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Wang D, Yang X, Ren Z, Hu B, Zhao H, Yang K, Shi P, Zhang Z, Feng Q, Nawenja CV, Obanda V, Robert K, Nalikka B, Waruhiu CN, Ochola GO, Onyuok SO, Ochieng H, Li B, Zhu Y, Si H, Yin J, Kristiansen K, Jin X, Xu X, Xiao M, Agwanda B, Ommeh S, Li J, Shi ZL. Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation. Microbiome 2024; 12:72. [PMID: 38600530 PMCID: PMC11005217 DOI: 10.1186/s40168-024-01782-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/26/2024] [Indexed: 04/12/2024]
Abstract
BACKGROUND Zoonotic viruses cause substantial public health and socioeconomic problems worldwide. Understanding how viruses evolve and spread within and among wildlife species is a critical step when aiming for proactive identification of viral threats to prevent future pandemics. Despite the many proposed factors influencing viral diversity, the genomic diversity and structure of viral communities in East Africa are largely unknown. RESULTS Using 38.3 Tb of metatranscriptomic data obtained via ultradeep sequencing, we screened vertebrate-associated viromes from 844 bats and 250 rodents from Kenya and Uganda collected from the wild. The 251 vertebrate-associated viral genomes of bats (212) and rodents (39) revealed the vast diversity, host-related variability, and high geographic specificity of viruses in East Africa. Among the surveyed viral families, Coronaviridae and Circoviridae showed low host specificity, high conservation of replication-associated proteins, high divergence among viral entry proteins, and frequent recombination. Despite major dispersal limitations, recurrent mutations, cocirculation, and occasional gene flow contribute to the high local diversity of viral genomes. CONCLUSIONS The present study not only shows the landscape of bat and rodent viromes in this zoonotic hotspot but also reveals genomic signatures driven by the evolution and dispersal of the viral community, laying solid groundwork for future proactive surveillance of emerging zoonotic pathogens in wildlife. Video Abstract.
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Affiliation(s)
- Daxi Wang
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China
| | - Xinglou Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Hubei Jiangxia Lab, Wuhan, 430071, China
| | - Zirui Ren
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Hailong Zhao
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China
| | - Kaixin Yang
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China
| | - Peibo Shi
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China
| | - Zhipeng Zhang
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China
| | - Qikai Feng
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China
| | - Carol Vannesa Nawenja
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Vincent Obanda
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | - Kityo Robert
- Department of Zoology, Entomology and Fisheries Sciences, School of BioSciences, Makerere University, Kampala, Uganda
| | - Betty Nalikka
- Department of Zoology, Entomology and Fisheries Sciences, School of BioSciences, Makerere University, Kampala, Uganda
| | - Cecilia Njeri Waruhiu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Griphin Ochieng Ochola
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Mammalogy Section, National Museums of Kenya, Nairobi, Kenya
| | - Samson Omondi Onyuok
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Mammalogy Section, National Museums of Kenya, Nairobi, Kenya
| | - Harold Ochieng
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Mammalogy Section, National Museums of Kenya, Nairobi, Kenya
| | - Bei Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yan Zhu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Haorui Si
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | | | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | - Xun Xu
- BGI Research, Shenzhen, 518083, China
| | - Minfeng Xiao
- BGI Research, Shenzhen, 518083, China.
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China.
| | - Bernard Agwanda
- Mammalogy Section, National Museums of Kenya, Nairobi, Kenya.
| | - Sheila Ommeh
- Center for Animal Science, Queensland Alliance for Agriculture & Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Junhua Li
- BGI Research, Shenzhen, 518083, China.
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI Research, Shenzhen, 518083, China.
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
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Snider MH, Helgen KM, Young HS, Agwanda B, Schuttler S, Titcomb GC, Branch D, Dommain R, Kays R. Shifting mammal communities and declining species richness along an elevational gradient on Mount Kenya. Ecol Evol 2024; 14:e11151. [PMID: 38601855 PMCID: PMC11004549 DOI: 10.1002/ece3.11151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 02/23/2024] [Accepted: 03/01/2024] [Indexed: 04/12/2024] Open
Abstract
Conservation areas encompassing elevation gradients are biodiversity hotspots because they contain a wide range of habitat types in a relatively small space. Studies of biodiversity patterns along elevation gradients, mostly on small mammal or bird species, have documented a peak in diversity at mid elevations. Here, we report on a field study of medium and large mammals to examine the impact of elevation, habitat type, and gross primary productivity on community structure. Species richness was observed using a camera trap transect with 219 sites situated across different habitat types from 2329 to 4657 m above the sea level on the western slope of Mt Kenya, the second highest mountain in Africa. We found that the lowest elevation natural habitats had the highest species richness and relative abundance and that both metrics decreased steadily as elevation increased, paralleling changes in gross primary productivity, and supporting the energy richness hypothesis. We found no evidence for the mid-domain effect on species diversity. The lowest elevation degraded Agro-Forestry lands adjacent to the National Park had high activity of domestic animals and reduced diversity and abundance of native species. The biggest difference in community structure was between protected and unprotected areas, followed by more subtle stepwise differences between habitats at different elevations. Large carnivore species remained relatively consistent but dominant herbivore species shifted along the elevation gradient. There was some habitat specialization and turnover in species, such that the elevation gradient predicts a high diversity of species, demonstrating the high conservation return for protecting mountain ecosystems for biodiversity conservation.
