abn0713] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
How acute pathogens persist and what curtails their epidemic growth in the absence of acquired immunity remains unknown. Canine rabies is a fatal zoonosis that circulates endemically at low prevalence among domestic dogs in low- and middle-income countries. We traced rabies transmission in a population of 50,000 dogs in Tanzania from 2002 to 2016 and applied individual-based models to these spatially resolved data to investigate the mechanisms modulating transmission and the scale over which they operate. Although rabies prevalence never exceeded 0.15%, the best-fitting models demonstrated appreciable depletion of susceptible animals that occurred at local scales because of clusters of deaths and dogs already incubating infection. Individual variation in rabid dog behavior facilitated virus dispersal and cocirculation of virus lineages, enabling metapopulation persistence. These mechanisms have important implications for prediction and control of pathogens that circulate in spatially structured populations.
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Affiliation(s)
- Rebecca Mancy
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Malavika Rajeev
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Ahmed Lugelo
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Sarah Cleaveland
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Elaine A. Ferguson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Karen Hotopp
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Rudovick Kazwala
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | | | - Kristyna Rysava
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Warwick, UK
| | - Daniel T. Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
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14
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N'dilimabaka N, Koumba Mavoungou D, Soami V, Bohou Kombila L, Mouguiama RM, Mondjo A, Mangombi Pambou JB, Ngoma JF, Ovengue FC, Alilangori TP, Koko J, Bitegue Methe L, Mboumba Mboumba H, Sima Zue A, Edjo Nkili G, Lekana-Douki SE, Maganga GD. Molecular analyses of human rabies virus associated with encephalitis in two children in Gabon. IJID REGIONS 2022; 2:180-183. [PMID: 35757081 PMCID: PMC9216393 DOI: 10.1016/j.ijregi.2022.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 10/25/2022]
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15
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Hayes S, Lushasi K, Sambo M, Changalucha J, Ferguson EA, Sikana L, Hampson K, Nouvellet P, Donnelly CA. Understanding the incidence and timing of rabies cases in domestic animals and wildlife in south-east Tanzania in the presence of widespread domestic dog vaccination campaigns. Vet Res 2022; 53:106. [PMID: 36510331 PMCID: PMC9743725 DOI: 10.1186/s13567-022-01121-1] [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: 11/11/2021] [Accepted: 10/17/2022] [Indexed: 12/14/2022] Open
Abstract
The "Zero by 30" strategic plan aims to eliminate human deaths from dog-mediated rabies by 2030 and domestic dog vaccination is a vital component of this strategic plan. In areas where domestic dog vaccination has been implemented, it is important to assess the impact of this intervention. Additionally, understanding temporal and seasonal trends in the incidence of animal rabies cases may assist in optimizing such interventions. Data on the incidence of probable rabies cases in domestic and wild animals were collected between January 2011 and December 2018 in thirteen districts of south-east Tanzania where jackals comprise over 40% of reported rabies cases. Vaccination coverage was estimated over this period, as five domestic dog vaccination campaigns took place in all thirteen districts between 2011 and 2016. Negative binomial generalized linear models were used to explore the impact of domestic dog vaccination on the annual incidence of animal rabies cases, whilst generalized additive models were used to investigate the presence of temporal and/or seasonal trends. Increases in domestic dog vaccination coverage were significantly associated with a decreased incidence of rabies cases in both domestic dogs and jackals. A 35% increase in vaccination coverage was associated with a reduction in the incidence of probable dog rabies cases of between 78.0 and 85.5% (95% confidence intervals ranged from 61.2 to 92.2%) and a reduction in the incidence of probable jackal rabies cases of between 75.3 and 91.2% (95% confidence intervals ranged from 53.0 to 96.1%). A statistically significant common seasonality was identified in the monthly incidence of probable rabies cases in both domestic dogs and jackals with the highest incidence from February to August and lowest incidence from September to January. These results align with evidence supporting the use of domestic dog vaccination as part of control strategies aimed at reducing animal rabies cases in both domestic dogs and jackals in this region. The presence of a common seasonal trend requires further investigation but may have implications for the timing of future vaccination campaigns.
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Affiliation(s)
- Sarah Hayes
- grid.7445.20000 0001 2113 8111Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, London, UK ,grid.4991.50000 0004 1936 8948Department of Statistics, University of Oxford, Oxford, UK
| | - Kennedy Lushasi
- grid.414543.30000 0000 9144 642XIfakara Health Institute, Ifakara, Tanzania ,grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK ,grid.451346.10000 0004 0468 1595Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Maganga Sambo
- grid.414543.30000 0000 9144 642XIfakara Health Institute, Ifakara, Tanzania
| | - Joel Changalucha
- grid.414543.30000 0000 9144 642XIfakara Health Institute, Ifakara, Tanzania ,grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Elaine A. Ferguson
- grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Lwitiko Sikana
- grid.414543.30000 0000 9144 642XIfakara Health Institute, Ifakara, Tanzania ,grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Katie Hampson
- grid.414543.30000 0000 9144 642XIfakara Health Institute, Ifakara, Tanzania ,grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Pierre Nouvellet
- grid.12082.390000 0004 1936 7590School of Life Sciences, University of Sussex, Sussex, UK
| | - Christl A. Donnelly
- grid.7445.20000 0001 2113 8111Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, London, UK ,grid.4991.50000 0004 1936 8948Department of Statistics, University of Oxford, Oxford, UK
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16
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Dog rabies control in West and Central Africa: A review. Acta Trop 2021; 224:105459. [PMID: 32404295 DOI: 10.1016/j.actatropica.2020.105459] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 03/16/2020] [Accepted: 03/24/2020] [Indexed: 02/06/2023]
Abstract
Rabies is a neglected but preventable zoonotic disease that predominantly affects the most vulnerable populations living in remote rural areas of resource-limited countries. To date, every country on the African mainland is considered endemic for dog-mediated rabies with an estimated 21'500 human rabies deaths occurring each year. In 2018, the United Against Rabies collaboration launched the Global Strategic Plan to end human deaths from dog-mediated rabies by 2030. The epidemiology of rabies from most Western and Central African countries remains poorly defined, making it difficult to assess the overall rabies situation and progress towards the 2030 goal. In this review, we attempt to provide an overview of the current rabies situation in 22 West and Central African countries based on published scientific literature and information obtained from rabies focal points. To this end, information was collected on i) established surveillance, ii) diagnostic capacity, iii) post-exposure prophylaxis (PEP) availability and coverage, iv) dog population estimates, v) dog vaccination campaigns, vi) animal and human health communication (One Health), vii) molecular studies, viii) Knowledge, Attitude and Practices (KAP), ix) cost estimates and x) national control strategies. Although rabies is a notifiable disease in the majority of the studied countries, national surveillance systems do not adequately capture the disease. A general lack of rabies diagnostic capacity has an additional negative impact on rabies surveillance and attempts to estimate rabies burden. Recurrent shortages of human rabies vaccine are reported by all of the countries, with vaccine availability usually limited to major urban centers but no country has yet adopted the new WHO-recommended 1-week intradermal vaccination regimen. Most countries carry out subsidized mass dog vaccination campaigns on World Rabies Day. Such activities are indispensable to keep rabies in the public consciousness but are not of the scale and intensity that is required to eliminate rabies from the dog population. Countries will need to scale up the intensity of their campaigns, if they are to progress towards the 2030 goal. But more than half of the countries do not yet have reliable figures on their dog populations. Only two countries reached stage 2 on the Stepwise Approach towards Rabies Elimination ladder - indicating that their national governments have truly prioritized rabies elimination and are thus providing the necessary support and political buy-in required to achieve success. In summary, the sub-region of West and Central Africa seems to be divided into countries which have accepted the challenge to eliminate rabies with governments committed to pushing forward rabies elimination, while other countries have achieved some progress, but elimination efforts remain stuck due to lacking government commitment and financial constraints. The possibility to meet the 2030 goal without international solidarity is low, because more than two-thirds of the countries rank in the low human development group (HDI ≤ 152). Leading countries should act as role models, sharing their experiences and capacities so that no country is left behind. Unified and with international support it is possible to reach the common goal of zero human rabies deaths by 2030.
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Parag KV, Cowling BJ, Donnelly CA. Deciphering early-warning signals of SARS-CoV-2 elimination and resurgence from limited data at multiple scales. J R Soc Interface 2021; 18:20210569. [PMID: 34905965 PMCID: PMC8672070 DOI: 10.1098/rsif.2021.0569] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/25/2021] [Indexed: 12/12/2022] Open
Abstract
Inferring the transmission potential of an infectious disease during low-incidence periods following epidemic waves is crucial for preparedness. In such periods, scarce data may hinder existing inference methods, blurring early-warning signals essential for discriminating between the likelihoods of resurgence versus elimination. Advanced insight into whether elevating caseloads (requiring swift community-wide interventions) or local elimination (allowing controls to be relaxed or refocussed on case-importation) might occur can separate decisive from ineffective policy. By generalizing and fusing recent approaches, we propose a novel early-warning framework that maximizes the information extracted from low-incidence data to robustly infer the chances of sustained local transmission or elimination in real time, at any scale of investigation (assuming sufficiently good surveillance). Applying this framework, we decipher hidden disease-transmission signals in prolonged low-incidence COVID-19 data from New Zealand, Hong Kong and Victoria, Australia. We uncover how timely interventions associate with averting resurgent waves, support official elimination declarations and evidence the effectiveness of the rapid, adaptive COVID-19 responses employed in these regions.
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Affiliation(s)
- Kris V. Parag
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Benjamin J. Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong
| | - Christl A. Donnelly
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
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18
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Chevalier V, Davun H, Sorn S, Ly P, Pov V, Ly S. Large scale dog population demography, dog management and bite risk factors analysis: A crucial step towards rabies control in Cambodia. PLoS One 2021; 16:e0254192. [PMID: 34237103 PMCID: PMC8266089 DOI: 10.1371/journal.pone.0254192] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/21/2021] [Indexed: 12/25/2022] Open
Abstract
Cambodia is a rabid-endemic country. However, data on dog population characteristics are lacking, and there is no national dog vaccination program. We implemented the first extensive door-to-door longitudinal survey in 2 Cambodian provinces, namely Kandal and Battambang, to estimate dog population demographic parameters, identify dog ownership determinants, analyze dog management practices and estimate the yearly cumulative bite incidence and associated factors. During the first session, more than 5000 dogs were recorded and identified. Data on families, dogs and cats characteristics, as well as the number of bites experienced the year before in the family, were recorded. One year later, a second session was performed in both provinces to record missing dogs and the reasons for missing. Age-specific survival rates of the dog populations were computed using Kaplan-Meier estimates. Ownership determinants and bite risk factors were identified using a negative binomial regression model. Dog trade and dog meat consumption were often reported. We estimated high dog-to-human ratios (1:3.8 in Kandal, and 1:3.3 in Battambang). The mean age of dog populations was 26.4 months in Kandal against 24.3 in Battambang, with a survival rate of 52% at 24 months in Kandal (34% only in Battambang). They were no feral dogs, but the large majority of recorded dogs were free roaming. In both provinces, the number of dogs significantly increased in families with children younger than 15, and when the head of the family was a male. The estimated yearly cumulative bite incidences were 2.3 and 3.1% in Kandal and Battambang provinces respectively, and are among the highest in the world. Our survey provides valuable data to focus information programs, parametrize transmission models and identify efficient vaccination strategies to control rabies in Cambodia in the future.
