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Current status and molecular epidemiology of rabies virus from different hosts and regions in Malawi. Arch Virol 2023; 168:61. [PMID: 36631547 PMCID: PMC9834359 DOI: 10.1007/s00705-022-05635-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/21/2022] [Indexed: 01/13/2023]
Abstract
Although rabies is endemic in Malawi, there have been no studies in which rabies virus was systematically investigated and characterized in multiple animal hosts in that country. In order to provide molecular epidemiological data on rabies virus in Malawi, 683 suspected rabies case reports from 2008 to 2021 were examined, and 46 (dog = 40, cow = 5, and cat = 1) viable rabies-positive brain samples archived at the Central Veterinary Laboratory (CVL), Lilongwe, Malawi, were analyzed genetically. The results showed an increase in the submission of brain samples from 2008 to 2010, with the highest number of submissions observed in 2020. Of the 683 case reports analyzed for the period under review, 38.1% (260/683) (CI: 34.44 - 41.84) were confirmed by direct fluorescent antibody test. Among the confirmed cases, 65.4% (170/260) (CI: 59.23 - 71.09) were canine rabies. Further, phylogenetic analysis revealed that sequences from different animal hosts clustered together within the Africa 1b lineage, suggesting that the strains circulating in livestock are similar to those in domestic dogs. This finding supports the hypothesis that canine rabies is spilling over to livestock and emphasizes the need for further studies to provide data for effective control of rabies in Malawi.
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Muturi EJ, Njoroge TM, Dunlap C, Cáceres CE. Blood meal source and mixed blood-feeding influence gut bacterial community composition in Aedes aegypti. Parasit Vectors 2021; 14:83. [PMID: 33509255 PMCID: PMC7841894 DOI: 10.1186/s13071-021-04579-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/01/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND The guts of blood-sucking insects host a community of bacteria that can shift dramatically in response to biotic and abiotic factors. Identifying the key factors structuring these microbial communities has important ecological and epidemiological implications. METHODS We used the yellow fever mosquito, Aedes aegypti, to investigate the impact of mixed blood meals on gut microbiota of vector mosquitoes. Adult females were experimentally fed on sugar or blood from chicken, rabbit or a mixture of chicken and rabbit blood, and their gut microbiota were characterized using 16S rRNA gene amplification and MiSeq sequencing. RESULTS The gut bacterial communities of mosquitoes fed on the three blood meal treatments clustered separately, suggesting that host species identity and mixed blood-feeding are key determinants of gut bacterial community composition in mosquitoes. Mixed blood meal had a synergistic effect on both operational taxonomic unit (OTU) richness and the Shannon diversity index, suggesting that mixed blood-feeding can offset the nutritional deficit of blood meals from certain host species. The microbial communities observed in this study were distinct from those identified from similarly fed Ae. aegypti from our previous study. CONCLUSIONS These findings demonstrate that vector host-feeding preferences can influence gut microbial composition and diversity, which could potentially impact pathogen acquisition and transmission by the vector. The results also demonstrate that different microenvironmental conditions within the laboratory may play an important role in structuring the microbial communities of independently reared mosquito colonies.
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Affiliation(s)
- Ephantus J Muturi
- Crop Bioprotection Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St, Peoria, 61604, IL, USA.
| | - Teresia M Njoroge
- Department of Entomology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Christopher Dunlap
- Crop Bioprotection Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St, Peoria, 61604, IL, USA
| | - Carla E Cáceres
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave, Urbana, 61801, IL, USA
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3
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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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4
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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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Mtui-Malamsha N, Sallu R, Mahiti GR, Mohamed H, OleNeselle M, Rubegwa B, Swai ES, Makungu S, Otieno EG, Lupindu AM, Komba E, Mdegela R, Assenga JA, Bernard J, Marandu W, Warioba J, Makondo Z, Chang'a J, Mramba F, Nonga H, Killewo J, Kafeero F, Makonnen YJ, Rivas AL, Fasina FO. Ecological and Epidemiological Findings Associated with Zoonotic Rabies Outbreaks and Control in Moshi, Tanzania, 2017-2018. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E2816. [PMID: 31394794 PMCID: PMC6719226 DOI: 10.3390/ijerph16162816] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/25/2019] [Accepted: 08/05/2019] [Indexed: 02/05/2023]
Abstract
Approximately 1500 people die annually due to rabies in the United Republic of Tanzania. Moshi, in the Kilimanjaro Region, reported sporadic cases of human rabies between 2017 and 2018. In response and following a One Health approach, we implemented surveillance, monitoring, as well as a mass vaccinations of domestic pets concurrently in >150 villages, achieving a 74.5% vaccination coverage (n = 29, 885 dogs and cats) by September 2018. As of April 2019, no single human or animal case has been recorded. We have observed a disparity between awareness and knowledge levels of community members on rabies epidemiology. Self-adherence to protective rabies vaccination in animals was poor due to the challenges of costs and distances to vaccination centers, among others. Incidence of dog bites was high and only a fraction (65%) of dog bite victims (humans) received post-exposure prophylaxis. A high proportion of unvaccinated dogs and cats and the relative intense interactions with wild dog species at interfaces were the risk factors for seropositivity to rabies virus infection in dogs. A percentage of the previously vaccinated dogs remained unimmunized and some unvaccinated dogs were seropositive. Evidence of community engagement and multi-coordinated implementation of One Health in Moshi serves as an example of best practice in tackling zoonotic diseases using multi-level government efforts. The district-level establishment of the One Health rapid response team (OHRRT), implementation of a carefully structured routine vaccination campaign, improved health education, and the implementation of barriers between domestic animals and wildlife at the interfaces are necessary to reduce the burden of rabies in Moshi and communities with similar profiles.