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Affiliation(s)
- Matthew H. Snider
- Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | | | - Hillary S. Young
- Department of Ecology, Evolution and Marine BiologyUniversity of California Santa BarbaraSanta BarbaraCaliforniaUSA
| | | | | | - Georgia C. Titcomb
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Douglas Branch
- Department of Applied SciencesUniversity of the West of EnglandBristolUK
| | - René Dommain
- Earth Observatory of SingaporeNanyang Technological UniversitySingaporeSingapore
- National Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
| | - Roland Kays
- Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNorth CarolinaUSA
- North Carolina Museum of Natural SciencesRaleighNorth CarolinaUSA
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3
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Lwande OW, Näslund J, Sjödin A, Lantto R, Luande VN, Bucht G, Ahlm C, Agwanda B, Obanda V, Evander M. Novel strains of Culex flavivirus and Hubei chryso-like virus 1 from the Anopheles mosquito in western Kenya. Virus Res 2024; 339:199266. [PMID: 37944758 PMCID: PMC10682293 DOI: 10.1016/j.virusres.2023.199266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
Surveillance of mosquito vectors is critical for early detection, prevention and control of vector borne diseases. In this study we used advanced molecular tools, such as DNA barcoding in combination with novel sequencing technologies to discover new and already known viruses in genetically identified mosquito species. Mosquitoes were captured using BG sentinel traps in Western Kenya during May and July 2019, and homogenized individually before pooled into groups of ten mosquitoes. The pools and individual samples were then used for molecular analysis and to infect cell cultures. Of a total of fifty-four (54) 10-pools, thirteen (13) showed cytopathic effect (CPE) on VeroB4 cells, eighteen (18) showed CPE on C6/36 cells. Eight (8) 10-pools out of the 31 CPE positive pools showed CPE on both VeroB4 and C6/36 cells. When using reverse transcriptase polymerase chain reaction (RT-PCR), Sanger sequencing and Twist Comprehensive Viral Research Panel (CVRP) (Twist Biosciences), all pools were found negative by RT-PCR when using genus specific primers targeting alphaviruses, orthobunyaviruses and virus specific primers towards o'nyong-nyong virus, chikungunya virus and Sindbis virus (previously reported to circulate in the region). Interestingly, five pools were RT-PCR positive for flavivirus. Two of the RT-PCR positive pools showed CPE on both VeroB4 and C6/36 cells, two pools showed CPE on C6/36 cells alone and one pool on VeroB4 cells only. Fifty individual mosquito homogenates from the five RT-PCR positive 10-pools were analyzed further for flavivirus RNA. Of these, 19 out of the 50 individual mosquito homogenates indicated the presence of flavivirus RNA. Barcoding of the flavivirus positive mosquitoes revealed the mosquito species as Aedes aegypti (1), Mansonia uniformis (6), Anopheles spp (3), Culex pipiens (5), Culex spp (1), Coquilletidia metallica (2) and Culex quinquefasciatus (1). Of the 19 flavivirus positive individual mosquitoes, five (5) virus positive homogenates were sequenced. Genome sequences of two viruses were completed. One was identified as the single-stranded RNA Culex flavivirus and the other as the double-stranded RNA Hubei chryso-like virus 1. Both viruses were found in the same Anopheles spp. homogenate extracted from a sample that showed CPE on both VeroB4 and C6/36 cells. The detection of both viruses in a single mosquito homogenate indicated coinfection. Phylogenetic analyses suggested that the Culex flavivirus sequence detected was closely related to a Culex flavivirus isolated from Uganda in 2008. All four Hubei chryso-like virus 1 segments clusters closely to Hubei chryso-like virus 1 strains isolated in Australia, China and USA. Two novel strains of insect-specific viruses in Anopheles mosquitoes were detected and characterized.
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Affiliation(s)
- Olivia Wesula Lwande
- Department of Clinical Microbiology, Umeå University, Umeå 901-85, Sweden; Umeå Centre for Microbial Research, Umeå University, Umeå 901-87, Sweden.