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Affiliation(s)
- Véronique Chevalier
- International Center of Research in Agriculture for Development (CIRAD), UMR ASTRE, Montpellier, France
- ASTRE, University of Montpellier, CIRAD, INRA, Phnom Penh, Cambodia
- Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
- * E-mail:
| | - Holl Davun
- General Directorate of Animal Health and Production, Ministry of Agriculture, Forestry and Fisheries, Phnom Penh, Cambodia
| | - Sopheak Sorn
- Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Pitou Ly
- Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
- Royal University of Agriculture, Phnom Penh, Cambodia
| | - Vutha Pov
- Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sowath Ly
- Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
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19
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Gold S, Donnelly CA, Woodroffe R, Nouvellet P. Modelling the influence of naturally acquired immunity from subclinical infection on outbreak dynamics and persistence of rabies in domestic dogs. PLoS Negl Trop Dis 2021; 15:e0009581. [PMID: 34283827 PMCID: PMC8330898 DOI: 10.1371/journal.pntd.0009581] [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: 11/26/2020] [Revised: 08/03/2021] [Accepted: 06/21/2021] [Indexed: 12/04/2022] Open
Abstract
A number of mathematical models have been developed for canine rabies to explore dynamics and inform control strategies. A common assumption of these models is that naturally acquired immunity plays no role in rabies dynamics. However, empirical studies have detected rabies-specific antibodies in healthy, unvaccinated domestic dogs, potentially due to immunizing, non-lethal exposure. We developed a stochastic model for canine rabies, parameterised for Laikipia County, Kenya, to explore the implications of different scenarios for naturally acquired immunity to rabies in domestic dogs. Simulating these scenarios using a non-spatial model indicated that low levels of immunity can act to limit rabies incidence and prevent depletion of the domestic dog population, increasing the probability of disease persistence. However, incorporating spatial structure and human response to high rabies incidence allowed the virus to persist in the absence of immunity. While low levels of immunity therefore had limited influence under a more realistic approximation of rabies dynamics, high rates of exposure leading to immunizing non-lethal exposure were required to produce population-level seroprevalences comparable with those reported in empirical studies. False positives and/or spatial variation may contribute to high empirical seroprevalences. However, if high seroprevalences are related to high exposure rates, these findings support the need for high vaccination coverage to effectively control this disease.
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Affiliation(s)
- Susannah Gold
- Institute of Zoology, Zoological Society of London, London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Christl A. Donnelly
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- Department of Statistics, University of Oxford, Oxfordshire, United Kingdom
| | - Rosie Woodroffe
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Pierre Nouvellet
- School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
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20
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Wobessi JNS, Kenmoe S, Mahamat G, Belobo JTE, Emoh CPD, Efietngab AN, Bebey SRK, Ngongang DT, Tchatchouang S, Nzukui ND, Modiyinji AF, Simo REG, Ka'e AC, Tazokong HR, Ngandji AB, Mbaga DS, Kengne-Nde C, Sadeuh-Mba SA, Njouom R. Incidence and seroprevalence of rabies virus in humans, dogs and other animal species in Africa, a systematic review and meta-analysis. One Health 2021; 13:100285. [PMID: 34258372 PMCID: PMC8254041 DOI: 10.1016/j.onehlt.2021.100285] [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: 11/06/2020] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 12/30/2022] Open
Abstract
Rabies is transmitted to humans mainly by dogs but also by other animal species. Reliable data on the incidence of Rabies virus (RABV) in humans, dogs, and other animal species in Africa, could be essential in the implementation of a global strategic plan to eliminate the RABV by 2030 as adopted by the WHO, OIE, and FAO. We searched the Pubmed, Embase, Scopus, African Journal Online, and African Index Medicus databases for relevant studies that report data on the incidence of RABV in Africa up to February 17, 2020. Information on active and past RABV exposures in various categories of dogs, humans and other animal species were extracted. Incidence and seroprevalence estimates were pooled using a random-effect meta-analysis. We included 73 articles which provided 142 RABV incidence and seroprevalence records in 21 African countries. The estimated incidence of RABV in 222 humans, 15,600 dogs, and 12,865 other animal species was 83.4% (95% CI = 64.6–96.5), 44.1% (95% CI = 35.1–53.4), and 41.4% (95% CI = 29.6–53.8), respectively. The estimated seroprevalence of RABV in 420 humans, 3577 dogs, and 8,55 other animal species was 33.8% (95% CI = 21.9–46.8), 19.8% (95% CI = 13.3–27.3), and 3.6% (95% CI = 0.3–9.2), respectively. The incidence of RABV in general was higher in suspected rabid dogs, other animal species of the Orders Perissodactyla, Artiodactyla and Carnivora. The incidence of RABV was higher for humans in regions of West and East Africa, for dogs in urban areas and in regions of Central and South Africa, and for animals of the order Perissodactyla in urban areas. This meta-analysis demonstrated a high incidence of RABV in Africa. Itis necessary to improve surveillance system to provide reliable data on RABV in Africa, essential for the implementation of an effective control strategy.
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Affiliation(s)
- Jocelyne Noel Sowe Wobessi
- Virology Department, Centre, Pasteur of Cameroon, Yaounde, Cameroon.,Ecole Doctorale Régionale d'Afrique Centrale, Franceville, Gabon
| | - Sebastien Kenmoe
- Virology Department, Centre, Pasteur of Cameroon, Yaounde, Cameroon
| | - Gadji Mahamat
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaounde, Cameroon
| | - Jean Thierry Ebogo Belobo
- Medical Research Centre, Institute of Medical Research and Medicinal Plants Studies, Yaoundé, Cameroon
| | | | - Atembeh Noura Efietngab
- Medical Research Centre, Institute of Medical Research and Medicinal Plants Studies, Yaoundé, Cameroon
| | | | - Dimitri Tchami Ngongang
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaounde, Cameroon
| | | | - Nathalie Diane Nzukui
- School of Health Sciences-Catholic University of Central Africa, Department of Medical Microbiology, Yaounde, Cameroon
| | - Abdou Fatawou Modiyinji
- Ecole Doctorale Régionale d'Afrique Centrale, Franceville, Gabon.,Department of Animals Biology and Physiology, Faculty of Science, The University of Yaounde I, Yaounde, Cameroon
| | | | - Aude Christelle Ka'e
- Virology Department, Chantal Biya International Reference Centre, Yaounde, Cameroon
| | - Hervé Raoul Tazokong
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaounde, Cameroon
| | - Arnol Bowo Ngandji
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaounde, Cameroon
| | - Donatien Serge Mbaga
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaounde, Cameroon
| | - Cyprien Kengne-Nde
- Epidemiological Surveillance, Evaluation and Research Unit, National AIDS Control Committee, Yaounde, Cameroon
| | | | - Richard Njouom
- Virology Department, Centre, Pasteur of Cameroon, Yaounde, Cameroon
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21
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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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Voupawoe G, Varkpeh R, Kamara V, Sieh S, Traoré A, De Battisti C, Angot A, Loureiro LFLDJ, Soumaré B, Dauphin G, Abebe W, Coetzer A, Scott T, Nel L, Blanton J, Dacheux L, Bonas S, Bourhy H, Gourlaouen M, Leopardi S, De Benedictis P, Léchenne M, Zinsstag J, Mauti S. Rabies control in Liberia: Joint efforts towards zero by 30. Acta Trop 2021; 216:105787. [PMID: 33385361 DOI: 10.1016/j.actatropica.2020.105787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 01/24/2023]
Abstract
Despite declaration as a national priority disease, dog rabies remains endemic in Liberia, with surveillance systems and disease control activities still developing. The objective of these initial efforts was to establish animal rabies diagnostics, foster collaboration between all rabies control stakeholders, and develop a short-term action plan with estimated costs for rabies control and elimination in Liberia. Four rabies diagnostic tests, the direct fluorescent antibody (DFA) test, the direct immunohistochemical test (dRIT), the reverse transcriptase polymerase chain reaction (RT-PCR) assay and the rapid immunochromatographic diagnostic test (RIDT), were implemented at the Central Veterinary Laboratory (CVL) in Monrovia between July 2017 and February 2018. Seven samples (n=7) out of eight suspected animals were confirmed positive for rabies lyssavirus, and molecular analyses revealed that all isolates belonged to the Africa 2 lineage, subgroup H. During a comprehensive in-country One Health rabies stakeholder meeting in 2018, a practical workplan, a short-term action plan and an accurately costed mass dog vaccination strategy were developed. Liberia is currently at stage 1.5/5 of the Stepwise Approach towards Rabies Elimination (SARE) tool, which corresponds with countries that are scaling up local-level interventions (e.g. dog vaccination campaigns) to the national level. Overall an estimated 5.3 - 8 million USD invested over 13 years is needed to eliminate rabies in Liberia by 2030. Liberia still has a long road to become free from dog-rabies. However, the dialogue between all relevant stakeholders took place, and disease surveillance considerably improved through implementing rabies diagnosis at the CVL. The joint efforts of diverse national and international stakeholders laid important foundations to achieve the goal of zero dog-mediated human rabies deaths by 2030.
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Kotzé JL, Duncan Grewar J, Anderson A. Modelling the factors affecting the probability for local rabies elimination by strategic control. PLoS Negl Trop Dis 2021; 15:e0009236. [PMID: 33661893 PMCID: PMC7963038 DOI: 10.1371/journal.pntd.0009236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/16/2021] [Accepted: 02/11/2021] [Indexed: 11/18/2022] Open
Abstract
Dog rabies has been recognized from ancient times and remains widespread across the developing world with an estimated 59,000 people dying annually from the disease. In 2011 a tri-partite alliance consisting of the OIE, the WHO and the FAO committed to globally eliminating dog-mediated human rabies by 2030. Regardless of global support, the responsibility remains with local program managers to implement successful elimination programs. It is well known that vaccination programs have a high probability of successful elimination if they achieve a population-coverage of 70%. It is often quoted that reducing population turnover (typically through sterilizations) raises the probability for local elimination by maintaining herd immunity for longer. Besides this, other factors that affect rabies elimination are rarely mentioned. This paper investigates the probability for local elimination as it relates to immunity, fecundity, dog population size, infectivity (bite rates), in-migration of immune-naïve dogs, and the initial incidence. To achieve this, an individual-based, stochastic, transmission model was manipulated to create a dataset covering combinations of factors that may affect elimination. The results thereof were analysed using a logistic regression model with elimination as the dependent variable. Our results suggest that smaller dog populations, lower infectivity and lower incidence (such as when epidemics start with single introductions) strongly increased the probability for elimination at wide ranges of vaccination levels. Lower fecundity and lower in-migration had weak effects. We discuss the importance of these findings in terms of their impact and their practical application in the design of dog-mediated rabies control programs. Most guidelines for rabies control call for at least 70% vaccination coverage of dogs. This level of immunity has a very high probability for the local elimination of rabies, but it is often not an achievable ideal due to resource constraints. Campaign managers can be strategic on how they allocate their resources. Lower infectivity rates are present in areas with more restricted dog movements and have higher probabilities for elimination at lower vaccination rates. Smaller sub-populations have higher probabilities for elimination at the same vaccination coverage levels compared to larger sub-populations. Vaccinating immune corridors can divide meta-populations into smaller sub-populations that are likely to result in elimination either due to their small size or due to the local low infectivity. Areas already free of rabies require lower vaccination levels to maintain freedom compared to endemic areas. Where donors do not specifically require sterilization campaigns, funds meant for rabies control should not be diverted to sterilizations.