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Affiliation(s)
- Niwael Mtui-Malamsha
- Food and Agriculture Organization of the United Nations, Dar es Salaam 14111, Tanzania
| | - Raphael Sallu
- Food and Agriculture Organization of the United Nations, Dar es Salaam 14111, Tanzania
| | - Gladys R Mahiti
- Department of Developmental Studies, Muhimbili University of Health and Allied Sciences, Dar es Salaam 11103, Tanzania
- One Health Central and Eastern Africa, Dar es Salaam 11103, Tanzania
| | - Hussein Mohamed
- Department of Developmental Studies, Muhimbili University of Health and Allied Sciences, Dar es Salaam 11103, Tanzania
- One Health Central and Eastern Africa, Dar es Salaam 11103, Tanzania
| | - Moses OleNeselle
- Food and Agriculture Organization of the United Nations, Dar es Salaam 14111, Tanzania
| | - Bachana Rubegwa
- Food and Agriculture Organization of the United Nations, Dar es Salaam 14111, Tanzania
| | | | | | - Edward G Otieno
- One Health Central and Eastern Africa, Dar es Salaam 11103, Tanzania
- College of Veterinary Medeicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro 67000, Tanzania
| | - Athuman M Lupindu
- One Health Central and Eastern Africa, Dar es Salaam 11103, Tanzania
- College of Veterinary Medeicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro 67000, Tanzania
| | - Erick Komba
- One Health Central and Eastern Africa, Dar es Salaam 11103, Tanzania
- College of Veterinary Medeicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro 67000, Tanzania
| | - Robinson Mdegela
- One Health Central and Eastern Africa, Dar es Salaam 11103, Tanzania
- College of Veterinary Medeicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro 67000, Tanzania
| | - Justine A Assenga
- Ministry of Livestock and Fisheries, Dodoma 41000, Tanzania
- One Health Coordination Desk, Prime Minister's Office, Dodoma 41000, Tanzania
| | - Jubilate Bernard
- One Health Coordination Desk, Prime Minister's Office, Dodoma 41000, Tanzania
- Ministry of Health, Community Development, Gender, Elderly and Children, Dodoma 41000, Tanzania
| | - Walter Marandu
- District Veterinary Office, Moshi District 25101, Tanzania
| | | | - Zacharia Makondo
- Tanzania Veterinary Laboratory Agency, Dar es Salaam 15101, Tanzania
| | - Jelly Chang'a
- Tanzania Veterinary Laboratory Agency, Dar es Salaam 15101, Tanzania
| | - Furaha Mramba
- Tanzania Veterinary Laboratory Agency, Dar es Salaam 15101, Tanzania
| | - Hezron Nonga
- Ministry of Livestock and Fisheries, Dodoma 41000, Tanzania
- College of Veterinary Medeicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro 67000, Tanzania
| | - Japhet Killewo
- Department of Developmental Studies, Muhimbili University of Health and Allied Sciences, Dar es Salaam 11103, Tanzania
- One Health Central and Eastern Africa, Dar es Salaam 11103, Tanzania
| | - Fred Kafeero
- Food and Agriculture Organization of the United Nations, Dar es Salaam 14111, Tanzania
| | - Yilma J Makonnen
- Food and Agriculture Organization of the United Nations, 00153 Rome, Italy
| | - Ariel L Rivas
- Center for Global Health, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
| | - Folorunso O Fasina
- Food and Agriculture Organization of the United Nations, Dar es Salaam 14111, Tanzania.
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa.
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6
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Bitek AO, Osoro E, Munyua PM, Nanyingi M, Muthiani Y, Kiambi S, Muturi M, Mwatondo A, Muriithi R, Cleaveland S, Hampson K, Njenga MK, Kitala PM, Thumbi SM. A hundred years of rabies in Kenya and the strategy for eliminating dog-mediated rabies by 2030. AAS Open Res 2019; 1:23. [PMID: 32259023 PMCID: PMC7117960 DOI: 10.12688/aasopenres.12872.2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2018] [Indexed: 12/24/2022] Open
Abstract
Background: Rabies causes an estimated 59,000 human deaths annually. In Kenya, rabies was first reported in a dog in 1912, with the first human case reported in 1928. Here we examine retrospective rabies data in Kenya for the period 1912 - 2017 and describe the spatial and temporal patterns of rabies occurrence in the country. Additionally, we detail Kenya's strategy for the elimination of dog-mediated human rabies by 2030. Methods: Data on submitted samples and confirmed cases in humans, domestic animals and wildlife were obtained from Kenya's Directorate of Veterinary Services. These data were associated with the geographical regions where the samples originated, and temporal and spatial trends examined. Results: Between 1912 and the mid 1970's, rabies spread across Kenya gradually, with fewer than 50 cases reported per year and less than half of the 47 counties affected. Following an outbreak in the mid 1970's, rabies spread rapidly to more than 85% of counties, with a 4 fold increase in the percent positivity of samples submitted and number of confirmed rabies cases. Since 1958, 7,584 samples from domestic animals (93%), wildlife (5%), and humans (2%) were tested. Over two-thirds of all rabies cases came from six counties, all in close proximity to veterinary diagnostic laboratories, highlighting a limitation of passive surveillance. Conclusions: Compulsory annual dog vaccinations between 1950's and the early 1970's slowed rabies spread. The rapid spread with peak rabies cases in the 1980's coincided with implementation of structural adjustment programs privatizing the veterinary sector leading to breakdown of rabies control programs. To eliminate human deaths from rabies by 2030, Kenya is implementing a 15-year step-wise strategy based on three pillars: a) mass dog vaccination, b) provision of post-exposure prophylaxis and public awareness and c) improved surveillance for rabies in dogs and humans with prompt responses to rabies outbreaks.
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Affiliation(s)
- Austine O Bitek
- Zoonotic Disease Unit, Ministry of Agriculture and Livestock, Nairobi, Kenya
| | - Eric Osoro
- Zoonotic Disease Unit, Ministry of Health, Nairobi, Kenya
| | - Peninah M Munyua
- Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Mark Nanyingi
- Department of Public Health, Pharmacology and Toxicology, University of Nairobi, Nairobi, Kenya
| | - Yvonne Muthiani
- Zoonotic Disease Unit, Ministry of Agriculture and Livestock, Nairobi, Kenya
| | - Stella Kiambi
- Zoonotic Disease Unit, Ministry of Agriculture and Livestock, Nairobi, Kenya
| | - Mathew Muturi
- Zoonotic Disease Unit, Ministry of Agriculture and Livestock, Nairobi, Kenya
| | | | - Rees Muriithi
- Directorate of Veterinary Services, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - Sarah Cleaveland
- Boyd Orr Centre for Population and Ecosystem Health, Institute for Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Katie Hampson
- Boyd Orr Centre for Population and Ecosystem Health, Institute for Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, UK
| | - M. Kariuki Njenga
- 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
| | - PM Kitala
- Department of Public Health, Pharmacology and Toxicology, University of Nairobi, Nairobi, Kenya
| | - SM Thumbi
- 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
- Rabies Free Africa, Washington State University, Pullman, WA, USA
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7
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Bitek AO, Osoro E, Munyua PM, Nanyingi M, Muthiani Y, Kiambi S, Muturi M, Mwatondo A, Muriithi R, Cleaveland S, Hampson K, Njenga MK, Kitala PM, Thumbi SM. A hundred years of rabies in Kenya and the strategy for eliminating dog-mediated rabies by 2030. AAS Open Res 2018. [DOI: 10.12688/aasopenres.12872.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: Rabies causes an estimated 59,000 human deaths annually. In Kenya, rabies was first reported in a dog in 1912, with the first human case reported in 1928. Here we examine retrospective rabies data in Kenya for the period 1912 – 2017 and describe the spatial and temporal patterns of rabies occurrence in the country. Additionally, we detail Kenya’s strategy for the elimination of dog-mediated human rabies by 2030. Methods: Data on submitted samples and confirmed cases in humans, domestic animals and wildlife were obtained from Kenya’s Directorate of Veterinary Services. These data were associated with the geographical regions where the samples originated, and temporal and spatial trends examined. Results: Between 1912 and the mid 1970’s, rabies spread across Kenya gradually, with fewer than 50 cases reported per year and less than half of the 47 counties affected. Following an outbreak in the mid 1970’s, rabies spread rapidly to more than 85% of counties, with a 4 fold increase in the percent positivity of samples submitted and number of confirmed rabies cases. Since 1958, 7,584 samples from domestic animals (93%), wildlife (5%), and humans (2%) were tested. Over two-thirds of all rabies cases came from six counties, all in close proximity to veterinary diagnostic laboratories, highlighting a limitation of passive surveillance. Conclusions: Compulsory annual dog vaccinations between 1950’s and the early 1970’s slowed rabies spread. The rapid spread with peak rabies cases in the 1980’s coincided with implementation of structural adjustment programs privatizing the veterinary sector leading to breakdown of rabies control programs. To eliminate human deaths from rabies by 2030, Kenya is implementing a 15-year step-wise strategy based on three pillars: a) mass dog vaccination, b) provision of post-exposure prophylaxis and public awareness and c) improved surveillance for rabies in dogs and humans with prompt responses to rabies outbreaks.