| | - Jonas Näslund
- Swedish Defence Research Agency, CBRN, Defence and Security, Umeå 901 82, Sweden
| | - Andreas Sjödin
- Swedish Defence Research Agency, CBRN, Defence and Security, Umeå 901 82, Sweden
| | - Rebecca Lantto
- Department of Clinical Microbiology, Umeå University, Umeå 901-85, Sweden
| | | | - Göran Bucht
- Department of Clinical Microbiology, Umeå University, Umeå 901-85, Sweden
| | - Clas Ahlm
- Department of Clinical Microbiology, Umeå University, Umeå 901-85, Sweden; Umeå Centre for Microbial Research, Umeå University, Umeå 901-87, Sweden
| | - Bernard Agwanda
- Mammalogy Section, National Museums of Kenya, Nairobi 40658-00100, Kenya
| | - Vincent Obanda
- Department of Research Permitting and Compliance Wildlife Research and Training Institute, Naivasha 842-20117, Kenya
| | - Magnus Evander
- Department of Clinical Microbiology, Umeå University, Umeå 901-85, Sweden; Umeå Centre for Microbial Research, Umeå University, Umeå 901-87, Sweden
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4
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Chen C, Granados A, Brodie JF, Kays R, Davies TJ, Liu R, Fisher JT, Ahumada J, McShea W, Sheil D, Mohd-Azlan J, Agwanda B, Andrianarisoa MH, Appleton RD, Bitariho R, Espinosa S, Grigione MM, Helgen KM, Hubbard A, Hurtado CM, Jansen PA, Jiang X, Jones A, Kalies EL, Kiebou-Opepa C, Li X, Lima MGM, Meyer E, Miller AB, Murphy T, Piana R, Quan RC, Rota CT, Rovero F, Santos F, Schuttler S, Uduman A, van Bommel JK, Young H, Burton AC. Combining camera trap surveys and IUCN range maps to improve knowledge of species distributions. Conserv Biol 2023:e14221. [PMID: 37937455 DOI: 10.1111/cobi.14221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 10/05/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023]
Abstract
Reliable maps of species distributions are fundamental for biodiversity research and conservation. The International Union for Conservation of Nature (IUCN) range maps are widely recognized as authoritative representations of species' geographic limits, yet they might not always align with actual occurrence data. In recent area of habitat (AOH) maps, areas that are not habitat have been removed from IUCN ranges to reduce commission errors, but their concordance with actual species occurrence also remains untested. We tested concordance between occurrences recorded in camera trap surveys and predicted occurrences from the IUCN and AOH maps for 510 medium- to large-bodied mammalian species in 80 camera trap sampling areas. Across all areas, cameras detected only 39% of species expected to occur based on IUCN ranges and AOH maps; 85% of the IUCN only mismatches occurred within 200 km of range edges. Only 4% of species occurrences were detected by cameras outside IUCN ranges. The probability of mismatches between cameras and the IUCN range was significantly higher for smaller-bodied mammals and habitat specialists in the Neotropics and Indomalaya and in areas with shorter canopy forests. Our findings suggest that range and AOH maps rarely underrepresent areas where species occur, but they may more often overrepresent ranges by including areas where a species may be absent, particularly at range edges. We suggest that combining range maps with data from ground-based biodiversity sensors, such as camera traps, provides a richer knowledge base for conservation mapping and planning.
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Affiliation(s)
- Cheng Chen
- Department of Forest Resources Management, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alys Granados
- Department of Forest Resources Management, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Felidae Conservation Fund, Mill Valley, California, USA
| | - Jedediah F Brodie
- Division of Biological Sciences and Wildlife Biology Program, University of Montana, Missoula, Montana, USA
| | - Roland Kays
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | - T Jonathan Davies
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Runzhe Liu
- Department of Forest Resources Management, University of British Columbia, Vancouver, British Columbia, Canada
- Biology Department, Lund University, Lund, Sweden
| | - Jason T Fisher
- School of Environmental Studies, University of Victoria, Victoria, British Columbia, Canada
| | - Jorge Ahumada
- Moore Center for Science, Conservation International, Arlington, Virginia, USA
| | - William McShea
- Conservation Ecology Center, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, Virginia, USA
| | - Douglas Sheil
- Forest Ecology and Forest Management Group, Wageningen University & Research, Wageningen, The Netherlands
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, Akershus, Norway
- Center for International Forestry Research, Bogor, Indonesia
| | - Jayasilan Mohd-Azlan
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia
| | | | | | - Robyn D Appleton
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Spectacled Bear Conservation Society Peru, Lambayeque, Peru
| | - Robert Bitariho
- Institute of Tropical Forest Conservation, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Santiago Espinosa
- Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
- Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | | | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Andy Hubbard
- National Park Service, Sonoran Desert Network, Tucson, Arizona, USA
| | - Cindy M Hurtado
- Department of Forest Resources Management, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick A Jansen
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Wageningen, The Netherlands
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Alex Jones
- Campus Natural Reserves, University of California, Santa Cruz, Santa Cruz, California, USA
| | | | | | - Xueyou Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Erik Meyer
- Sequoia & Kings Canyon National Parks, Three Rivers, California, USA
| | - Anna B Miller
- Department of Environment and Society, Institute of Outdoor Recreation and Tourism, Utah State University, Logan, Utah, USA
| | - Thomas Murphy
- Department of Anthropology, Edmonds College, Lynwood, Washington, USA
| | - Renzo Piana
- Spectacled Bear Conservation Society Peru, Lambayeque, Peru
| | - Rui-Chang Quan
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Christopher T Rota
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia, USA
| | - Francesco Rovero
- Department of Biology, University of Florence, Trento, Italy
- MUSE - Museo delle Scienze, Trento, Italy
| | | | | | - Aisha Uduman
- Department of Forest Resources Management, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joanna Klees van Bommel
- Department of Forest Resources Management, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hilary Young
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA
| | - A Cole Burton
- Department of Forest Resources Management, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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5
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Ochola GO, Li B, Obanda V, Ommeh S, Ochieng H, Yang XL, Onyuok SO, Shi ZL, Agwanda B, Hu B. Discovery of novel DNA viruses in small mammals from Kenya. Virol Sin 2022; 37:491-502. [PMID: 35680114 PMCID: PMC9437603 DOI: 10.1016/j.virs.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/17/2022] [Indexed: 11/29/2022] Open
Abstract
Emergence and re-emergence of infectious diseases of wildlife origin have led pre-emptive pathogen surveillances in animals to be a public health priority. Rodents and shrews are among the most numerically abundant vertebrate taxa and are known as natural hosts of important zoonotic viruses. Many surveillance programs focused more on RNA viruses. In comparison, much less is known about DNA viruses harbored by these small mammals. To fill this knowledge gap, tissue specimens of 232 animals including 226 rodents, five shrews and one hedgehog were collected from 5 counties in Kenya and tested for the presence of DNA viruses belonging to 7 viral families by PCR. Diverse DNA sequences of adenoviruses, adeno-associated viruses, herpesviruses and polyomaviruses were detected. Phylogenetic analyses revealed that most of these viruses showed distinction from previously described viruses and formed new clusters. Furthermore, this is the first report of the discovery and full-length genome characterization of a polyomavirus in Lemniscomys species. This novel polyomavirus, named LsPyV KY187, has less than 60% amino acid sequence identity to the most related Glis glis polyomavirus 1 and Sciurus carolinensis polyomavirus 1 in both large and small T-antigen proteins and thus can be putatively allocated to a novel species within Betapolyomavirus. Our findings help us better understand the genetic diversity of DNA viruses in rodent and shrew populations in Kenya and provide new insights into the evolution of those DNA viruses in their small mammal reservoirs. It demonstrates the necessity of ongoing pathogen discovery studies targeting rodent-borne viruses in East Africa.