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Affiliation(s)
- Johann L. Kotzé
- Department of Production Animal Studies, University of Pretoria, Onderstepoort, South Africa
- * E-mail:
| | - John Duncan Grewar
- Department of Production Animal Studies, University of Pretoria, Onderstepoort, South Africa
- jDATA (Pty) Ltd, Sandbaai, South Africa
| | - Aaron Anderson
- USDA National Wildlife Research Centre, Fort Collins, Colorado, United States of America
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24
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Bourhy H, de Melo GD, Tarantola A. [New aspects of rabies control]. BULLETIN DE L'ACADEMIE NATIONALE DE MEDECINE 2020; 204:1000-1009. [PMID: 32981935 PMCID: PMC7500396 DOI: 10.1016/j.banm.2020.09.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/10/2020] [Indexed: 12/25/2022]
Abstract
Rabies still causes about 60,000 human deaths per year, mainly in poor populations in Africa and Asia. However, since Louis Pasteur developed the first vaccine 130 years ago, prophylactic measures have been considerably improved and simplified. They now consist of the vaccine combined with purified rabies immunoglobulins of equine or human origin. In general, however, post-exposure prophylaxis protocols are long and expensive. Furthermore, the immunoglobulins used for associated serotherapy are costly and not widely available in developing countries. Approaches have been developed to deal with these two issues that offer hope for a paradigm shift for the benefit of exposed populations. Finally, mass rabies vaccination in dogs, which are the most cost-effective measure for preventing rabies in humans, are difficult to implement and sometimes have moderate effectiveness. The identification and analysis of the epidemiological drivers conditioning the circulation of the virus in dog populations allow a better understanding of the key control points that need to be associated with these campaigns for a better efficacy.
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Affiliation(s)
- H Bourhy
- Unité lyssavirus, épidémiologie et neuropathologie, centre collaborateur de l'Organisation mondiale de la santé de référence et de recherche sur la rage, institut Pasteur, 28, rue du Docteur Roux, 75724 Paris cedex 15, France
| | - G D de Melo
- Unité lyssavirus, épidémiologie et neuropathologie, centre collaborateur de l'Organisation mondiale de la santé de référence et de recherche sur la rage, institut Pasteur, 28, rue du Docteur Roux, 75724 Paris cedex 15, France
| | - A Tarantola
- Unité lyssavirus, épidémiologie et neuropathologie, centre collaborateur de l'Organisation mondiale de la santé de référence et de recherche sur la rage, institut Pasteur, 28, rue du Docteur Roux, 75724 Paris cedex 15, France
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Rysava K, Mancero T, Caldas E, de Carvalho MF, Castro APB, Gutiérrez V, Haydon DT, Johnson PCD, Mancy R, Montebello LR, Rocha SM, Gonzalez Roldan JF, Vigilato MAN, Vilas VDR, Hampson K. Towards the elimination of dog-mediated rabies: development and application of an evidence-based management tool. BMC Infect Dis 2020; 20:778. [PMID: 33081712 PMCID: PMC7574347 DOI: 10.1186/s12879-020-05457-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/27/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND International organizations advocate for the elimination of dog-mediated rabies, but there is only limited guidance on interpreting surveillance data for managing elimination programmes. With the regional programme in Latin America approaching elimination of dog-mediated rabies, we aimed to develop a tool to evaluate the programme's performance and generate locally-tailored rabies control programme management guidance to overcome remaining obstacles. METHODS We developed and validated a robust algorithm to classify progress towards rabies elimination within sub-national administrative units, which we applied to surveillance data from Brazil and Mexico. The method combines criteria that are easy to understand, including logistic regression analysis of case detection time series, assessment of rabies virus variants, and of incursion risk. Subjecting the algorithm to robustness testing, we further employed simulated data sub-sampled at differing levels of case detection to assess the algorithm's performance and sensitivity to surveillance quality. RESULTS Our tool demonstrated clear epidemiological transitions in Mexico and Brazil: most states progressed rapidly towards elimination, but a few regressed due to incursions and control lapses. In 2015, dog-mediated rabies continued to circulate in the poorest states, with foci remaining in only 1 of 32 states in Mexico, and 2 of 27 in Brazil, posing incursion risks to the wider region. The classification tool was robust in determining epidemiological status irrespective of most levels of surveillance quality. In endemic settings, surveillance would need to detect less than 2.5% of all circulating cases to result in misclassification, whereas in settings where incursions become the main source of cases the threshold detection level for correct classification should not be less than 5%. CONCLUSION Our tool provides guidance on how to progress effectively towards elimination targets and tailor strategies to local epidemiological situations, while revealing insights into rabies dynamics. Post-campaign assessments of dog vaccination coverage in endemic states, and enhanced surveillance to verify and maintain freedom in states threatened by incursions were identified as priorities to catalyze progress towards elimination. Our finding suggests genomic surveillance should become increasingly valuable during the endgame for discriminating circulating variants and pinpointing sources of incursions.
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Affiliation(s)
- Kristyna Rysava
- University of Warwick, School of Life Sciences, Gibbet Hill Road, Coventry, UK
- University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr building, MVLS, Glasgow, G12 8QQ UK
| | - Tamara Mancero
- Pan American Health Organization (PAHO), Duque de Caxias, Rio de Janeiro, Brazil
| | - Eduardo Caldas
- Virology, Central Laboratory, State Center for Health Surveillance, State Department of Health, São Paulo, Rio Grande do Sul Brazil
| | | | | | | | - Daniel T. Haydon
- University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr building, MVLS, Glasgow, G12 8QQ UK
| | - Paul C. D. Johnson
- University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr building, MVLS, Glasgow, G12 8QQ UK
| | - Rebecca Mancy
- University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr building, MVLS, Glasgow, G12 8QQ UK
| | | | | | | | | | - Victor Del Rio Vilas
- Pan American Health Organization (PAHO), Duque de Caxias, Rio de Janeiro, Brazil
- University of Surrey, School of Veterinary Medicine, VSM Building, Guildford, UK
| | - Katie Hampson
- University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr building, MVLS, Glasgow, G12 8QQ UK
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26
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Zero human deaths from dog-mediated rabies by 2030: perspectives from quantitative and mathematical modelling. Gates Open Res 2020; 3:1564. [PMID: 32596645 PMCID: PMC7308633 DOI: 10.12688/gatesopenres.13074.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2020] [Indexed: 11/20/2022] Open
Abstract
Dog-mediated rabies continues to kill tens of thousands of people every year in low- and middle-income countries despite being an entirely vaccine-preventable disease. WHO and partners have launched a global campaign to reach zero human deaths from dog-mediated rabies by 2030. The primary tools for reaching this target are mass dog vaccination to interrupt transmission in domestic dog populations that maintain infection, appropriate post-exposure prophylaxis (PEP) for rabies-exposed persons to prevent the fatal onset of disease, together with education to support their effective uptake. Models have been developed to assess the feasibility, impact and cost-effectiveness of these measures. From these models, we argue that the 2030 target of zero human rabies deaths is achievable, but will require concerted effort, engagement and investment. A proposed Gavi investment in human rabies vaccines has potential to drive progress towards the 2030 target; however, concomitant investment is needed to scale up mass dog vaccination or this target will be missed. Predicted economic benefits of mass dog vaccination vary according to national PEP provisioning and healthcare access. Integrated Bite Case Management can enhance surveillance and rationalize PEP use, but needs adapting to and integrating within local health systems and international reporting systems to improve PEP accountability, monitor impacts and support verification of disease freedom. Modelling approaches need refining to project realistic and geographically specific timelines for achieving targets. Model iterations informed by data on the implementation of interventions can be used to evaluate progress and guide future strategies. Critically such models are needed to advocate for investment, since the greatest risk to the ‘Zero by 30’ strategy is the limited long-term cross-sectoral or targeted financing to support countries to deliver and sustain mass dog vaccination.
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27
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Brunker K, Jaswant G, Thumbi S, Lushasi K, Lugelo A, Czupryna AM, Ade F, Wambura G, Chuchu V, Steenson R, Ngeleja C, Bautista C, Manalo DL, Gomez MRR, Chu MYJV, Miranda ME, Kamat M, Rysava K, Espineda J, Silo EAV, Aringo AM, Bernales RP, Adonay FF, Tildesley MJ, Marston DA, Jennings DL, Fooks AR, Zhu W, Meredith LW, Hill SC, Poplawski R, Gifford RJ, Singer JB, Maturi M, Mwatondo A, Biek R, Hampson K. Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes. Wellcome Open Res 2020; 5:3. [PMID: 32090172 PMCID: PMC7001756 DOI: 10.12688/wellcomeopenres.15518.2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.
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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
| | - Gurdeep Jaswant
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- University of Nairobi Institute of Tropical and Infectious Diseases (UNITID), Nairobi, Kenya
| | - S.M. Thumbi
- University of Nairobi Institute of Tropical and Infectious Diseases (UNITID), Nairobi, Kenya
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | | | - Ahmed Lugelo
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Anna M. Czupryna
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fred Ade
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Gati Wambura
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Veronicah Chuchu
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Rachel Steenson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Chanasa Ngeleja
- Tanzania Veterinary Laboratory Agency, Ministry of Livestock and Fisheries Development, Dar es Salaam, Tanzania
| | - Criselda Bautista
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
| | - Daria L. Manalo
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
| | | | | | - Mary Elizabeth Miranda
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
- Field Epidemiology Training Program Alumni Foundation (FETPAFI), Manilla, Philippines
| | - Maya Kamat
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Kristyna Rysava
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematical Institute, University of Warwick, Coventry, UK
| | - Jason Espineda
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Eva Angelica V. Silo
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Ariane Mae Aringo
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Rona P. Bernales
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Florencio F. Adonay
- Albay Veterinary Office, Provincial Government of Albay, Albay Farmers' Bounty Village, Cabangan, Camalig, Albay, Philippines
| | - Michael J. Tildesley
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematical Institute, University of Warwick, Coventry, UK
| | - Denise A. Marston
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
| | - Daisy L. Jennings
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
| | - Anthony R. Fooks
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
- Institute of Infection and Global Health,, University of Liverpool, Liverpool, UK
| | - Wenlong Zhu
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | | | - Radoslaw Poplawski
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
- Advanced Research Computing, University of Birmingham, Birmingham, B15 2TT, UK
| | - Robert J. Gifford
- MRC-University of Glasgow Centre for Virus Research (CVR), University of Glasgow, Glasgow, UK
| | - Joshua B. Singer
- MRC-University of Glasgow Centre for Virus Research (CVR), University of Glasgow, Glasgow, UK
| | - Mathew Maturi
- Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - Athman Mwatondo
- Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - 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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28
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Colombi D, Poletto C, Nakouné E, Bourhy H, Colizza V. Long-range movements coupled with heterogeneous incubation period sustain dog rabies at the national scale in Africa. PLoS Negl Trop Dis 2020; 14:e0008317. [PMID: 32453756 PMCID: PMC7274467 DOI: 10.1371/journal.pntd.0008317] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 06/05/2020] [Accepted: 04/22/2020] [Indexed: 12/25/2022] Open
Abstract
Dog-transmitted rabies is responsible for more than 98% of human cases worldwide, remaining a persistent problem in developing countries. Mass vaccination targets predominantly major cities, often compromising disease control due to re-introductions. Previous work suggested that areas neighboring cities may behave as the source of these re-introductions. To evaluate this hypothesis, we introduce a spatially explicit metapopulation model for rabies diffusion in Central African Republic. Calibrated on epidemiological data for the capital city, Bangui, the model predicts that long-range movements are essential for continuous re-introductions of rabies-exposed dogs across settlements, eased by the large fluctuations of the incubation period. Bangui's neighborhood, instead, would not be enough to self-sustain the epidemic, contrary to previous expectations. Our findings suggest that restricting long-range travels may be very efficient in limiting rabies persistence in a large and fragmented dog population. Our framework can be applied to other geographical contexts where dog rabies is endemic.