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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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9
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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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10
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Moreno-Torres KI, Pomeroy LW, Moritz M, Saville W, Wolfe B, Garabed R. Host species heterogeneity in the epidemiology of Nesopora caninum. PLoS One 2017; 12:e0183900. [PMID: 28850580 PMCID: PMC5574622 DOI: 10.1371/journal.pone.0183900] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/14/2017] [Indexed: 11/18/2022] Open
Abstract
Pathogen transmission across species drives disease emergence; however, mechanisms by which multi-host pathogens cross species boundaries are not well identified. This knowledge gap prevents integrated and targeted control in an epidemiologically continuous ecosystem. Our goal is to describe the impact of host species heterogeneity on the epidemiology of Neospora caninum circulating between livestock and wildlife in southeastern Ohio. We collected biological samples from Père David’s deer (Elaphurus davidianus) located at an outdoor wildlife conservation center; from cattle raised at farms adjacent to the center; and from wild white-tailed deer that roamed across farm and center boundaries. We designed nested infectious disease models of competing hypotheses about transmission and used collected data to fit the models, thereby estimating important immunological and transmission quantities which describe the species-specific contribution to the persistence of this pathogen in the community. We applied these data and models to suggest appropriate species-specific disease control methods. Results show that immunity in cattle and Pére David’s deer wanes over time, while in white-tailed deer immunity appears to be lifelong. Transmission quantities for cattle were estimated at values below the threshold for an outbreak (Rt < 1), meaning that chains of transmission are not maintained within this population and infections must occur due to reintroduction from an outside source. Pére David’s deer and white-tailed deer both could maintain continuous chains of transmission within their group (Rt > 1). Therefore, we propose that control of contact with outside sources will be useful for disease control in cattle; boosting immunity with vaccines might be an avenue to prevent infection in cattle and Père David’s deer. White-tailed deer are a potential maintenance host for infection and require further study to determine optimal control methods. Community-level investigations like this allow us to better evaluate heterogeneities in transmission processes that ultimately guide targeted control.
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Affiliation(s)
- Karla I. Moreno-Torres
- The Ohio State University, Department of Veterinary Preventive Medicine, Columbus, Ohio, United States of America
- * E-mail:
| | - Laura W. Pomeroy
- The Ohio State University, Department of Veterinary Preventive Medicine, Columbus, Ohio, United States of America
| | - Mark Moritz
- The Ohio State University, Department of Anthropology, Columbus, Ohio, United States of America
| | - William Saville
- The Ohio State University, Department of Veterinary Preventive Medicine, Columbus, Ohio, United States of America
| | - Barbara Wolfe
- Morris Animal Foundation, Denver, Colorado, United States of America
| | - Rebecca Garabed
- The Ohio State University, Department of Veterinary Preventive Medicine, Columbus, Ohio, United States of America
- The Ohio State University, Public Health Preparedness for Infectious Diseases Program, Columbus, Ohio, United States of America
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11
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Ecology and Demography of Free-Roaming Domestic Dogs in Rural Villages near Serengeti National Park in Tanzania. PLoS One 2016; 11:e0167092. [PMID: 27893866 PMCID: PMC5125679 DOI: 10.1371/journal.pone.0167092] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/07/2016] [Indexed: 12/24/2022] Open
Abstract
Free-roaming dogs (Canis lupus familiaris) are of public health and conservation concern because of their potential to transmit diseases, such as rabies, to both people and wildlife. Understanding domestic dog population dynamics and how they could potentially be impacted by interventions, such as rabies vaccination, is vital for such disease control efforts. For four years, we measured demographic data on 2,649 free-roaming domestic dogs in four rural villages in Tanzania: two villages with and two without a rabies vaccination campaign. We examined the effects of body condition, sex, age and village on survivorship and reproduction. Furthermore, we compared sources of mortality among villages. We found that adult dogs (>12mos) had higher survival than puppies in all villages. We observed a male-biased sex ratio across all age classes. Overall survival in one non-vaccination village was lower than in the other three villages, all of which had similar survival probabilities. In all villages, dogs in poor body condition had lower survival than dogs in ideal body condition. Sickness and spotted hyena (Crocuta crocuta) predation were the two main causes of dog death. Within vaccination villages, vaccinated dogs had higher survivorship than unvaccinated dogs. Dog population growth, however, was similar in all the villages suggesting village characteristics and ownership practices likely have a greater impact on overall dog population dynamics than vaccination. Free-roaming domestic dogs in rural communities exist in the context of their human owners as well as the surrounding wildlife. Our results did not reveal a clear effect of vaccination programs on domestic dog population dynamics. An investigation of the role of dogs and their care within these communities could provide additional insight for planning and implementing rabies control measures such as mass dog vaccination.
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12
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Fenton A, Streicker DG, Petchey OL, Pedersen AB. Are All Hosts Created Equal? Partitioning Host Species Contributions to Parasite Persistence in Multihost Communities. Am Nat 2015; 186:610-22. [PMID: 26655774 DOI: 10.1086/683173] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Many parasites circulate endemically within communities of multiple host species. To understand disease persistence within these communities, it is essential to know the contribution each host species makes to parasite transmission and maintenance. However, quantifying those contributions is challenging. We present a conceptual framework for classifying multihost sharing, based on key thresholds for parasite persistence. We then develop a generalized technique to quantify each species' contribution to parasite persistence, allowing natural systems to be located within the framework. We illustrate this approach using data on gastrointestinal parasites circulating within rodent communities and show that, although many parasites infect several host species, parasite persistence is often driven by just one host species. In some cases, however, parasites require multiple host species for maintenance. Our approach provides a quantitative method for differentiating these cases using minimal reliance on system-specific parameters, enabling informed decisions about parasite management within poorly understood multihost communities.