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Affiliation(s)
- Griphin Ochieng Ochola
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; Mammalogy Section, National Museums of Kenya, Nairobi, 40658-00100, Kenya; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bei Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Vincent Obanda
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, 40241-00100, Kenya
| | - Sheila Ommeh
- Institute of Biotechnology Research, Jomo Kenyatta University of Science and Technology, Nairobi, 62000-00200, Kenya
| | - Harold Ochieng
- Mammalogy Section, National Museums of Kenya, Nairobi, 40658-00100, Kenya
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Samson Omondi Onyuok
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Mammalogy Section, National Museums of Kenya, Nairobi, 40658-00100, Kenya
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Bernard Agwanda
- Mammalogy Section, National Museums of Kenya, Nairobi, 40658-00100, Kenya.
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
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6
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Chen C, Brodie JF, Kays R, Davies TJ, Liu R, Fisher JT, Ahumada J, McShea W, Sheil D, Agwanda B, Andrianarisoa MH, Appleton RD, Bitariho R, Espinosa S, Grigione MM, Helgen KM, Hubbard A, Hurtado CM, Jansen PA, Jiang X, Jones A, Kalies EL, Kiebou‐Opepa C, Li X, Lima MGM, Meyer E, Miller AB, Murphy T, Piana R, Quan R, Rota CT, Rovero F, Santos F, Schuttler S, Uduman A, Bommel JK, Young H, Burton AC. Global camera trap synthesis highlights the importance of protected areas in maintaining mammal diversity. Conserv Lett 2022. [DOI: 10.1111/conl.12865] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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7
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Ogada S, Otecko NO, Moraa Kennedy G, Musina J, Agwanda B, Obanda V, Lichoti J, Peng M, Ommeh S. Demographic history and genetic diversity of wild African harlequin quail ( Coturnix delegorguei delegorguei) populations of Kenya. Ecol Evol 2021; 11:18562-18574. [PMID: 35003693 PMCID: PMC8717324 DOI: 10.1002/ece3.8458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 11/24/2022] Open
Abstract
Hunting wild African harlequin quails (Coturnix delegorguei delegorguei) using traditional methods in Western Kenya has been ongoing for generations, yet their genetic diversity and evolutionary history are largely unknown. In this study, the genetic variation and demographic history of wild African harlequin quails were assessed using a 347bp mitochondrial DNA (mtDNA) control region fragment and 119,339 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS) data. Genetic diversity analyses revealed that the genetic variation in wild African harlequin quails was predominantly among individuals than populations. Demographic analyses indicated a signal of rapid demographic expansion, and the estimated time since population expansion was found to be 150,000-350,000 years ago, corresponding to around the Pliocene-Pleistocene boundary. A gradual decline in their effective population size was also observed, which raised concerns about their conservation status. These results provide the first account of the genetic diversity of wild African harlequin quails of Siaya, thereby creating a helpful foundation in their biodiversity conservation.
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Affiliation(s)
- Stephen Ogada
- Institute For Biotechnology ResearchJomo Kenyatta University of Agriculture and TechnologyNairobiKenya
| | - Newton O. Otecko
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Sino‐Africa Joint Research CenterChinese Academy of SciencesNairobiKenya
| | - Grace Moraa Kennedy
- Institute For Biotechnology ResearchJomo Kenyatta University of Agriculture and TechnologyNairobiKenya
| | - John Musina
- Department of ZoologyNational Museums of KenyaNairobiKenya
| | | | - Vincent Obanda
- Department of Veterinary ServicesKenya Wildlife ServiceNairobiKenya
| | - Jacqueline Lichoti
- Central Veterinary Laboratories KabeteState Department of LivestockMinistry of Agriculture, Livestock and FisheriesNairobiKenya
| | - Min‐Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Sino‐Africa Joint Research CenterChinese Academy of SciencesNairobiKenya
| | - Sheila Ommeh
- Institute For Biotechnology ResearchJomo Kenyatta University of Agriculture and TechnologyNairobiKenya
- Department of ZoologyNational Museums of KenyaNairobiKenya
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8
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Zhang Y, Hu B, Agwanda B, Fang Y, Wang J, Kuria S, Yang J, Masika M, Tang S, Lichoti J, Fan Z, Shi Z, Ommeh S, Wang H, Deng F, Shen S. Viromes and surveys of RNA viruses in camel-derived ticks revealing transmission patterns of novel tick-borne viral pathogens in Kenya. Emerg Microbes Infect 2021; 10:1975-1987. [PMID: 34570681 PMCID: PMC8525980 DOI: 10.1080/22221751.2021.1986428] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Tick-borne viruses (TBVs) capable of transmitting between ticks and hosts have been increasingly recognized as a global public health concern. In this study, Hyalomma ticks and serum samples from camels were collected using recorded sampling correlations in eastern Kenya. Viromes of pooled ticks were profiled by metagenomic sequencing, revealing a diverse community of viruses related to at least 11 families. Five highly abundant viruses, including three novel viruses (Iftin tick virus, Mbalambala tick virus [MATV], and Bangali torovirus [BanToV]) and new strains of previously identified viruses (Bole tick virus 4 [BLTV4] and Liman tick virus [LMTV]), were characterized in terms of genome sequences, organizations, and phylogeny, and their molecular prevalence was investigated in individual ticks. Moreover, viremia and antibody responses to these viruses have been investigated in camels. MATV, BLTV4, LMTV, and BanToV were identified as viral pathogens that can potentially cause zoonotic diseases. The transmission patterns of these viruses were summarized, suggesting three different types according to the sampling relationships between viral RNA-positive ticks and camels positive for viral RNA and/or antibodies. They also revealed the frequent transmission of BanToV and limited but effective transmission of other viruses between ticks and camels. Furthermore, follow-up surveys on TBVs from tick, animal, and human samples with definite sampling relationships are suggested. The findings revealed substantial threats from the emerging TBVs and may guide the prevention and control of TBV-related zoonotic diseases in Kenya and in other African countries.