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Affiliation(s)
- Davide Colombi
- INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP, Paris, France
- Computational Epidemiology Laboratory, Institute for Scientific Interchange (ISI), Turin, Italy
- Physics Department and INFN, University of Turin, Turin, Italy
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP, Paris, France
| | | | - Hervé Bourhy
- Institut Pasteur, Unit Lyssavirus Epidemiology and Neuropathology, WHO Collaborating Center for Reference and Research on Rabies, Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP, Paris, France
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29
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Gibson AD, Wallace RM, Rahman A, Bharti OK, Isloor S, Lohr F, Gamble L, Mellanby RJ, King A, Day MJ. Reviewing Solutions of Scale for Canine Rabies Elimination in India. Trop Med Infect Dis 2020; 5:E47. [PMID: 32210019 PMCID: PMC7157614 DOI: 10.3390/tropicalmed5010047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/14/2020] [Accepted: 03/18/2020] [Indexed: 12/18/2022] Open
Abstract
Canine rabies elimination can be achieved through mass vaccination of the dog population, as advocated by the WHO, OIE and FAO under the 'United Against Rabies' initiative. Many countries in which canine rabies is endemic are exploring methods to access dogs for vaccination, campaign structures and approaches to resource mobilization. Reviewing aspects that fostered success in rabies elimination campaigns elsewhere, as well as examples of largescale resource mobilization, such as that seen in the global initiative to eliminate poliomyelitis, may help to guide the planning of sustainable, scalable methods for mass dog vaccination. Elimination of rabies from the majority of Latin America took over 30 years, with years of operational trial and error before a particular approach gained the broad support of decision makers, governments and funders to enable widespread implementation. The endeavour to eliminate polio now enters its final stages; however, there are many transferrable lessons to adopt from the past 32 years of global scale-up. Additionally, there is a need to support operational research, which explores the practicalities of mass dog vaccination roll-out and what are likely to be feasible solutions at scale. This article reviews the processes that supported the scale-up of these interventions, discusses pragmatic considerations of campaign duration and work-force size and finally provides an examples hypothetical resource requirements for implementing mass dog vaccination at scale in Indian cities, with a view to supporting the planning of pilot campaigns from which expanded efforts can grow.
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Affiliation(s)
- Andrew D. Gibson
- Mission Rabies, 4 Castle Street, Cranborne, Dorset BH21 5PZ, UK
- The Royal (Dick) School of Veterinary Studies and the Roslin Institute, Easter Bush Campus, The University of Edinburgh, Roslin, Midlothian EH25 9RG, UK;
| | - Ryan M. Wallace
- United States Centers for Disease Control and Prevention, Poxvirus and Rabies Branch, Atlanta, GA 30333, USA
| | - Abdul Rahman
- Commonwealth Veterinary Association 123, 7th B Main Road, 4th Block West, Jayanagar, Bangalore 560011, Karnataka, India
| | - Omesh K. Bharti
- State Institute of Health and Family Welfare, Parimahal, Kasumpti, Shimla 171009, Himachal Pradesh, India
| | - Shrikrishna Isloor
- Bangalore Veterinary College, KVAFSU, Hebbal, Bangalore 560024, Karnataka, India
| | - Frederic Lohr
- Mission Rabies, 4 Castle Street, Cranborne, Dorset BH21 5PZ, UK
| | - Luke Gamble
- Mission Rabies, 4 Castle Street, Cranborne, Dorset BH21 5PZ, UK
| | - Richard J. Mellanby
- The Royal (Dick) School of Veterinary Studies and the Roslin Institute, Easter Bush Campus, The University of Edinburgh, Roslin, Midlothian EH25 9RG, UK;
| | | | - Michael J. Day
- World Small Animal Veterinary Association and School of Veterinary and Life Sciences, Murdoch University, Murdoch 6150, Australia
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30
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Zero human deaths from dog-mediated rabies by 2030: perspectives from quantitative and mathematical modelling. Gates Open Res 2020; 3:1564. [PMID: 32596645 PMCID: PMC7308633 DOI: 10.12688/gatesopenres.13074.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2020] [Indexed: 09/09/2023] Open
Abstract
Dog-mediated rabies continues to kill tens of thousands of people every year in low- and middle-income countries despite being an entirely vaccine-preventable disease. WHO and partners have launched a global campaign to reach zero human deaths from dog-mediated rabies by 2030. The primary tools for reaching this target are mass dog vaccination to interrupt transmission in domestic dog populations that maintain infection, appropriate post-exposure prophylaxis (PEP) for rabies-exposed persons to prevent the fatal onset of disease, together with education to support their effective uptake. Models have been developed to assess the feasibility, impact and cost-effectiveness of these measures. From these models, we argue that the 2030 target of zero human rabies deaths is achievable, but will require concerted effort, engagement and investment. A proposed Gavi investment in human rabies vaccines has potential to drive progress towards the 2030 target; however, concomitant investment is needed to scale up mass dog vaccination or this target will be missed. Predicted economic benefits of mass dog vaccination vary according to national PEP provisioning and healthcare access. Integrated Bite Case Management can enhance surveillance and rationalize PEP use, but needs adapting to and integrating within local health systems and international reporting systems to improve PEP accountability, monitor impacts and support verification of disease freedom. Modelling approaches need refining to project realistic and geographically specific timelines for achieving targets. Model iterations informed by data on the implementation of interventions can be used to evaluate progress and guide future strategies. Critically such models are needed to advocate for investment, since the greatest risk to the 'Zero by 30' strategy is the limited long-term cross-sectoral or targeted financing to support countries to deliver and sustain mass dog vaccination.
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31
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Rasolonjatovo FS, Guis H, Rajeev M, Dacheux L, Arivony Nomenjanahary L, Razafitrimo G, Rafisandrantantsoa JT, Cêtre-Sossah C, Heraud JM, Andriamandimby SF. Enabling animal rabies diagnostic in low-access areas: Sensitivity and specificity of a molecular diagnostic test from cerebral tissue dried on filter paper. PLoS Negl Trop Dis 2020; 14:e0008116. [PMID: 32142519 PMCID: PMC7135319 DOI: 10.1371/journal.pntd.0008116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/06/2020] [Accepted: 02/05/2020] [Indexed: 02/03/2023] Open
Abstract
Rabies is a lethal zoonotic encephalomyelitis that causes an estimated 59,000 human deaths yearly worldwide. Although developing countries of Asia and Africa bear the heaviest burden, surveillance and disease detection in these countries is often hampered by the absence of local laboratories able to diagnose rabies and/or the difficulties of sample shipment from low-access areas to national reference laboratories. Filter papers offer a convenient cost-effective alternative for the sampling, shipment, and storage of biological materials for the diagnosis of many pathogens including rabies virus, yet the properties of diagnostic tests using this support have not been evaluated thoroughly. Sensitivity and specificity of molecular diagnosis of rabies infection using a reverse transcription followed by a hemi-nested polymerase chain reaction (RT-hn-PCR) either directly on brain tissue or using brain tissue dried on filter paper were assessed on 113 suspected field animal samples in comparison to the direct fluorescent antibody test (FAT) recommended by the World Health Organization as one of the reference tests for rabies diagnosis. Impact of the duration of the storage was also evaluated. The sensitivity and the specificity of RT-hn-PCR i) on brain tissue were 96.6% (95% CI: [88.1-99.6]) and 92.7% (95% CI: [82.4-98.0]) respectively and ii) on brain tissue dried on filter paper 100% (95% CI: [93.8-100.0]) and 90.9% (95% CI: [80.0-97.0]) respectively. No loss of sensitivity of RT-hn-PCR on samples of brain tissue dried on filter paper left 7 days at ambient temperature was detected indicating that this method would enable analyzing impregnated filter papers sent to the national reference laboratory at ambient temperature within a 1-week shipment time. It could therefore be an effective alternative to facilitate storage and shipment of samples from low-access areas to enhance and expand rabies surveillance.
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Affiliation(s)
- Felana Suzah Rasolonjatovo
- Rabies National Reference Laboratory, Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- CIRAD, UMR ASTRE, 101 Antananarivo, Madagascar
- Faculty of Medicine, Department of Veterinary Medecine, Antananarivo, Madagascar
- Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Hélène Guis
- CIRAD, UMR ASTRE, 101 Antananarivo, Madagascar
- Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- ASTRE, Univ Montpellier, CIRAD, INRAE, Montpellier, France
- FOFIFA-DRZVP, Antananarivo, Madagascar
| | - Malavika Rajeev
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States of America
| | - Laurent Dacheux
- Institut Pasteur, Lyssavirus Epidemiology and Neuropathology Unit, National Reference Centre for Rabies, WHO Collaborating Center for Reference and Research on Rabies, Paris, France
| | | | - Girard Razafitrimo
- Rabies National Reference Laboratory, Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Catherine Cêtre-Sossah
- ASTRE, Univ Montpellier, CIRAD, INRAE, Montpellier, France
- CIRAD, UMR ASTRE, F-97491 Sainte-Clotilde, La Réunion, France
| | - Jean-Michel Heraud
- Rabies National Reference Laboratory, Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Soa Fy Andriamandimby
- Rabies National Reference Laboratory, Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
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32
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Brunker K, Jaswant G, Thumbi S, Lushasi K, Lugelo A, Czupryna AM, Ade F, Wambura G, Chuchu V, Steenson R, Ngeleja C, Bautista C, Manalo DL, Gomez MRR, Chu MYJV, Miranda ME, Kamat M, Rysava K, Espineda J, Silo EAV, Aringo AM, Bernales RP, Adonay FF, Tildesley MJ, Marston DA, Jennings DL, Fooks AR, Zhu W, Meredith LW, Hill SC, Poplawski R, Gifford RJ, Singer JB, Maturi M, Mwatondo A, Biek R, Hampson K. Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes. Wellcome Open Res 2020; 5:3. [PMID: 32090172 PMCID: PMC7001756 DOI: 10.12688/wellcomeopenres.15518.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2019] [Indexed: 08/27/2023] Open
Abstract
Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.