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Affiliation(s)
- Andy Fenton
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, United Kingdom
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13
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Brunker K, Marston DA, Horton DL, Cleaveland S, Fooks AR, Kazwala R, Ngeleja C, Lembo T, Sambo M, Mtema ZJ, Sikana L, Wilkie G, Biek R, Hampson K. Elucidating the phylodynamics of endemic rabies virus in eastern Africa using whole-genome sequencing. Virus Evol 2015; 1:vev011. [PMID: 27774283 PMCID: PMC5014479 DOI: 10.1093/ve/vev011] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Many of the pathogens perceived to pose the greatest risk to humans are viral zoonoses, responsible for a range of emerging and endemic infectious diseases. Phylogeography is a useful tool to understand the processes that give rise to spatial patterns and drive dynamics in virus populations. Increasingly, whole-genome information is being used to uncover these patterns, but the limits of phylogenetic resolution that can be achieved with this are unclear. Here, whole-genome variation was used to uncover fine-scale population structure in endemic canine rabies virus circulating in Tanzania. This is the first whole-genome population study of rabies virus and the first comprehensive phylogenetic analysis of rabies virus in East Africa, providing important insights into rabies transmission in an endemic system. In addition, sub-continental scale patterns of population structure were identified using partial gene data and used to determine population structure at larger spatial scales in Africa. While rabies virus has a defined spatial structure at large scales, increasingly frequent levels of admixture were observed at regional and local levels. Discrete phylogeographic analysis revealed long-distance dispersal within Tanzania, which could be attributed to human-mediated movement, and we found evidence of multiple persistent, co-circulating lineages at a very local scale in a single district, despite on-going mass dog vaccination campaigns. This may reflect the wider endemic circulation of these lineages over several decades alongside increased admixture due to human-mediated introductions. These data indicate that successful rabies control in Tanzania could be established at a national level, since most dispersal appears to be restricted within the confines of country borders but some coordination with neighbouring countries may be required to limit transboundary movements. Evidence of complex patterns of rabies circulation within Tanzania necessitates the use of whole-genome sequencing to delineate finer scale population structure that can that can guide interventions, such as the spatial scale and design of dog vaccination campaigns and dog movement controls to achieve and maintain freedom from disease.
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Affiliation(s)
- Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow G12 8QQ, UK; Animal and Plant Health Agency, Weybridge, Woodham Lane, KT15 3NB, UK
| | - Denise A Marston
- Animal and Plant Health Agency, Weybridge, Woodham Lane, KT15 3NB, UK
| | - Daniel L Horton
- Animal and Plant Health Agency, Weybridge, Woodham Lane, KT15 3NB, UK; School of Veterinary Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Sarah Cleaveland
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow G12 8QQ, UK
| | - Anthony R Fooks
- Animal and Plant Health Agency, Weybridge, Woodham Lane, KT15 3NB, UK
| | - Rudovick Kazwala
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, United Republic of Tanzania
| | - Chanasa Ngeleja
- Tanzania Veterinary Laboratory Agency, Dar es Salaam, United Republic of Tanzania, Temeke Veterinary, Mandela Road, P.O. BOX 9254
| | - Tiziana Lembo
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow G12 8QQ, UK
| | - Maganga Sambo
- Ifakara Health Institute, Ifakara, United Republic of Tanzania, P.O. Box 53
| | - Zacharia J Mtema
- Ifakara Health Institute, Ifakara, United Republic of Tanzania, P.O. Box 53
| | - Lwitiko Sikana
- Ifakara Health Institute, Ifakara, United Republic of Tanzania, P.O. Box 53
| | - Gavin Wilkie
- MRC Centre for Virus Research, University of Glasgow, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow G12 8QQ, UK
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow G12 8QQ, UK
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14
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Collapse of amphibian communities due to an introduced Ranavirus. Curr Biol 2014; 24:2586-91. [PMID: 25438946 DOI: 10.1016/j.cub.2014.09.028] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/13/2014] [Accepted: 09/09/2014] [Indexed: 11/22/2022]
Abstract
The emergence of infectious diseases with a broad host range can have a dramatic impact on entire communities and has become one of the main threats to biodiversity. Here, we report the simultaneous exploitation of entire communities of potential hosts with associated severe declines following invasion by a novel viral pathogen. We found two phylogenetically related, highly virulent viruses (genus Ranavirus, family Iridoviridae) causing mass mortality in multiple, diverse amphibian hosts in northern Spain, as well as a third, relatively avirulent virus. We document host declines in multiple species at multiple sites in the region. Our work reveals a group of pathogens that seem to have preexisting capacity to infect and evade immunity in multiple diverse and novel hosts, and that are exerting massive impacts on host communities. This report provides an exceptional record of host population trends being tracked in real time following emergence of a wildlife disease and a striking example of a novel, generalist pathogen repeatedly crossing the species barrier with catastrophic consequences at the level of host communities.
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15
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Zeynalova S, Shikhiyev M, Aliyeva T, Ismayilova R, Wise E, Abdullayev R, Asadov K, Rustamova S, Quliyev F, Whatmore AM, Marshall ES, Fooks AR, Horton DL. Epidemiological characteristics of human and animal rabies in Azerbaijan. Zoonoses Public Health 2014; 62:111-8. [PMID: 24845953 DOI: 10.1111/zph.12119] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Indexed: 12/25/2022]
Abstract
The Caucasus is a region of geopolitical importance, in the gateway between Europe and Asia. This geographical location makes the region equally important in the epidemiology and control of transboundary infectious diseases such as rabies. Azerbaijan is the largest country in the Caucasus, and although rabies is notifiable and considered endemic, there is little information on the burden of human and animal rabies. Here, we describe a cross-disciplinary international collaboration aimed at improving rabies control in Azerbaijan. Partial nucleoprotein gene sequences were obtained from animal rabies cases for comparison with those from surrounding areas. Reported human and animal rabies cases between 2000 and 2010 were also reviewed and analysed by region and year. Comparison of rabies virus strains circulating in Azerbaijan demonstrates more than one lineage of rabies virus circulating concurrently in Azerbaijan and illustrates the need for further sample collection and characterization. Officially reported rabies data showed an increase in human and animal rabies cases, and an increase in animal bites requiring provision of post-exposure prophylaxis, since 2006. This is despite apparently consistent levels of dog vaccination and culling of stray dogs.