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Affiliation(s)
- You Zhang
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Yaohui Fang
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jun Wang
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Stephen Kuria
- Institute For Biotechnology Research (IBR), Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Juan Yang
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Moses Masika
- Department of Medical Microbiology, University of Nairobi Nairobi, Kenya
| | - Shuang Tang
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Jacqueline Lichoti
- Directorate of Veterinary Services, State Department of Livestock, Ministry of Agriculture, Livestock, Fisheries and Irrigation, Nairobi, Kenya
| | - Zhaojun Fan
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Zhengli Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Sheila Ommeh
- Institute For Biotechnology Research (IBR), Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Hualin Wang
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Fei Deng
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Shu Shen
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
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9
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Obanda V, Agwanda B, Blanco-Penedo I, Mwangi IA, King'ori E, Omondi GP, Ahlm C, Evander M, Lwande OW. Livestock Presence Influences the Seroprevalence of Crimean Congo Hemorrhagic Fever Virus on Sympatric Wildlife in Kenya. Vector Borne Zoonotic Dis 2021; 21:809-816. [PMID: 34559011 DOI: 10.1089/vbz.2021.0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Crimean Congo Hemorrhagic Fever (CCHF) is an emerging tick-borne zoonotic viral disease with the potential of causing public health emergencies. However, less is known about the role of wildlife and livestock in spreading the virus. Therefore, we aimed to assess how the interactions between African buffalo (Syncerus caffer) and cattle may influence the seroprevalence of CCHF across livestock-wildlife management systems in Kenya. The study included archived sera samples from buffalo and cattle from wildlife only habitats (Lake Nakuru National Park and Solio conservancy), open wildlife-livestock integrated habitats (Maasai Mara ecosystem and Meru National Park), and closed wildlife-livestock habitats (Ol Pejeta Conservancy) in Kenya. We analyzed 191 buffalo and 139 cattle sera using IDvet multispecies, double-antigen IgG enzyme-linked immunosorbent assay (ELISA). The seroprevalence toward Crimean Congo hemorrhagic fever virus (CCHFV) was significantly higher for buffalo compared to cattle (75.3% and 28.1%, respectively, p < 0.001). We obtained the highest seroprevalence among buffalo of 92.1% in closed wildlife only systems compared to 28.8% and 46.1% prevalence in closed-integrated and open-integrated systems, respectively. The regression coefficients were all negative for cattle compared to buffalo in both closed-integrated and open-integrated compared to wildlife only system. Our results show that CCHFV circulates among the diverse animal community in Kenya in spatially disconnected foci. The habitat overlap between cattle and buffalo makes cattle a "bridge species" or superspreader host for CCHFV and increases transmission risks to humans. The effect of animal management system on prevalence is depended on tick control on the cattle and not the animal per se. We conclude that buffalo, a host with a longer life span than livestock, is a reservoir and may serve as a sentinel population for longitudinal surveillance of CCHFV.