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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
| | - Gurdeep Jaswant
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- University of Nairobi Institute of Tropical and Infectious Diseases (UNITID), Nairobi, Kenya
| | - S.M. Thumbi
- University of Nairobi Institute of Tropical and Infectious Diseases (UNITID), Nairobi, Kenya
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | | | - Ahmed Lugelo
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Anna M. Czupryna
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fred Ade
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Gati Wambura
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Veronicah Chuchu
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Rachel Steenson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Chanasa Ngeleja
- Tanzania Veterinary Laboratory Agency, Ministry of Livestock and Fisheries Development, Dar es Salaam, Tanzania
| | - Criselda Bautista
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
| | - Daria L. Manalo
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
| | | | | | - Mary Elizabeth Miranda
- Research Institute for Tropical Medicine (RITM), Manilla, Philippines
- Field Epidemiology Training Program Alumni Foundation (FETPAFI), Manilla, Philippines
| | - Maya Kamat
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Kristyna Rysava
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematical Institute, University of Warwick, Coventry, UK
| | - Jason Espineda
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Eva Angelica V. Silo
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Ariane Mae Aringo
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Rona P. Bernales
- Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory, Cabangan, Camalig, Albay, Philippines
| | - Florencio F. Adonay
- Albay Veterinary Office, Provincial Government of Albay, Albay Farmers' Bounty Village, Cabangan, Camalig, Albay, Philippines
| | - Michael J. Tildesley
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematical Institute, University of Warwick, Coventry, UK
| | - Denise A. Marston
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
| | - Daisy L. Jennings
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
| | - Anthony R. Fooks
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge, UK
- Institute of Infection and Global Health,, University of Liverpool, Liverpool, UK
| | - Wenlong Zhu
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | | | - Radoslaw Poplawski
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
- Advanced Research Computing, University of Birmingham, Birmingham, B15 2TT, UK
| | - Robert J. Gifford
- MRC-University of Glasgow Centre for Virus Research (CVR), University of Glasgow, Glasgow, UK
| | - Joshua B. Singer
- MRC-University of Glasgow Centre for Virus Research (CVR), University of Glasgow, Glasgow, UK
| | - Mathew Maturi
- Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - Athman Mwatondo
- Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - 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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Streicker DG, Fallas González SL, Luconi G, Barrientos RG, Leon B. Phylodynamics reveals extinction-recolonization dynamics underpin apparently endemic vampire bat rabies in Costa Rica. Proc Biol Sci 2019; 286:20191527. [PMID: 31594511 PMCID: PMC6790760 DOI: 10.1098/rspb.2019.1527] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/17/2019] [Indexed: 12/21/2022] Open
Abstract
Variation in disease incidence in wildlife is often assumed to reflect environmental or demographic changes acting on an endemic pathogen. However, apparent endemicity might instead arise from spatial processes that are challenging to identify from traditional data sources including time series and field studies. Here, we analysed longitudinal sequence data collected from rabies virus outbreaks over 14 years in Costa Rica, a Central American country that has recorded continuous vampire bat-transmitted rabies outbreaks in humans and livestock since 1985. We identified five phylogenetically distinct lineages which shared most recent common ancestors with viruses from North and South America. Bayesian phylogeographic reconstructions supported bidirectional viral dispersals involving countries to the north and south of Costa Rica at different time points. Within Costa Rica, viruses showed little contemporaneous spatial overlap and no lineage was detected across all years of surveillance. Statistical models suggested that lineage disappearances were more likely to be explained by viral extinctions than undetected viral circulation. Our results highlight the importance of international viral dispersal for shaping the burden of rabies in Costa Rica, suggest a Central American corridor of rabies virus invasions between continents, and show that apparent disease endemicity may arise through recurrent pathogen extinctions and reinvasions which can be readily detected in relatively small datasets by joining phylodynamic and modelling approaches.
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Affiliation(s)
- Daniel G. Streicker
- MRC—University of Glasgow Centre for Virus Research, Glasgow, UK
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Rocío González Barrientos
- Laboratorio de Bioseguridad, Laboratorio Nacional de Servicios Veterinarios, Servicio Nacional de Salud Animal, Heredia, Costa Rica
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Bernal Leon
- Laboratorio de Bioseguridad, Laboratorio Nacional de Servicios Veterinarios, Servicio Nacional de Salud Animal, Heredia, Costa Rica
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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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Rakotomalala M, Vrancken B, Pinel-Galzi A, Ramavovololona P, Hébrard E, Randrianangaly JS, Dellicour S, Lemey P, Fargette D. Comparing patterns and scales of plant virus phylogeography: Rice yellow mottle virus in Madagascar and in continental Africa. Virus Evol 2019; 5:vez023. [PMID: 31384483 PMCID: PMC6671560 DOI: 10.1093/ve/vez023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Rice yellow mottle virus (RYMV) in Madagascar Island provides an opportunity to study the spread of a plant virus disease after a relatively recent introduction in a large and isolated country with a heterogeneous host landscape ecology. Here, we take advantage of field survey data on the occurrence of RYMV disease throughout Madagascar dating back to the 1970s, and of virus genetic data from ninety-four isolates collected since 1989 in most regions of the country to reconstruct the epidemic history. We find that the Malagasy isolates belong to a unique recombinant strain that most likely entered Madagascar through a long-distance introduction from the most eastern part of mainland Africa. We infer the spread of RYMV as a continuous process using a Bayesian statistical framework. In order to calibrate the time scale in calendar time units in this analysis, we pool the information about the RYMV evolutionary rate from several geographical partitions. Whereas the field surveys and the phylogeographic reconstructions both point to a rapid southward invasion across hundreds of kilometers throughout Madagascar within three to four decades, they differ on the inferred origin location and time of the epidemic. The phylogeographic reconstructions suggest a lineage displacement and unveil a re-invasion of the northern regions that may have remained unnoticed otherwise. Despite ecological differences that could affect the transmission potential of RYMV in Madagascar and in mainland Africa, we estimate similar invasion and dispersal rates. We could not identify environmental factors that have a relevant impact on the lineage dispersal velocity of RYMV in Madagascar. This study highlights the value and complementarity of (historical) nongenetic and (more contemporaneous) genetic surveillance data for reconstructing the history of spread of plant viruses.
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Affiliation(s)
- Mbolarinosy Rakotomalala
- Centre Régional de Recherche du Nord-Ouest du FOFIFA, BP 289, Mahavoky Avaratra, Mahajanga 401, Madagascar
| | - Bram Vrancken
- Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Herestraat 49 box 1040, 3000 Leuven, Belgium
| | - Agnès Pinel-Galzi
- IRD, Cirad, Université Montpellier, IPME, 911 avenue Agropolis, BP 64501 34934 Montpellier cedex 5, France
| | - Perle Ramavovololona
- Département de Biologie et d'Ecologie Végétales, Faculté des Sciences, Université d'Antananarivo, BP 906
| | - Eugénie Hébrard
- IRD, Cirad, Université Montpellier, IPME, 911 avenue Agropolis, BP 64501 34934 Montpellier cedex 5, France
| | | | - Simon Dellicour
- Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Herestraat 49 box 1040, 3000 Leuven, Belgium.,Spatial Epidemiology Lab, Université Libre de Bruxelles, CP 264 / 3,50 av FD Roosevelt, B-1050 Brussels, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Herestraat 49 box 1040, 3000 Leuven, Belgium
| | - Denis Fargette
- IRD, Cirad, Université Montpellier, IPME, 911 avenue Agropolis, BP 64501 34934 Montpellier cedex 5, France
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Coetzer A, Gwenhure L, Makaya P, Markotter W, Nel L. Epidemiological aspects of the persistent transmission of rabies during an outbreak (2010 - 2017) in Harare, Zimbabwe. PLoS One 2019; 14:e0210018. [PMID: 30629634 PMCID: PMC6328171 DOI: 10.1371/journal.pone.0210018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 12/14/2018] [Indexed: 12/25/2022] Open
Abstract
Canine-mediated human rabies is endemic to the entire African continent, where the disease burden is often highest in rural communities of resource-limited countries. In this study, we analysed an animal rabies outbreak, which had persisted since 2010 in the predominantly metropolitan capital city of Zimbabwe, Harare. As rabies is considered to disproportionally affect rural communities, the persistence of urban rabies in this metropolitan setting is of interest. In order to gain an improved understanding of the epidemiology of the outbreak under investigation, we utilised both routine surveillance data that had been collected during the first eight years of the outbreak (2010-2017), as well as molecular epidemiological analyses relying on the Bayesian Markov Chain Monte Carlo methodology. This approach allowed us to characterize virus transmission by identifying specific suburbs within the city limits where persistent disease transmission took place, while also confirming that immunologically naïve dogs were the most likely reservoir species in and around the city. In addition to gaining an improved local understanding of the outbreak, we are also able to infer that rabies was likely introduced to the city in 2010 when a rabid animal was moved from the north-east of Zimbabwe into Harare-resulting in an epizootic event. The work presented here not only showcased the value of combining conventional and molecular epidemiological data, but also highlighted the importance of maintaining rabies vaccination coverage and continued public awareness in urban areas where the risk appears to be low. By educating the general population on rabies and relying on owners to bring their companion animals to strategically placed vaccination points, the control and elimination of rabies from Harare may be feasible.
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Affiliation(s)
- Andre Coetzer
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
- Global Alliance for Rabies Control SA NPC, Pretoria, Gauteng, South Africa
| | - Lambert Gwenhure
- Department of Livestock & Veterinary Services, Central Veterinary Research and Diagnostic Laboratory, Harare, Harare metropolitan province, Zimbabwe
| | - Pious Makaya
- Department of Livestock & Veterinary Services, Central Veterinary Research and Diagnostic Laboratory, Harare, Harare metropolitan province, Zimbabwe
| | - Wanda Markotter
- Department of Medical Virology, Centre for Viral Zoonoses, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Louis Nel
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
- Global Alliance for Rabies Control SA NPC, Pretoria, Gauteng, South Africa
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Rysava K, Miranda ME, Zapatos R, Lapiz S, Rances P, Miranda LM, Roces MC, Friar J, Townsend SE, Hampson K. On the path to rabies elimination: The need for risk assessments to improve administration of post-exposure prophylaxis. Vaccine 2018; 37 Suppl 1:A64-A72. [PMID: 30573356 PMCID: PMC6863041 DOI: 10.1016/j.vaccine.2018.11.066] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/12/2018] [Accepted: 11/27/2018] [Indexed: 12/24/2022]
Abstract
Incidence of bite-injury patients and costs of PEP are high in Bohol Province, Philippines. Dog vaccination has controlled rabies so few patients (<2%) are bitten by rabid dogs. Risk assessments with bite patients can identify potential rabid dog bites. Investigations triggered by patient risk assessments enable early detection of rabies. This One health approach to surveillance could guide judicious PEP provision and improve PEP access.