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Affiliation(s)
- S Zeynalova
- Republican Veterinary Laboratory, Baku, Azerbaijan
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16
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Kuzmina NA, Lemey P, Kuzmin IV, Mayes BC, Ellison JA, Orciari LA, Hightower D, Taylor ST, Rupprecht CE. The phylogeography and spatiotemporal spread of south-central skunk rabies virus. PLoS One 2013; 8:e82348. [PMID: 24312657 PMCID: PMC3849458 DOI: 10.1371/journal.pone.0082348] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 10/25/2013] [Indexed: 12/25/2022] Open
Abstract
The south-central skunk rabies virus (SCSK) is the most broadly distributed terrestrial viral lineage in North America. Skunk rabies has not been efficiently targeted by oral vaccination campaigns and represents a natural system of pathogen invasion, yielding insights to rabies emergence. In the present study we reconstructed spatiotemporal spread of SCSK in the whole territory of its circulation using a combination of Bayesian methods. The analysis based on 241 glycoprotein gene sequences demonstrated that SCSK is much more divergent phylogenetically than was appreciated previously. According to our analyses the SCSK originated in the territory of Texas ~170 years ago, and spread geographically during the following decades. The wavefront velocity in the northward direction was significantly greater than in the eastward and westward directions. Rivers (except the Mississippi River and Rio Grande River) did not constitute significant barriers for epizootic spread, in contrast to deserts and mountains. The mean dispersal rate of skunk rabies was lower than that of the raccoon and fox rabies. Viral lineages circulate in their areas with limited evidence of geographic spread during decades. However, spatiotemporal reconstruction shows that after a long period of stability the dispersal rate and wavefront velocity of SCSK are increasing. Our results indicate that there is a need to develop control measures for SCSK, and suggest how such measure can be implemented most efficiently. Our approach can be extrapolated to other rabies reservoirs and used as a tool for investigation of epizootic patterns and planning interventions towards disease elimination.
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Affiliation(s)
- Natalia A. Kuzmina
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Philippe Lemey
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Ivan V. Kuzmin
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Bonny C. Mayes
- Zoonosis Control Branch, Texas Department of State Health Services, Austin, Texas, United States of America
| | - James A. Ellison
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Lillian A. Orciari
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Dillon Hightower
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Steven T. Taylor
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Charles E. Rupprecht
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Department of Epidemiology and Public Health, Ross University School of Veterinary Medicine, Basseterre, St. Kitts, West Indies
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17
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Berentsen AR, Dunbar MR, Becker MS, M'soka J, Droge E, Sakuya NM, Matandiko W, McRobb R, Hanlon CA. Rabies, canine distemper, and canine parvovirus exposure in large carnivore communities from two Zambian ecosystems. Vector Borne Zoonotic Dis 2013; 13:643-9. [PMID: 23805791 DOI: 10.1089/vbz.2012.1233] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Disease transmission within and among wild and domestic carnivores can have significant impacts on populations, particularly for threatened and endangered species. We used serology to evaluate potential exposure to rabies virus, canine distemper virus (CDV), and canine parvovirus (CPV) for populations of African lions (Panthera leo), African wild dogs (Lycaon pictus), and spotted hyenas (Crocuta crocuta) in Zambia's South Luangwa National Park (SLNP) and Liuwa Plain National Park (LPNP) as well as community lands bordering these areas. In addition, domestic dogs in the study region were evaluated for exposure to CDV and rabies. We provide the first comprehensive disease exposure data for these species in these ecosystems. Twenty-one lions, 20 hyenas, 13 wild dogs, and 38 domestic dogs were sampled across both regions from 2009 to 2011. Laboratory results show 10.5% of domestic dogs, 5.0% of hyenas, and 7.7% of wild dogs sampled were positive for CDV exposure. All lions were negative. Exposure to CPV was 10.0% and 4.8% for hyenas and lions, respectively. All wild dogs were negative, and domestic dogs were not tested due to insufficient serum samples. All species sampled were negative for rabies virus neutralizing antibodies except lions. Forty percent of lions tested positive for rabies virus neutralizing antibodies. Because these lions appeared clinically healthy, this finding is consistent with seroconversion following exposure to rabies antigen. To our knowledge, this finding represents the first ever documentation of rabies virus neutralizing antibodies consistent with rabies exposure that did not lead to clinical disease in free-ranging African lions from this region. With ever-increasing human pressure on these ecosystems, understanding disease transmission dynamics is essential for proper management and conservation of these carnivore species.
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Affiliation(s)
- Are R Berentsen
- 1 U.S. Department of Agriculture, Wildlife Services, National Wildlife Research Center , Fort Collins, Colorado
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18
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Streicker DG, Fenton A, Pedersen AB. Differential sources of host species heterogeneity influence the transmission and control of multihost parasites. Ecol Lett 2013; 16:975-84. [PMID: 23714379 PMCID: PMC4282463 DOI: 10.1111/ele.12122] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 03/05/2013] [Accepted: 04/07/2013] [Indexed: 11/29/2022]
Abstract
Controlling parasites that infect multiple host species often requires targeting single species that dominate transmission. Yet, it is rarely recognised that such ‘key hosts’ can arise through disparate mechanisms, potentially requiring different approaches for control. We identify three distinct, but not mutually exclusive, processes that underlie host species heterogeneity: infection prevalence, population abundance and infectiousness. We construct a theoretical framework to isolate the role of each process from ecological data and to explore the outcome of different control approaches. Applying this framework to data on 11 gastrointestinal parasites in small mammal communities across the eastern United States reveals variation not only in the magnitude of transmission asymmetries among host species but also in the processes driving heterogeneity. These differences influence the efficiency by which different control strategies reduce transmission. Identifying and tailoring interventions to a specific type of key host may therefore enable more effective management of multihost parasites.
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Silva SR, Katz ISS, Mori E, Carnieli P, Vieira LFP, Batista HBCR, Chaves LB, Scheffer KC. Biotechnology advances: a perspective on the diagnosis and research of Rabies Virus. Biologicals 2013; 41:217-23. [PMID: 23683880 DOI: 10.1016/j.biologicals.2013.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 04/05/2013] [Accepted: 04/06/2013] [Indexed: 11/15/2022] Open
Abstract
Rabies is a widespread zoonotic disease responsible for approximately 55,000 human deaths/year. The direct fluorescent antibody test (DFAT) and the mouse inoculation test (MIT) used for rabies diagnosis, have high sensitivity and specificity, but are expensive and time-consuming. These disadvantages and the identification of new strains of the virus encourage the use of new techniques that are rapid, sensitive, specific and economical for the detection and research of the Rabies Virus (RABV). Real-time RT-PCR, phylogeographic analysis, proteomic assays and DNA recombinant technology have been used in research laboratories. Together, these techniques are effective on samples with low virus titers in the study of molecular epidemiology or in the identification of new disease markers, thus improving the performance of biological assays. In this context, modern advances in molecular technology are now beginning to complement more traditional approaches and promise to revolutionize the diagnosis of rabies. This brief review presents some of the recent molecular tools used for RABV analysis, with emphasis on rabies diagnosis and research.
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Affiliation(s)
- S R Silva
- Pasteur Institute, São Paulo, Brazil.