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Affiliation(s)
- Vincent Obanda
- Department of Veterinary Services, Kenya Wildlife Service, Nairobi, Kenya
| | - Bernard Agwanda
- Department of Mammalogy, National Museums of Kenya, Nairobi, Kenya
| | - Isabel Blanco-Penedo
- Unit of Veterinary Epidemiology, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Irene Ann Mwangi
- Department of Medical Microbiology, Kenya AIDs Vaccine Initiative Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Edward King'ori
- Department of Veterinary Services, Kenya Wildlife Service, Nairobi, Kenya
| | - George P Omondi
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota, USA.,Ahadi Veterinary Resource Center, Nairobi, Kenya
| | - Clas Ahlm
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Magnus Evander
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
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10
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Shen QK, Peng MS, Adeola AC, Kui L, Duan S, Miao YW, Eltayeb NM, Lichoti JK, Otecko NO, Strillacci MG, Gorla E, Bagnato A, Charles OS, Sanke OJ, Dawuda PM, Okeyoyin AO, Musina J, Njoroge P, Agwanda B, Kusza S, Nanaei HA, Pedar R, Xu MM, Du Y, Nneji LM, Murphy RW, Wang MS, Esmailizadeh A, Dong Y, Ommeh SC, Zhang YP. Erratum to: Genomic analyses unveil helmeted guinea fowl (Numida meleagris) domestication in West Africa. Genome Biol Evol 2021; 13:6355925. [PMID: 34417609 PMCID: PMC8379371 DOI: 10.1093/gbe/evab174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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11
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Zeng L, Liu HQ, Tu XL, Ji CM, Gou X, Esmailizadeh A, Wang S, Wang MS, Wang MC, Li XL, Charati H, Adeola AC, Moshood Adedokun RA, Oladipo O, Olaogun SC, Sanke OJ, Godwin F M, Cecily Ommeh S, Agwanda B, Kasiiti Lichoti J, Han JL, Zheng HK, Wang CF, Zhang YP, Frantz LAF, Wu DD. Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation. Zool Res 2021; 42:450-460. [PMID: 34156172 PMCID: PMC8317180 DOI: 10.24272/j.issn.2095-8137.2021.095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Over the last several hundred years, donkeys have adapted to high-altitude conditions on the Tibetan Plateau. Interestingly, the kiang, a closely related equid species, also inhabits this region. Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau. Here, we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred. We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys (including 24 from the Tibetan Plateau). Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs. In Tibetan donkeys, however, another gene, i.e., EGLN1, was likely involved in their adaptation to high altitude. In addition, admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys. Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau, as well as the existence of a closely related species already adapted to hypoxia, Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.
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Affiliation(s)
- Lin Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Xiao-Long Tu
- Annoroad Gene Tech. (Beijing) Co., Ltd., Beijing 100176, China
| | - Chang-Mian Ji
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.,Biomarker Technologies Corporation, Beijing 101300, China
| | - Xiao Gou
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | | | - Xiao-Long Li
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Hadi Charati
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | | | - Olatunbosun Oladipo
- Federal College of Animal Health and Production Technology, Moor-Plantation, Ibadan, Nigeria
| | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo 660221, Nigeria
| | | | - Sheila Cecily Ommeh
- Institute For Biotechnology Research Jomo Kenyatta University of Agriculture and Technology, Nairobi 62000-00200, Kenya.,Department of Zoology, National Museums of Kenya, Nairobi 40658-00100, Kenya
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi 40658-00100, Kenya
| | - Jacqueline Kasiiti Lichoti
- State Department of Livestock, Ministry of Agriculture, Livestock, Fisheries and Irrigation, Nairobi, Kenya
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Hong-Kun Zheng
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Chang-Fa Wang
- Equus Laboratory, Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong 250131, China.,Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, Shandong 252059, China. E-mail:
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK. E-mail:
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Institute of Three-River-Source National Park, Chinese Academy of Sciences, Qinghai 810008, China. E-mail:
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12
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Shen QK, Peng MS, Adeola AC, Kui L, Duan S, Miao YW, Eltayeb NM, Lichoti JK, Otecko NO, Strillacci MG, Gorla E, Bagnato A, Charles OS, Sanke OJ, Dawuda PM, Okeyoyin AO, Musina J, Njoroge P, Agwanda B, Kusza S, Nanaei HA, Pedar R, Xu MM, Du Y, Nneji LM, Murphy RW, Wang MS, Esmailizadeh A, Dong Y, Ommeh SC, Zhang YP. Genomic Analyses of Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa. Genome Biol Evol 2021; 13:6261762. [PMID: 34009300 PMCID: PMC8214406 DOI: 10.1093/gbe/evab090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 12/22/2022] Open
Abstract
Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long- and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.
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Affiliation(s)
- Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Ling Kui
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Yong-Wang Miao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Nada M Eltayeb
- Department of Animal breeding and Reproduction Technology, College of Animal Production, University of Bahri, Khartoum, Sudan
| | - Jacqueline K Lichoti
- State Department of Livestock, Ministry of Agriculture Livestock Fisheries and Irrigation, Nairobi, Kenya
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | | | - Erica Gorla
- Department of Veterinary Medicine, Università degli Studi di Milano, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Italy
| | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Philip M Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture, Makurdi, Nigeria
| | - Agboola O Okeyoyin
- National Park Service Headquarter, Federal Capital Territory, Abuja, Nigeria
| | - John Musina
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Peter Njoroge
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, Hungary
| | | | - Rana Pedar
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Iran
| | - Ming-Min Xu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yuan Du
- Nowbio Biotechnology Company, Kunming, China
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya
| | - Robert W Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, California, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, California, USA
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Iran
| | - Yang Dong
- College of Biological Big Data, Yunnan Agriculture University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.,Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Sheila C Ommeh
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya.,Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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13
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Weinstein SB, Malanga KN, Agwanda B, Maldonado JE, Dearing MD. The secret social lives of African crested rats, Lophiomys imhausi. J Mammal 2020; 101:1680-1691. [PMID: 33510587 DOI: 10.1093/jmammal/gyaa127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
The crested rat, Lophiomys imhausi, is the only mammal known to sequester plant toxins. Found in eastern Africa, this large rodent is thought to defend against predation by coating specialized hairs along its sides with cardenolide toxins from the poison arrow tree, Acokanthera schimperi. To better understand the ecology of this unusual poisonous mammal, we used camera traps, livetrapping, and captive behavioral observations, to study L. imhausi in central Kenya. Although crested rats were rarely detected with camera traps, 25 individuals were caught in live traps, with estimated densities of up to 15 rats/km2 at one of nine trapping sites. Trapping records and behavioral observations suggest that L. imhausi live in male-female pairs, with juveniles that might exhibit delayed dispersal. We observed chewing of A. schimperi and/or anointing in 10 of 22 individuals, confirming the previous poison sequestration observation. We monitored crested rat activity using cameras and found that chewing on A. schimperi and cardenolide exposure had no effect on feeding, movement, or total activity. One crested rat also fed on milkweed (Gomphocarpus physocarpus; Gentaniales: Apocynaceae), but did not anoint with this cardenolide containing plant. This observation, combined with L. imhausi's selective use of A. schimperi, suggests the potential for use of alternative poison sources. This research provides novel insight into the ecology of L. imhausi, while also suggesting that more field observations, feeding trials, and chemical analyses are needed to understand their behavior and physiology. Furthermore, their complex social interactions, slow life history, and fragmented populations suggest that L. imhausi could be at risk of decline.