Background Costs of rabies post-exposure prophylaxis (PEP) often remain high in regions where rabies has been controlled in dogs, presenting a challenge for sustaining rabies elimination programmes. We investigated the potential for bite patient risk assessments to improve PEP provision and surveillance in settings approaching elimination of dog-mediated rabies. Methods We conducted a longitudinal study of patients presenting to animal bite treatment centres (ABTCs) on the island province of Bohol in the Philippines to investigate the health status of biting dogs and to quantify current expenditure on PEP. Results Incidence of bite patients presenting to ABTCs was high (>300/100,000 persons/year) and increasing, resulting in substantial health provider costs. Over $142,000 was spent on PEP in 2013 for a population of 1.3 million. From follow up of 3820 bite patients we found that >92% were bitten by healthy dogs (alive 14 days after the bite) and just 1.4% were bitten by probable or confirmed rabid dogs. The status of dogs that bit 6% of patients could not be determined. During the course of investigations of bites by suspect dogs, we were able to obtain samples for case confirmation, identify exposed persons who had not sought PEP as well as in-contact dogs at risk of developing rabies. We calculate that expenditure on PEP could at least be halved through more judicious approaches to provision of PEP, based on the histories of biting animals determined through risk assessments with bite patients. Conclusions We conclude that a One Health approach to surveillance based on Integrated Bite Case Management could improve the sustainability and effectiveness of rabies elimination programmes while also improving patient care by identifying those genuinely in need of lifesaving PEP.
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Affiliation(s)
- K Rysava
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences, University of Warwick, Coventry, UK; Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, UK
| | - M E Miranda
- Field Epidemiology Training Program Alumni Foundation Inc. Quezon City, Philippines; Global Alliance for Rabies Control Inc., Laguna, Philippines
| | - R Zapatos
- Provincial Health Office, Capitol Annex, Tagbilaran City, Philippines
| | - S Lapiz
- Office of the Provincial Veterinarian, Capitol Annex, Tagbilaran City, Philippines
| | - P Rances
- Provincial Health Office, Capitol Annex, Tagbilaran City, Philippines
| | - L M Miranda
- Global Alliance for Rabies Control Inc., Laguna, Philippines; Asian Development Bank, Manila, Philippines
| | - M C Roces
- Global Alliance for Rabies Control Inc., Laguna, Philippines
| | - J Friar
- Wise Monkey Foundation, Washington, USA
| | - S E Townsend
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, UK
| | - K Hampson
- The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences, University of Warwick, Coventry, UK; Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, UK.
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Cori A, Nouvellet P, Garske T, Bourhy H, Nakouné E, Jombart T. A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies. PLoS Comput Biol 2018; 14:e1006554. [PMID: 30557340 PMCID: PMC6312344 DOI: 10.1371/journal.pcbi.1006554] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 12/31/2018] [Accepted: 10/09/2018] [Indexed: 11/23/2022] Open
Abstract
Early assessment of infectious disease outbreaks is key to implementing timely and effective control measures. In particular, rapidly recognising whether infected individuals stem from a single outbreak sustained by local transmission, or from repeated introductions, is crucial to adopt effective interventions. In this study, we introduce a new framework for combining several data streams, e.g. temporal, spatial and genetic data, to identify clusters of related cases of an infectious disease. Our method explicitly accounts for underreporting, and allows incorporating preexisting information about the disease, such as its serial interval, spatial kernel, and mutation rate. We define, for each data stream, a graph connecting all cases, with edges weighted by the corresponding pairwise distance between cases. Each graph is then pruned by removing distances greater than a given cutoff, defined based on preexisting information on the disease and assumptions on the reporting rate. The pruned graphs corresponding to different data streams are then merged by intersection to combine all data types; connected components define clusters of cases related for all types of data. Estimates of the reproduction number (the average number of secondary cases infected by an infectious individual in a large population), and the rate of importation of the disease into the population, are also derived. We test our approach on simulated data and illustrate it using data on dog rabies in Central African Republic. We show that the outbreak clusters identified using our method are consistent with structures previously identified by more complex, computationally intensive approaches. Early assessment of infectious disease outbreaks is key to implementing timely and effective control measures. In particular, rapidly recognising whether infected individuals stem from a single outbreak sustained by local transmission, or from repeated introductions, is crucial to adopt effective interventions. In this study, we introduce a new approach which combines different types of data to identify clusters of related cases of an infectious disease. This approach relies on representing each type of data (e.g. temporal, spatial, or genetic) as a graph where nodes are cases, and two nodes are connected if the corresponding cases are closely related for this data. Our method then identifies clusters of cases which likely stem from the same introduction. Furthermore, we can use the size of these clusters to infer transmissibility of the disease and the number of importations of the pathogen into the population. We apply this approach to analyse dog rabies epidemics in Central African Republic. We show that outbreak clusters identified using our method are consistent with structures previously identified by more complex and computationally intensive approaches. Using simulated rabies epidemics, we show that our method has excellent potential for optimally detecting outbreak clusters. We also identify promising areas of research for transforming our method into a routine analysis tool for processing disease surveillance data.
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Affiliation(s)
- Anne Cori
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail: (AC); (TJ)
| | - Pierre Nouvellet
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Tini Garske
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Hervé Bourhy
- Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Paris, France
| | - Emmanuel Nakouné
- Département fièvres hémorragiques virales, Institut Pasteur de Bangui, Bangui, République Centrafricaine
| | - Thibaut Jombart
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail: (AC); (TJ)
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Tian H, Feng Y, Vrancken B, Cazelles B, Tan H, Gill MS, Yang Q, Li Y, Yang W, Zhang Y, Zhang Y, Lemey P, Pybus OG, Stenseth NC, Zhang H, Dellicour S. Transmission dynamics of re-emerging rabies in domestic dogs of rural China. PLoS Pathog 2018; 14:e1007392. [PMID: 30521641 PMCID: PMC6283347 DOI: 10.1371/journal.ppat.1007392] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/08/2018] [Indexed: 12/17/2022] Open
Abstract
Despite ongoing efforts to control transmission, rabies prevention remains a challenge in many developing countries, especially in rural areas of China where re-emerging rabies is under-reported due to a lack of sustained animal surveillance. By taking advantage of detailed genomic and epidemiological data for the re-emerging rabies outbreak in Yunnan Province, China, collected between 1999 and 2015, we reconstruct the demographic and dispersal history of domestic dog rabies virus (RABV) as well as the dynamics of dog-to-dog and dog-to-human transmission. Phylogeographic analyses reveal a lower diffusion coefficient than previously estimated for dog RABV dissemination in northern Africa. Furthermore, epidemiological analyses reveal transmission rates between dogs, as well as between dogs and humans, lower than estimates for Africa. Finally, we show that reconstructed epidemic history of RABV among dogs and the dynamics of rabid dogs are consistent with the recorded human rabies cases. This work illustrates the benefits of combining phylogeographic and epidemic modelling approaches for uncovering the spatiotemporal dynamics of zoonotic diseases, with both approaches providing estimates of key epidemiological parameters.
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Affiliation(s)
- Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
- * E-mail: (HT); (HZ); (SD)
| | - Yun Feng
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Bram Vrancken
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
| | - Bernard Cazelles
- Institut de Biologie de l’École Normale Supérieure UMR 8197, Eco-Evolutionary Mathematics, École Normale Supérieure, France
- Unité Mixte Internationnale 209, Mathematical and Computational Modeling of Complex Systems, Institut de Recherche pour le Développement et Université Pierre et Marie Curie, Bondy, France
| | - Hua Tan
- School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Mandev S. Gill
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
| | - Qiqi Yang
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Yidan Li
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Weihong Yang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Yuzhen Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Yunzhi Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Philippe Lemey
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Nils Chr. Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Blindern, Oslo, Norway
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing, China
| | - Hailin Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
- * E-mail: (HT); (HZ); (SD)
| | - Simon Dellicour
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- * E-mail: (HT); (HZ); (SD)
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Laager M, Léchenne M, Naissengar K, Mindekem R, Oussiguere A, Zinsstag J, Chitnis N. A metapopulation model of dog rabies transmission in N'Djamena, Chad. J Theor Biol 2018; 462:408-417. [PMID: 30500602 DOI: 10.1016/j.jtbi.2018.11.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 12/24/2022]
Abstract
Rabies transmission was interrupted for several months in N'Djamena, the capital city of Chad, after two mass vaccination campaigns of dogs. However, there was a resurgence in cases, which was not predicted by previous models of rabies transmission. We developed a deterministic metapopulation model with importation of latent dogs, calibrated to four years of weekly incidence data from passive surveillance, to investigate possible causes for the early resurgence. Our results indicate that importation of latently infective dogs better explains the data than heterogeneity or underreporting. Stochastic implementations of the model suggest that the two vaccination campaigns averted approximately 67 cases of dog rabies (out of an estimated 74 cases without vaccination) and 124 human exposures (out of an estimated 148 human exposures without vaccination) over two years. Dog rabies vaccination is therefore an effective way of preventing rabies in the dog population and to subsequently reduce human exposure. However, vaccination campaigns have to be repeated to maintain the effect or reintroduction through importation has to be prevented.
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Affiliation(s)
- Mirjam Laager
- Swiss Tropical and Public Health Institue, Socinstrasse 57, Basel 4051, Switzerland; University of Basel, Petersplatz 1, Basel 4001, Switzerland.
| | - Monique Léchenne
- Swiss Tropical and Public Health Institue, Socinstrasse 57, Basel 4051, Switzerland; University of Basel, Petersplatz 1, Basel 4001, Switzerland
| | - Kemdongarti Naissengar
- Institut de Recherches en Elevage pour le Développement, BP 433, Farcha, N'Djamena, Chad
| | - Rolande Mindekem
- Centre de Support en Santé Internationale, BP 972, Moursal, N'Djamena, Chad
| | - Assandi Oussiguere
- Institut de Recherches en Elevage pour le Développement, BP 433, Farcha, N'Djamena, Chad
| | - Jakob Zinsstag
- Swiss Tropical and Public Health Institue, Socinstrasse 57, Basel 4051, Switzerland; University of Basel, Petersplatz 1, Basel 4001, Switzerland
| | - Nakul Chitnis
- Swiss Tropical and Public Health Institue, Socinstrasse 57, Basel 4051, Switzerland; University of Basel, Petersplatz 1, Basel 4001, Switzerland
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Laager M, Mbilo C, Madaye EA, Naminou A, Léchenne M, Tschopp A, Naïssengar SK, Smieszek T, Zinsstag J, Chitnis N. The importance of dog population contact network structures in rabies transmission. PLoS Negl Trop Dis 2018; 12:e0006680. [PMID: 30067733 PMCID: PMC6089439 DOI: 10.1371/journal.pntd.0006680] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 08/13/2018] [Accepted: 07/10/2018] [Indexed: 11/19/2022] Open
Abstract
Canine rabies transmission was interrupted in N'Djaména, Chad, following two mass vaccination campaigns. However, after nine months cases resurged with re-establishment of endemic rabies transmission to pre-intervention levels. Previous analyses investigated district level spatial heterogeneity of vaccination coverage, and dog density; and importation, identifying the latter as the primary factor for rabies resurgence. Here we assess the impact of individual level heterogeneity on outbreak probability, effectiveness of vaccination campaigns and likely time to resurgence after a campaign. Geo-located contact sensors recorded the location and contacts of 237 domestic dogs in N'Djaména over a period of 3.5 days. The contact network data showed that urban dogs are socially related to larger communities and constrained by the urban architecture. We developed a network generation algorithm that extrapolates this empirical contact network to networks of large dog populations and applied it to simulate rabies transmission in N'Djaména. The model predictions aligned well with the rabies incidence data. Using the model we demonstrated, that major outbreaks are prevented when at least 70% of dogs are vaccinated. The probability of a minor outbreak also decreased with increasing vaccination coverage, but reached zero only when coverage was near total. Our results suggest that endemic rabies in N'Djaména may be explained by a series of importations with subsequent minor outbreaks. We show that highly connected dogs hold a critical role in transmission and that targeted vaccination of such dogs would lead to more efficient vaccination campaigns.