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Integrating the landscape epidemiology and genetics of RNA viruses: rabies in domestic dogs as a model. Parasitology 2012; 139:1899-913. [PMID: 22814380 PMCID: PMC3526958 DOI: 10.1017/s003118201200090x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Landscape epidemiology and landscape genetics combine advances in molecular techniques, spatial analyses and epidemiological models to generate a more real-world understanding of infectious disease dynamics and provide powerful new tools for the study of RNA viruses. Using dog rabies as a model we have identified how key questions regarding viral spread and persistence can be addressed using a combination of these techniques. In contrast to wildlife rabies, investigations into the landscape epidemiology of domestic dog rabies requires more detailed assessment of the role of humans in disease spread, including the incorporation of anthropogenic landscape features, human movements and socio-cultural factors into spatial models. In particular, identifying and quantifying the influence of anthropogenic features on pathogen spread and measuring the permeability of dispersal barriers are important considerations for planning control strategies, and may differ according to cultural, social and geographical variation across countries or continents. Challenges for dog rabies research include the development of metapopulation models and transmission networks using genetic information to uncover potential source/sink dynamics and identify the main routes of viral dissemination. Information generated from a landscape genetics approach will facilitate spatially strategic control programmes that accommodate for heterogeneities in the landscape and therefore utilise resources in the most cost-effective way. This can include the efficient placement of vaccine barriers, surveillance points and adaptive management for large-scale control programmes.
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Marston DA, Horton DL, Ngeleja C, Hampson K, McElhinney LM, Banyard AC, Haydon D, Cleaveland S, Rupprecht CE, Bigambo M, Fooks AR, Lembo T. Ikoma lyssavirus, highly divergent novel lyssavirus in an African civet. Emerg Infect Dis 2012; 18:664-7. [PMID: 22469151 PMCID: PMC3309678 DOI: 10.3201/eid1804.111553] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Evidence in support of a novel lyssavirus was obtained from brain samples of an African civet in Tanzania. Results of phylogenetic analysis of nucleoprotein gene sequences from representative Lyssavirus species and this novel lyssavirus provided strong empirical evidence that this is a new lyssavirus species, designated Ikoma lyssavirus.
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Affiliation(s)
- Denise A Marston
- Animal Health and Veterinary Laboratories Agency, Addlestone, UK
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Beyer HL, Hampson K, Lembo T, Cleaveland S, Kaare M, Haydon DT. The implications of metapopulation dynamics on the design of vaccination campaigns. Vaccine 2012; 30:1014-22. [PMID: 22198516 DOI: 10.1016/j.vaccine.2011.12.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 12/07/2011] [Accepted: 12/09/2011] [Indexed: 12/25/2022]
Abstract
Control programmes for vaccine preventable diseases typically operate under logistic constraints such as limited resources and in spatially structured populations where the assumption of homogeneous mixing is invalid. It is unclear, therefore, how to maximise the effectiveness of campaigns in such populations. We investigate how to deploy vaccine in metapopulations by comparing the effectiveness of alternative vaccination strategies on reducing disease occurrence (presence/absence), using canine rabies as a model system, and a domestic dog population within a Tanzanian district divided into sub-populations corresponding to villages. We use patch-occupancy models to quantify the contribution of sub-populations to disease occurrence ("risk") and model allocation strategies for a limited number of vaccine doses that prioritize villages based on their size, risk, or the reduction in risk for the entire population that would result from vaccination. We assume that a maximum of 70% of susceptible individuals in a village could be vaccinated, and that only susceptible dogs are vaccinated. The most effective strategy maximised the reduction in risk of the entire population, and was up to 62% more effective than the other strategies. Large, single-pulse campaigns provided the greatest short-term protection, but higher frequencies of smaller pulses were more effective at reducing long-term disease occurrence. Vaccine allocation on a per-dose basis was substantially more effective than a per-village strategy, indicating that operational constraints can reduce control effectiveness. The spatial distribution and abundance of hosts have an important influence on disease dynamics and these results demonstrate that metapopulation models can be used to substantially improve the effectiveness of vaccination campaigns and optimize the allocation of limited control resources.
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Affiliation(s)
- Hawthorne L Beyer
- The Boyd Orr Centre for Population and Ecosystem Health, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom.
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Höner OP, Wachter B, Goller KV, Hofer H, Runyoro V, Thierer D, Fyumagwa RD, Müller T, East ML. The impact of a pathogenic bacterium on a social carnivore population. J Anim Ecol 2012; 81:36-46. [PMID: 21631499 PMCID: PMC7194172 DOI: 10.1111/j.1365-2656.2011.01873.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
1. The long-term ecological impact of pathogens on group-living, large mammal populations is largely unknown. We evaluated the impact of a pathogenic bacterium, Streptococcus equi ruminatorum, and other key ecological factors on the dynamics of the spotted hyena Crocuta crocuta population in the Ngorongoro Crater, Tanzania. 2. We compared key demographic parameters during two years when external signs of bacterial infection were prevalent ('outbreak') and periods of five years before and after the outbreak when such signs were absent or rare. We also tested for density dependence and calculated the basic reproductive rate R(0) of the bacterium. 3. During the five pre-outbreak years, the mean annual hyena mortality rate was 0.088, and annual population growth was relatively high (13.6%). During the outbreak, mortality increased by 78% to a rate of 0.156, resulting in an annual population decline of 4.3%. After the outbreak, population size increased moderately (5.1%) during the first three post-outbreak years before resuming a growth similar to pre-outbreak levels (13.9%). We found no evidence that these demographic changes were driven by density dependence or other ecological factors. 4. Most hyenas showed signs of infection when prey abundance in their territory was low. During the outbreak, mortality increased among adult males and yearlings, but not among adult females - the socially dominant group members. These results suggest that infection and mortality were modulated by factors linked to low social status and poor nutrition. During the outbreak, we estimated R(0) for the bacterium to be 2.7, indicating relatively fast transmission. 5. Our results suggest that the short-term 'top-down' impact of S. equi ruminatorum during the outbreak was driven by 'bottom-up' effects on nutritionally disadvantaged age-sex classes, whereas the longer-term post-outbreak reduction in population growth was caused by poor survival of juveniles during the outbreak and subsequent poor recruitment of breeding females. These results suggest synergistic effects of 'bottom-up' and 'top-down' processes on host population dynamics.
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Affiliation(s)
- Oliver P Höner
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany.