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Affiliation(s)
- Sara B Weinstein
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA.,Mpala Research Centre, Nanyuki, Kenya
| | - Katrina Nyawira Malanga
- Mpala Research Centre, Nanyuki, Kenya.,Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | | | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA.,Department of Biology and Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | - M Denise Dearing
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
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14
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Amin R, Wacher T, Ogwoka B, Khayale C, Kariuki L, Agwanda B. Habitat use of the endangered golden‐rumped sengi
Rhynchocyon chrysopygus. Afr J Ecol 2020. [DOI: 10.1111/aje.12804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Rajan Amin
- Conservation Programmes Zoological Society of LondonRegent's Park London UK
| | - Tim Wacher
- Conservation Programmes Zoological Society of LondonRegent's Park London UK
| | | | | | | | - Bernard Agwanda
- Section of Mammalogy National Museums of Kenya Nairobi Kenya
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15
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Zhang W, Zheng XS, Agwanda B, Ommeh S, Zhao K, Lichoti J, Wang N, Chen J, Li B, Yang XL, Mani S, Ngeiywa KJ, Zhu Y, Hu B, Onyuok SO, Yan B, Anderson DE, Wang LF, Zhou P, Shi ZL. Serological evidence of MERS-CoV and HKU8-related CoV co-infection in Kenyan camels. Emerg Microbes Infect 2020; 8:1528-1534. [PMID: 31645223 PMCID: PMC6818114 DOI: 10.1080/22221751.2019.1679610] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Dromedary camels are important reservoir hosts of various coronaviruses, including Middle East respiratory syndrome coronavirus (MERS-CoV) that cause human infections. CoV genomes regularly undergo recombination during infection as observed in bat SARS-related CoVs. Here we report for the first time that only a small proportion of MERS-CoV receptor-binding domain positive (RBD) of spike protein positive camel sera in Kenya were also seropositive to MERS-CoV nucleocapsid (NP). In contrast, many of them contain antibodies against bat HKU8-related (HKU8r)-CoVs. Among 584 camel samples that were positive against MERS-CoV RBD, we found only 0.48 (8.22%) samples were also positive for NP. Furthermore, we found bat HKU8r-CoV NP antibody in 73 (12.5%) of the MERS-CoV RBD positive and NP negative samples, yet found only 3 (0.43%) of the HKU8r-CoV S1 antibody in the same samples. These findings may indicate co-infection with MERS-CoV and a HKU8r-CoV in camels. It may also raise the possibility of the circulation of a recombinant coronavirus virus with the spike of MERS-CoV and the NP of a HKU8r-CoV in Kenya. We failed to find molecular evidence of an HKU8r-CoV or a putative recombinant virus. Our findings should alert other investigators to look for molecular evidence of HKU8r-CoV or recombinants.
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Affiliation(s)
- Wei Zhang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Xiao-Shuang Zheng
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China.,University of Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya , Nairobi , Kenya
| | - Sheila Ommeh
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology , Nairobi , Kenya
| | - Kai Zhao
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China.,University of Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Jacqueline Lichoti
- Directorate of Veterinary Services, State Department of Livestock, Ministry of Agriculture , Livestock and Fisheries , Kenya
| | - Ning Wang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Jing Chen
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China.,University of Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Bei Li
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Shailendra Mani
- Programme in Emerging Infectious Diseases Duke-NUS Medical School , Singapore , Singapore
| | - Kisa-Juma Ngeiywa
- Directorate of Veterinary Services, State Department of Livestock, Ministry of Agriculture , Livestock and Fisheries , Kenya.,Kenya Camel Association , Nairobi , Kenya
| | - Yan Zhu
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Samson Omondi Onyuok
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Bing Yan
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases Duke-NUS Medical School , Singapore , Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases Duke-NUS Medical School , Singapore , Singapore
| | - Peng Zhou
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences , Wuhan , People's Republic of China
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16
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Onyuok SO, Hu B, Li B, Fan Y, Kering K, Ochola GO, Zheng XS, Obanda V, Ommeh S, Yang XL, Agwanda B, Shi ZL. Molecular Detection and Genetic Characterization of Novel RNA Viruses in Wild and Synanthropic Rodents and Shrews in Kenya. Front Microbiol 2019; 10:2696. [PMID: 31824465 PMCID: PMC6881279 DOI: 10.3389/fmicb.2019.02696] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
The majority of emerging and reemerging zoonotic viral pathogens are RNA viruses. Pathogen discovery programs of emerging infectious diseases (EIDs) in wildlife have implicated rodents and shrews as hosts of diverse human pathogens, such as hantaviruses, arenaviruses, paramyxoviruses, etc. Despite these threats, little is known about the diversity of viruses circulating among rodents and shrews in Kenya, meaning the risk of infectious disease outbreak from these small mammals could be oblivious. This study reports the first surveillance toward understanding the diversity of RNA viruses carried by rodents and shrews in areas of high-potential contact with humans in Kenya through molecular detection. A total of 617 samples comprising fecal, urine, and tissues from 138 rodents and 5 shrews were screened for eight different families of viruses using RT-PCR assays. The results highlight the presence of diverse astroviruses, paramyxoviruses, hepeviruses, and arenavirus, circulating in both wild and synanthropic Kenyan rodents and shrews. Most of the viruses detected in this study are novel strains and some belong to the families that contain important human viral pathogens. Notably, a novel arenavirus was detected in Grammomys macmillani, a rodent species newly identified to harbor arenavirus, and it potentially represent a novel arenavirus species. Our findings demonstrate the need for continued pathogen surveillance among these small mammals as well as among the vulnerable and exposed livestock and humans. This would help in development and implementation of effective preventive and control strategies on EIDs in countries with rich wildlife biodiversity like Kenya.