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Affiliation(s)
- Mirjam Laager
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Céline Mbilo
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Abakar Naminou
- Institut de Recherches en Elevage pour le Développement, Farcha, N’Djaména, Chad
| | - Monique Léchenne
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Aurélie Tschopp
- Veterinary Public Health Institute, Vetsuisse Faculty, University of Bern, Liebefeld, Switzerland
| | | | - Timo Smieszek
- Modelling and Economics Unit, National Infection Service, Public Health England, London, United Kingdom
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College School of Public Health, London, United Kingdom
| | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nakul Chitnis
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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Zinsstag J, Lechenne M, Laager M, Mindekem R, Naïssengar S, Oussiguéré A, Bidjeh K, Rives G, Tessier J, Madjaninan S, Ouagal M, Moto DD, Alfaroukh IO, Muthiani Y, Traoré A, Hattendorf J, Lepelletier A, Kergoat L, Bourhy H, Dacheux L, Stadler T, Chitnis N. Vaccination of dogs in an African city interrupts rabies transmission and reduces human exposure. Sci Transl Med 2018; 9:9/421/eaaf6984. [PMID: 29263230 DOI: 10.1126/scitranslmed.aaf6984] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 12/07/2016] [Accepted: 08/15/2017] [Indexed: 01/16/2023]
Abstract
Despite the existence of effective rabies vaccines for dogs, dog-transmitted human rabies persists and has reemerged in Africa. Two consecutive dog vaccination campaigns took place in Chad in 2012 and 2013 (coverage of 71% in both years) in the capital city of N'Djaména, as previously published. We developed a deterministic model of dog-human rabies transmission fitted to weekly incidence data of rabid dogs and exposed human cases in N'Djaména. Our analysis showed that the effective reproductive number, that is, the number of new dogs infected by a rabid dog, fell to below one through November 2014. The modeled incidence of human rabies exposure fell to less than one person per million people per year. A phylodynamic estimation of the effective reproductive number from 29 canine rabies virus genetic sequences of the viral N-protein confirmed the results of the deterministic transmission model, implying that rabies transmission between dogs was interrupted for 9 months. However, new dog rabies cases appeared earlier than the transmission and phylodynamic models predicted. This may have been due to the continuous movement of rabies-exposed dogs into N'Djaména from outside the city. Our results show that canine rabies transmission to humans can be interrupted in an African city with currently available dog rabies vaccines, provided that the vaccination area includes larger adjacent regions, and local communities are informed and engaged.
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Affiliation(s)
- Jakob Zinsstag
- Swiss Tropical and Public Health Institute, P.O. Box, 4002 Basel, Switzerland. .,University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Monique Lechenne
- Swiss Tropical and Public Health Institute, P.O. Box, 4002 Basel, Switzerland.,University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Mirjam Laager
- Swiss Tropical and Public Health Institute, P.O. Box, 4002 Basel, Switzerland.,University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Rolande Mindekem
- Centre de Support en Santé Internationale, BP 972, N'Djaména, Chad
| | - Service Naïssengar
- Institut de Recherche en Elevage pour le Développement, BP 433, N'Djaména, Chad
| | - Assandi Oussiguéré
- Institut de Recherche en Elevage pour le Développement, BP 433, N'Djaména, Chad
| | - Kebkiba Bidjeh
- Institut de Recherche en Elevage pour le Développement, BP 433, N'Djaména, Chad
| | - Germain Rives
- Swiss Tropical and Public Health Institute, P.O. Box, 4002 Basel, Switzerland.,University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Julie Tessier
- Swiss Tropical and Public Health Institute, P.O. Box, 4002 Basel, Switzerland.,University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | | | - Mahamat Ouagal
- Institut de Recherche en Elevage pour le Développement, BP 433, N'Djaména, Chad
| | - Daugla D Moto
- Centre de Support en Santé Internationale, BP 972, N'Djaména, Chad
| | - Idriss O Alfaroukh
- Institut de Recherche en Elevage pour le Développement, BP 433, N'Djaména, Chad
| | - Yvonne Muthiani
- Swiss Tropical and Public Health Institute, P.O. Box, 4002 Basel, Switzerland.,University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | | | - Jan Hattendorf
- Swiss Tropical and Public Health Institute, P.O. Box, 4002 Basel, Switzerland.,University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Anthony Lepelletier
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Lauriane Kergoat
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Hervé Bourhy
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Laurent Dacheux
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, Federal Institute of Technology (ETH), Mattenstrasse 26, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nakul Chitnis
- Swiss Tropical and Public Health Institute, P.O. Box, 4002 Basel, Switzerland.,University of Basel, Petersplatz 1, 4003 Basel, Switzerland
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43
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Cleaveland S, Hampson K. Rabies elimination research: juxtaposing optimism, pragmatism and realism. Proc Biol Sci 2018; 284:rspb.2017.1880. [PMID: 29263285 PMCID: PMC5745407 DOI: 10.1098/rspb.2017.1880] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 11/27/2017] [Indexed: 12/17/2022] Open
Abstract
More than 100 years of research has now been conducted into the prevention, control and elimination of rabies with safe and highly efficacious vaccines developed for use in human and animal populations. Domestic dogs are a major reservoir for rabies, and although considerable advances have been made towards the elimination and control of canine rabies in many parts of the world, the disease continues to kill tens of thousands of people every year in Africa and Asia. Policy efforts are now being directed towards a global target of zero human deaths from dog-mediated rabies by 2030 and the global elimination of canine rabies. Here we demonstrate how research provides a cause for optimism as to the feasibility of these goals through strategies based around mass dog vaccination. We summarize some of the pragmatic insights generated from rabies epidemiology and dog ecology research that can improve the design of dog vaccination strategies in low- and middle-income countries and which should encourage implementation without further delay. We also highlight the need for realism in reaching the feasible, although technically more difficult and longer-term goal of global elimination of canine rabies. Finally, we discuss how research on rabies has broader relevance to the control and elimination of a suite of diseases of current concern to human and animal health, providing an exemplar of the value of a ‘One Health’ approach.
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Affiliation(s)
- Sarah Cleaveland
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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44
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Brunker K, Lemey P, Marston DA, Fooks AR, Lugelo A, Ngeleja C, Hampson K, Biek R. Landscape attributes governing local transmission of an endemic zoonosis: Rabies virus in domestic dogs. Mol Ecol 2018; 27:773-788. [PMID: 29274171 PMCID: PMC5900915 DOI: 10.1111/mec.14470] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 12/24/2022]
Abstract
Landscape heterogeneity plays an important role in disease spread and persistence, but quantifying landscape influences and their scale dependence is challenging. Studies have focused on how environmental features or global transport networks influence pathogen invasion and spread, but their influence on local transmission dynamics that underpin the persistence of endemic diseases remains unexplored. Bayesian phylogeographic frameworks that incorporate spatial heterogeneities are promising tools for analysing linked epidemiological, environmental and genetic data. Here, we extend these methodological approaches to decipher the relative contribution and scale-dependent effects of landscape influences on the transmission of endemic rabies virus in Serengeti district, Tanzania (area ~4,900 km2 ). Utilizing detailed epidemiological data and 152 complete viral genomes collected between 2004 and 2013, we show that the localized presence of dogs but not their density is the most important determinant of diffusion, implying that culling will be ineffective for rabies control. Rivers and roads acted as barriers and facilitators to viral spread, respectively, and vaccination impeded diffusion despite variable annual coverage. Notably, we found that landscape effects were scale-dependent: rivers were barriers and roads facilitators on larger scales, whereas the distribution of dogs was important for rabies dispersal across multiple scales. This nuanced understanding of the spatial processes that underpin rabies transmission can be exploited for targeted control at the scale where it will have the greatest impact. Moreover, this research demonstrates how current phylogeographic frameworks can be adapted to improve our understanding of endemic disease dynamics at different spatial scales.
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Affiliation(s)
- Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- The Boyd Orr Centre for Population and Ecosystem HealthUniversity of GlasgowGlasgowUK
- Animal and Plant Health AgencyAddlestoneUK
| | - Philippe Lemey
- Department of Microbiology and ImmunologyKU Leuven – University of LeuvenLeuvenBelgium
| | | | | | - Ahmed Lugelo
- Department of Veterinary Medicine and Public HealthSokoine University of AgricultureMorogoroUnited Republic of Tanzania
| | - Chanasa Ngeleja
- Tanzania Veterinary Laboratory AgencyDar es SalaamUnited Republic of Tanzania
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- The Boyd Orr Centre for Population and Ecosystem HealthUniversity of GlasgowGlasgowUK
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- The Boyd Orr Centre for Population and Ecosystem HealthUniversity of GlasgowGlasgowUK
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45
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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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46
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Fountain-Jones NM, Craft ME, Funk WC, Kozakiewicz C, Trumbo DR, Boydston EE, Lyren LM, Crooks K, Lee JS, VandeWoude S, Carver S. Urban landscapes can change virus gene flow and evolution in a fragmentation-sensitive carnivore. Mol Ecol 2017; 26:6487-6498. [PMID: 28987024 DOI: 10.1111/mec.14375] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/18/2017] [Accepted: 09/14/2017] [Indexed: 12/15/2022]
Abstract
Urban expansion has widespread impacts on wildlife species globally, including the transmission and emergence of infectious diseases. However, there is almost no information about how urban landscapes shape transmission dynamics in wildlife. Using an innovative phylodynamic approach combining host and pathogen molecular data with landscape characteristics and host traits, we untangle the complex factors that drive transmission networks of feline immunodeficiency virus (FIV) in bobcats (Lynx rufus). We found that the urban landscape played a significant role in shaping FIV transmission. Even though bobcats were often trapped within the urban matrix, FIV transmission events were more likely to occur in areas with more natural habitat elements. Urban fragmentation also resulted in lower rates of pathogen evolution, possibly owing to a narrower range of host genotypes in the fragmented area. Combined, our findings show that urban landscapes can have impacts on a pathogen and its evolution in a carnivore living in one of the most fragmented and urban systems in North America. The analytical approach used here can be broadly applied to other host-pathogen systems, including humans.