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Molecular epidemiology and a loop-mediated isothermal amplification method for diagnosis of infection with rabies virus in Zambia. Virus Res 2011; 163:160-8. [PMID: 21930165 DOI: 10.1016/j.virusres.2011.09.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 09/02/2011] [Accepted: 09/04/2011] [Indexed: 11/23/2022]
Abstract
The National Livestock Epidemiology and Information Center (NALEIC) in Zambia reported over 132 cases of canine rabies diagnosed by the direct fluorescent antibody test (DFAT) from 2004 to 2009. In this study, the lineage of rabies virus (RABV) in Zambia was determined by phylogenetic analysis of the nucleoprotein (N) and glycoprotein (G) gene sequences. Total RNA was extracted from 87-DFAT brain specimens out of which only 35 (40%) were positive on nested reverse transcription polymerase chain reaction (RT-PCR) for each gene, and 26 being positive for both genes. Positive specimens for the N (n=33) and G (n=35) genes were used for phylogenetic analysis. Phylogenetic analysis of the N gene showed two phylogenetic clusters in Zambia belonging to the Africa 1b lineage present in eastern and southern Africa. While one cluster exclusively comprised Zambian strains, the other was more heterogeneous regarding the RABV origins and included strains from Tanzania, Mozambique and Zambia. Phylogenetic analysis of the G gene revealed similar RABV strains in different hosts and regions of Zambia. We designed primers for reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay from the consensus sequence of the N gene in an attempt to improve the molecular diagnosis of RABV in Zambia. The specificity and reproducibility of the RT-LAMP assay was confirmed with actual clinical specimens. Therefore, the RT-LAMP assay presented in this study may prove to be useful for routine diagnosis of rabies in Zambia.
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Abstract
Numerous bat species have been identified as important reservoirs of zoonotic viral pathogens. Rabies and rabies-related viruses constitute one of the most important viral zoonoses and pose a significant threat to public health across the globe. Whereas rabies virus (RABV) appears to be restricted to bats of the New World, related lyssavirus species have not been detected in the Americas and have only been detected in bat populations across Africa, Eurasia, and Australia. Currently, 11 distinct species of lyssavirus have been identified, 10 of which have been isolated from bat species and all of which appear to be able to cause encephalitis consistent with that seen with RABV infection of humans. In contrast, whereas lyssaviruses are apparently able to cause clinical disease in bats, it appears that these lyssaviruses may also be able to circulate within bat populations in the absence of clinical disease. This feature of these highly encephalitic viruses, alongside many other aspects of lyssavirus infection in bats, is poorly understood. Here, we review what is known of the complex relationship between bats and lyssaviruses, detailing both natural and experimental infections of these viruses in both chiropteran and nonchiropteran models. We also discuss potential mechanisms of virus excretion, transmission both to conspecifics and spill-over of virus into nonvolant species, and mechanisms of maintenance within bat populations. Importantly, we review the significance of neutralizing antibodies reported within bat populations and discuss the potential mechanisms by which highly neurovirulent viruses such as the lyssaviruses are able to infect bat species in the absence of clinical disease.
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Affiliation(s)
- Ashley C Banyard
- Rabies and Wildlife Zoonoses Group, Department of Virology, Veterinary Laboratories Agency, Weybridge, New Haw, Addlestone, Surrey, United Kingdom
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26
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Abstract
Rabies virus (RABV) is enzootic throughout Africa, with the domestic dog (Canis familiaris) being the principal vector. Dog rabies is estimated to cause 24,000 human deaths per year in Africa, however, this estimate is still considered to be conservative. Two sub-Saharan African RABV lineages have been detected in West Africa. Lineage 2 is present throughout West Africa, whereas Africa 1a dominates in northern and eastern Africa, but has been detected in Nigeria and Gabon, and Africa 1b was previously absent from West Africa. We confirmed the presence of RABV in a cohort of 76 brain samples obtained from rabid animals in Ghana collected over an eighteen-month period (2007-2009). Phylogenetic analysis of the sequences obtained confirmed all viruses to be RABV, belonging to lineages previously detected in sub-Saharan Africa. However, unlike earlier reported studies that suggested a single lineage (Africa 2) circulates in West Africa, we identified viruses belonging to the Africa 2 lineage and both Africa 1 (a and b) sub-lineages. Phylogeographic Bayesian Markov chain Monte Carlo analysis of a 405 bp fragment of the RABV nucleoprotein gene from the 76 new sequences derived from Ghanaian animals suggest that within the Africa 2 lineage three clades co-circulate with their origins in other West African countries. Africa 1a is probably a western extension of a clade circulating in central Africa and the Africa 1b virus a probable recent introduction from eastern Africa. We also developed and tested a novel reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of RABV in African laboratories. This RT-LAMP was shown to detect both Africa 1 and 2 viruses, including its adaptation to a lateral flow device format for product visualization. These data suggest that RABV epidemiology is more complex than previously thought in West Africa and that there have been repeated introductions of RABV into Ghana. This analysis highlights the potential problems of individual developing nations implementing rabies control programmes in the absence of a regional programme.
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Lembo T, Hampson K, Kaare MT, Ernest E, Knobel D, Kazwala RR, Haydon DT, Cleaveland S. The feasibility of canine rabies elimination in Africa: dispelling doubts with data. PLoS Negl Trop Dis 2010; 4:e626. [PMID: 20186330 PMCID: PMC2826407 DOI: 10.1371/journal.pntd.0000626] [Citation(s) in RCA: 212] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 01/22/2010] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Canine rabies causes many thousands of human deaths every year in Africa, and continues to increase throughout much of the continent. METHODOLOGY/PRINCIPAL FINDINGS This paper identifies four common reasons given for the lack of effective canine rabies control in Africa: (a) a low priority given for disease control as a result of lack of awareness of the rabies burden; (b) epidemiological constraints such as uncertainties about the required levels of vaccination coverage and the possibility of sustained cycles of infection in wildlife; (c) operational constraints including accessibility of dogs for vaccination and insufficient knowledge of dog population sizes for planning of vaccination campaigns; and (d) limited resources for implementation of rabies surveillance and control. We address each of these issues in turn, presenting data from field studies and modelling approaches used in Tanzania, including burden of disease evaluations, detailed epidemiological studies, operational data from vaccination campaigns in different demographic and ecological settings, and economic analyses of the cost-effectiveness of dog vaccination for human rabies prevention. CONCLUSIONS/SIGNIFICANCE We conclude that there are no insurmountable problems to canine rabies control in most of Africa; that elimination of canine rabies is epidemiologically and practically feasible through mass vaccination of domestic dogs; and that domestic dog vaccination provides a cost-effective approach to the prevention and elimination of human rabies deaths.
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Affiliation(s)
- Tiziana Lembo
- Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, United Kingdom.
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Hirano S, Itou T, Shibuya H, Kashiwazaki Y, Sakai T. Molecular epidemiology of rabies virus isolates in Uganda. Virus Res 2010; 147:135-8. [DOI: 10.1016/j.virusres.2009.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 10/05/2009] [Accepted: 10/06/2009] [Indexed: 11/25/2022]
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Hampson K, Dushoff J, Cleaveland S, Haydon DT, Kaare M, Packer C, Dobson A. Transmission dynamics and prospects for the elimination of canine rabies. PLoS Biol 2009; 7:e53. [PMID: 19278295 PMCID: PMC2653555 DOI: 10.1371/journal.pbio.1000053] [Citation(s) in RCA: 309] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 01/21/2009] [Indexed: 01/10/2023] Open
Abstract
Rabies has been eliminated from domestic dog populations in Western Europe and North America, but continues to kill many thousands of people throughout Africa and Asia every year. A quantitative understanding of transmission dynamics in domestic dog populations provides critical information to assess whether global elimination of canine rabies is possible. We report extensive observations of individual rabid animals in Tanzania and generate a uniquely detailed analysis of transmission biology, which explains important epidemiological features, including the level of variation in epidemic trajectories. We found that the basic reproductive number for rabies, R0, is very low in our study area in rural Africa (approximately 1.2) and throughout its historic global range (<2). This finding provides strong support for the feasibility of controlling endemic canine rabies by vaccination, even near wildlife areas with large wild carnivore populations. However, we show that rapid turnover of domestic dog populations has been a major obstacle to successful control in developing countries, thus regular pulse vaccinations will be required to maintain population-level immunity between campaigns. Nonetheless our analyses suggest that with sustained, international commitment, global elimination of rabies from domestic dog populations, the most dangerous vector to humans, is a realistic goal.
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Affiliation(s)
- Katie Hampson
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
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Abstract
The dynamics of infectious disease spread depend on host population contact structure. Heterogeneities in this contact structure can arise from various forms of demographic and spatial phenomena. Craft et al. (this issue) have constructed an exploratory simulation model of the spread of canine distemper virus through a multispecies carnivore community. Each species in this community is modelled with a contact structure reflecting host social organization, ranging behaviour, and likely interspecific contact patterns. The results are used to infer the possible roles of different species in determining the observed spatio-temporal incidence of canine distemper virus in Serengeti lions during an outbreak in 1993-94.
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Affiliation(s)
- Daniel T Haydon
- Division of Environmental and Evolutionary Biology, University of Glasgow, Glasgow.
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Hampson K, Dobson A, Kaare M, Dushoff J, Magoto M, Sindoya E, Cleaveland S. Rabies exposures, post-exposure prophylaxis and deaths in a region of endemic canine rabies. PLoS Negl Trop Dis 2008; 2:e339. [PMID: 19030223 PMCID: PMC2582685 DOI: 10.1371/journal.pntd.0000339] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 10/31/2008] [Indexed: 11/18/2022] Open
Abstract
Background Thousands of human deaths from rabies occur annually despite the availability of effective vaccines following exposure, and for disease control in the animal reservoir. Our aim was to assess risk factors associated with exposure and to determine why human deaths from endemic canine rabies still occur. Methods and Findings Contact tracing was used to gather data on rabies exposures, post-exposure prophylaxis (PEP) delivered and deaths in two rural districts in northwestern Tanzania from 2002 to 2006. Data on risk factors and the propensity to seek and complete courses of PEP was collected using questionnaires. Exposures varied from 6–141/100,000 per year. Risk of exposure to rabies was greater in an area with agropastoralist communities (and larger domestic dog populations) than an area with pastoralist communities. Children were at greater risk than adults of being exposed to rabies and of developing clinical signs. PEP dramatically reduced the risk of developing rabies (odds ratio [OR] 17.33, 95% confidence interval [CI] 6.39–60.83) and when PEP was not delivered the risks were higher in the pastoralist than the agro-pastoralist area (OR 6.12, 95% CI 2.60–14.58). Low socioeconomic class and distance to medical facilities lengthened delays before PEP delivery. Over 20% of rabies-exposed individuals did not seek medical treatment and were not documented in official records and <65% received PEP. Animal bite injury records were an accurate indicator of rabies exposure incidence. Conclusions Insufficient knowledge about rabies dangers and prevention, particularly prompt PEP, but also wound management, was the main cause of rabies deaths. Education, particularly in poor and marginalized communities, but also for medical and veterinary workers, would prevent future deaths. Thousands of human deaths from rabies occur annually despite availability of effective vaccines for humans following exposure, and for disease control in domestic dog populations. We established a 5-year contact-tracing study in northwest Tanzania to investigate risk factors associated with rabies exposure and to determine why human deaths from canine rabies still occur. We found that children were at greater risk of being bitten and of developing rabies than adults and that incidence of bites by suspected rabid animals was higher in an area with larger domestic dog populations. A large proportion (>20%) of those bitten by rabid animals are not recorded in official records because they do not seek post-exposure prophylaxis (PEP), which is crucial for preventing the onset of rabies. Of those that seek medical attention, a significant proportion do not receive PEP because of the expense or because of hospital shortages; and victims who are poorer, and who live further from medical facilities, typically experience greater delays before obtaining PEP. Our work highlights the need to raise awareness about rabies dangers and prevention, particularly prompt PEP, but also wound management. We outline practical recommendations to prevent future deaths, stressing the importance of education, particularly in poor and marginalized communities, as well as for medical and veterinary workers.
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Affiliation(s)
- Katie Hampson
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom.
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Lembo T, Hampson K, Haydon DT, Craft M, Dobson A, Dushoff J, Ernest E, Hoare R, Kaare M, Mlengeya T, Mentzel C, Cleaveland S. Exploring reservoir dynamics: a case study of rabies in the Serengeti ecosystem. J Appl Ecol 2008; 45:1246-1257. [PMID: 22427710 DOI: 10.1111/j.1365-2664.2008.01468.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Knowledge of infection reservoir dynamics is critical for effective disease control, but identifying reservoirs of multi-host pathogens is challenging. Here, we synthesize several lines of evidence to investigate rabies reservoirs in complex carnivore communities of the Serengeti ecological region in northwest Tanzania, where the disease has been confirmed in 12 carnivore species.Long-term monitoring data suggest that rabies persists in high-density domestic dog Canis familiaris populations (> 11 dogs km(-2)) and occurs less frequently in lower-density (< 5 dogs km(-2)) populations and only sporadically in wild carnivores.Genetic data show that a single rabies virus variant belonging to the group of southern Africa canid-associated viruses (Africa 1b) circulates among a range of species, with no evidence of species-specific virus-host associations.Within-species transmission was more frequently inferred from high-resolution epidemiological data than between-species transmission. Incidence patterns indicate that spill-over of rabies from domestic dog populations sometimes initiates short-lived chains of transmission in other carnivores.Synthesis and applications. The balance of evidence suggests that the reservoir of rabies in the Serengeti ecosystem is a complex multi-host community where domestic dogs are the only population essential for persistence, although other carnivores contribute to the reservoir as non-maintenance populations. Control programmes that target domestic dog populations should therefore have the greatest impact on reducing the risk of infection in all other species including humans, livestock and endangered wildlife populations, but transmission in other species may increase the level of vaccination coverage in domestic dog populations necessary to eliminate rabies.
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Affiliation(s)
- Tiziana Lembo
- Centre for Tropical Veterinary Medicine, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK
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Fooks AR. Rabies awareness. Vet Rec 2007. [DOI: 10.1136/vr.161.20.704-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Anthony R. Fooks
- Rabies and Wildlife Zoonoses Group; Veterinary Laboratories Agency - Weybridge; WHO Collaborating Centre for the Characterisation of Rabies and Rabies-related Viruses; New Haw Addlestone Surrey KT15 3NB
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