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Affiliation(s)
- Nicholas M Fountain-Jones
- School of Biological Sciences, University of Tasmania, Hobart, Australia.,Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, USA
| | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, USA
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Chris Kozakiewicz
- School of Biological Sciences, University of Tasmania, Hobart, Australia
| | - Daryl R Trumbo
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Erin E Boydston
- Western Ecological Research Center, U.S. Geological Survey, Thousand Oaks, CA, USA
| | - Lisa M Lyren
- Western Ecological Research Center, U.S. Geological Survey, Thousand Oaks, CA, USA
| | - Kevin Crooks
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, USA
| | - Justin S Lee
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Scott Carver
- School of Biological Sciences, University of Tasmania, Hobart, Australia
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Sadeuh-Mba SA, Momo JB, Besong L, Loul S, Njouom R. Molecular characterization and phylogenetic relatedness of dog-derived Rabies Viruses circulating in Cameroon between 2010 and 2016. PLoS Negl Trop Dis 2017; 11:e0006041. [PMID: 29084223 PMCID: PMC5679643 DOI: 10.1371/journal.pntd.0006041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 11/09/2017] [Accepted: 10/15/2017] [Indexed: 12/25/2022] Open
Abstract
Rabies is enzootic among dog populations in some parts of Cameroon and the risk of human rabies is thought to be steadily high in these regions. However, the molecular epidemiology of circulating Rabies Virus (RABV) has been hardly considered in Cameroon as well as in most neighboring central African countries. To address this fundamental gap, 76 nucleoprotein (N) gene sequences of dog-derived RABV were obtained from 100 brain specimens sampled in Cameroon from 2010 to 2016. Studied sequences were subjected to molecular and phylogenetic analyses with reference strains retrieved from databases. The 71 studied Africa-1 isolates displayed 93.5–100% nucleotide (nt) and 98.3–100% amino-acid (aa) identities to each other while, the 5 studied Africa-2 isolates shared 99.4–99.7% sequence similarities at nt and aa levels. Maximum Likelihood based phylogenies inferred from nucleotide sequences confirmed all studied RABV isolates as members of the dog-related species 1 of the Lyssavirus genus. Individual isolates could be unambiguously assigned as either the Africa-1 subclade of the Cosmopolitan clade or the Africa 2 clade. The Africa-1 subclade appeared to be more prevalent and diversified. Indeed, 70 studied isolates segregated into 3 distinct circulating variants within Africa-1a lineage while a unique isolate was strikingly related to the Africa-1b lineage known to be prevalent in the neighboring Central African Republic and eastern Africa. Interestingly, all five Africa-2 isolates fell into the group-E lineage even though they appeared to be loosely related to databases available reference RABV; including those previously documented in Cameroon. This study uncovered the co-circulation of several Africa-1 and Africa-2 lineages in the southern regions of Cameroon. Striking phylogenetic outcasts to the geographic differentiation of RABV variants indicated that importation from close regions or neighboring countries apparently contributes to the sustainment of the enzootic cycle of domestic rabies in Cameroon. Rabies has been repeatedly reported among dog populations in Cameroon, especially in Yaounde, its capital city. However, the relative rates and genetic variability of Rabies Virus (RABV) variants circulating among dog populations in Cameroon are still to be documented. This study aimed to estimate the frequency and genetic diversity of RABV isolates originating from rabid dogs in the southern regions of Cameroon from 2010 to 2016. Overall, 76 of the 100 dog-derived RABV isolates sampled in Cameroon from 2010 to 2016 were successfully characterized. Our findings revealed that studied isolates belonged to the dog-related species 1 of the Lyssavirus genus, specifically 70 Africa-1a, 1 Africa-1b and 5 Africa-2 group-E lineages. The general phylogenetic pattern suggested an in-country geographic differentiation of the circulating RABV variants. This apparent geographic differentiation was contradicted by striking outcasts indicating importation from close or distant regions. Overall, this study uncovered the co-circulation of several Africa-1 and Africa-2 lineages in some southern regions of Cameroon, thus providing base-line molecular data that would be of interest for future stages of implementation of the rabies surveillance and control plan that is being setup in Cameroon.
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Affiliation(s)
- Serge Alain Sadeuh-Mba
- Virology Service, Centre Pasteur du Cameroun, Yaounde, Centre region, Cameroon
- * E-mail: ,
| | - Jean Blaise Momo
- Virology Service, Centre Pasteur du Cameroun, Yaounde, Centre region, Cameroon
| | - Laura Besong
- Ministry of Livestock, Fisheries and Animal Industries (MINEPIA), Yaounde, Centre region, Cameroon
| | - Sévérin Loul
- Ministry of Livestock, Fisheries and Animal Industries (MINEPIA), Yaounde, Centre region, Cameroon
| | - Richard Njouom
- Virology Service, Centre Pasteur du Cameroun, Yaounde, Centre region, Cameroon
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48
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Zhang Y, Vrancken B, Feng Y, Dellicour S, Yang Q, Yang W, Zhang Y, Dong L, Pybus OG, Zhang H, Tian H. Cross-border spread, lineage displacement and evolutionary rate estimation of rabies virus in Yunnan Province, China. Virol J 2017; 14:102. [PMID: 28578663 PMCID: PMC5457581 DOI: 10.1186/s12985-017-0769-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/25/2017] [Indexed: 12/12/2022] Open
Abstract
Background Rabies is an important but underestimated threat to public health, with most cases reported in Asia. Since 2000, a new epidemic wave of rabies has emerged in Yunnan Province, southwestern China, which borders three countries in Southeast Asia. Method We estimated gene-specific evolutionary rates for rabies virus using available data in GenBank, then used this information to calibrate the timescale of rabies virus (RABV) spread in Asia. We used 452 publicly available geo-referenced complete nucleoprotein (N) gene sequences, including 52 RABV sequences that were recently generated from samples collected in Yunnan between 2008 and 2012. Results The RABV N gene evolutionary rate was estimated to be 1.88 × 10−4 (1.37–2.41 × 10−4, 95% Bayesian credible interval, BCI) substitutions per site per year. Phylogenetic reconstructions show that the currently circulating RABV lineages in Yunnan result from at least seven independent introductions (95% BCI: 6–9 introductions) and represent each of the three main Asian RABV lineages, SEA-1, -2 and -3. We find that Yunnan is a sink location for the domestic spread of RABV and connects RABV epidemics in North China, South China, and Southeast Asia. Cross-border spread from southeast Asia (SEA) into South China, and intermixing of the North and South China epidemics is also well supported. The influx of RABV into Yunnan from SEA was not well-supported, likely due to the poor sampling of SEA RABV diversity. We found evidence for a lineage displacement of the Yunnan SEA-2 and -3 lineages by Yunnan SEA-1 strains, and considered whether this could be attributed to fitness differences. Conclusion Overall, our study contributes to a better understanding of the spread of RABV that could facilitate future rabies virus control and prevention efforts. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0769-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuzhen Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Bram Vrancken
- Department of Microbiology and Immunology, Division of Clinical and Epidemiological Virology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Yun Feng
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Simon Dellicour
- Department of Microbiology and Immunology, Division of Clinical and Epidemiological Virology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Qiqi Yang
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Weihong Yang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Yunzhi Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | | | - Hailin Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China.
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China.
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49
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Mindekem R, Lechenne MS, Naissengar KS, Oussiguéré A, Kebkiba B, Moto DD, Alfaroukh IO, Ouedraogo LT, Salifou S, Zinsstag J. Cost Description and Comparative Cost Efficiency of Post-Exposure Prophylaxis and Canine Mass Vaccination against Rabies in N'Djamena, Chad. Front Vet Sci 2017; 4:38. [PMID: 28421186 PMCID: PMC5376597 DOI: 10.3389/fvets.2017.00038] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/02/2017] [Indexed: 12/25/2022] Open
Abstract
Rabies claims approximately 59,000 human lives annually and is a potential risk to 3.3 billion people in over 100 countries worldwide. Despite being fatal in almost 100% of cases, human rabies can be prevented by vaccinating dogs, the most common vector, and the timely administration of post-exposure prophylaxis (PEP) to exposed victims. For the control and prevention of human rabies in N'Djamena, the capital city of Chad, a free mass vaccination campaign for dogs was organized in 2012 and 2013. The campaigns were monitored by parallel studies on the incidence of canine rabies based on diagnostic testing of suspect animals and the incidence of human bite exposure recorded at selected health facilities. Based on the cost description of the campaign and the need for PEP registered in health centers, three cost scenarios were compared: cumulative cost-efficiency of (1) PEP alone, (2) dog mass vaccination and PEP, (3) dog mass vaccination, PEP, and maximal communication between human health and veterinary workers (One Health communication). Assuming ideal One Health communication, the cumulative prospective cost of dog vaccination and PEP break even with the cumulative prospective cost of PEP alone in the 10th year from the start of the calculation (2012). The cost efficiency expressed in cost per human exposure averted is much higher with canine vaccination and One Health communication than with PEP alone. As shown in other studies, our cost-effectiveness analysis highlights that canine vaccination is financially the best option for animal rabies control and rabies prevention in humans. This study also provides evidence of the beneficial effect of One Health communication. Only with close communication between the human and animal health sectors will the decrease in animal rabies incidence be translated into a decline for PEP. An efficiently applied One Health concept would largely reduce the cost of PEP in resource poor countries and should be implemented for zoonosis control in general.
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Affiliation(s)
| | - Monique Sarah Lechenne
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Assandi Oussiguéré
- Institut de Recherches en Elevage pour le Développement, N'Djamena, Chad
| | - Bidjeh Kebkiba
- Institut de Recherches en Elevage pour le Développement, N'Djamena, Chad
| | | | | | | | | | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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50
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Troupin C, Dacheux L, Tanguy M, Sabeta C, Blanc H, Bouchier C, Vignuzzi M, Duchene S, Holmes EC, Bourhy H. Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts. PLoS Pathog 2016; 12:e1006041. [PMID: 27977811 PMCID: PMC5158080 DOI: 10.1371/journal.ppat.1006041] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 11/03/2016] [Indexed: 12/25/2022] Open
Abstract
The natural evolution of rabies virus (RABV) provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics. Zoonoses account for most recently emerged infectious diseases of humans, although little is known about the evolutionary mechanisms involved in cross-species virus transmission. Understanding the evolutionary patterns and processes that underpin such cross-species transmission is of importance for predicting the spread of zoonotic infections, and hence to their ultimate control. We present a large-scale and detailed reconstruction of the evolutionary history of rabies virus (RABV) in domestic and wildlife animal species. RABV is of particular interest as it is capable of infecting many mammals but, paradoxically, is only maintained in distinct epidemiological cycles associated with animal species from the orders Carnivora and Chiroptera. We show that bat-related RABV and dog-related RABV have experienced very different evolutionary dynamics, and that host jumps are sometimes characterized by significant increases in evolutionary rate. Among Carnivora, the association between RABV and particular host species most likely arose from a combination of the historical human-mediated spread of the virus and jumps into new primary host species. In addition, we show that changes in host species are associated with multiple evolutionary pathways including the occurrence of host-specific parallel evolution. Overall, our data indicate that the establishment of dog-related RABV in new carnivore hosts may only require subtle adaptive evolution.
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Affiliation(s)
- Cécile Troupin
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Laurent Dacheux
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Marion Tanguy
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
- Institut Pasteur, Genomics Platform, Paris, France
| | - Claude Sabeta
- Agricultural Research Council, Onderstepoort Veterinary Institute, OIE Rabies Reference Laboratory, Pretoria, South Africa
| | - Hervé Blanc
- Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, Viral Populations and Pathogenesis Unit, Paris, France
| | | | - Marco Vignuzzi
- Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, Viral Populations and Pathogenesis Unit, Paris, France
| | - Sebastián Duchene
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
- Centre for Systems Genomics, University of Melbourne, Parkville, Victoria, Australia
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Hervé Bourhy
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
- * E-mail:
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