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Affiliation(s)
- Samson Omondi Onyuok
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,Mammalogy Section, National Museums of Kenya, Nairobi, Kenya.,University of Chinese Academy of Sciences, Beijing, China
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bei Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yi Fan
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Kelvin Kering
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Griphin Ochieng Ochola
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,Mammalogy Section, National Museums of Kenya, Nairobi, Kenya.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Shuang Zheng
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Vincent Obanda
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | - Sheila Ommeh
- Institute of Biotechnology Research, Jomo Kenyatta University of Science and Technology, Nairobi, Kenya
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bernard Agwanda
- Mammalogy Section, National Museums of Kenya, Nairobi, Kenya
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
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17
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Otecko NO, Ogali I, Ng'ang'a SI, Mauki DH, Ogada S, Moraa GK, Lichoti J, Agwanda B, Peng MS, Ommeh SC, Zhang YP. Phenotypic and morphometric differentiation of indigenous chickens from Kenya and other tropical countries augments perspectives for genetic resource improvement and conservation. Poult Sci 2019; 98:2747-2755. [PMID: 30850827 PMCID: PMC6591685 DOI: 10.3382/ps/pez097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 02/25/2019] [Indexed: 12/20/2022] Open
Abstract
Indigenous chickens at the Swahili coast and other traditional migratory corridors in Kenya represent important populations that are inconclusively characterized. Using a comprehensive dataset of Kenyan indigenous chickens and additional mined data of chickens from 8 African and 5 Asian countries, we performed univariate and multivariate assessments to uncover the underlying phenotypic and morphometric variability. Kenyan indigenous chickens expressed differentiation of several qualitative and quantitative traits, both among different counties in the Swahili coast, and among coastal, western, and northern migratory corridors. There was a substantial population stratification of these chickens, particularly distinctive clustering of chickens from Marsabit, Lamu, and Kilifi counties. The pooled dataset further clarified a closer phenotypic and morphometric proximity of chickens within different geographical regions. We additionally revealed a preponderance of bantam and rumpless traits to hot and humid locales, and feathered shanks to cooler regions. Currently, most chicken breeding programs in developing countries rely on phenotypic and morphometric properties. Hence, the high chicken diversity and population stratification observed in our study, possibly shaped by natural and artificial selective pressures, reveal opportunities for complementary phenotypic and genotypic assessments to identify resources for effective breed improvement and conservation strategies of indigenous chickens in the tropics.
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Affiliation(s)
- Newton O Otecko
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Sino-Africa Joint Research Center, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya
| | - Irene Ogali
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya.,Veterinary Research Institute, Kenya Agriculture and Livestock Research Organization, Nairobi 00200, Kenya
| | - Said I Ng'ang'a
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China
| | - David H Mauki
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China
| | - Stephen Ogada
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya.,Sino-Africa Joint Research Center, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya
| | - Grace K Moraa
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya.,Sino-Africa Joint Research Center, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya
| | - Jacqueline Lichoti
- Directorate of Veterinary Services, State Department of Livestock, Ministry of Agriculture, Livestock and Fisheries, Nairobi 00625, Kenya
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi 00100, Kenya
| | - Min-Shen Peng
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China
| | - Sheila C Ommeh
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya.,Sino-Africa Joint Research Center, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya
| | - Ya-Ping Zhang
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
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18
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Atoni E, Zhao L, Karungu S, Obanda V, Agwanda B, Xia H, Yuan Z. The discovery and global distribution of novel mosquito-associated viruses in the last decade (2007-2017). Rev Med Virol 2019; 29:e2079. [PMID: 31410931 DOI: 10.1002/rmv.2079] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 07/10/2019] [Accepted: 07/23/2019] [Indexed: 01/21/2023]
Abstract
In the last decade, virus hunting and discovery has gained pace. This achievement has been driven by three major factors: (a) advancements in sequencing technologies, (b) scaled-up routine arbovirus surveillance strategies, and (c) the "hunt" for emerging pathogens and novel viruses. Many novel viruses have been discovered from a myriad of hosts, vectors, and environmental samples. To help promote understanding of the global diversity and distribution of mosquito-associated viruses and facilitate future studies, we review mosquito-associated viruses discovered between years 2007 and 2017, across the world. In the analyzed period, novel mosquito-associated viruses belonging to 25 families and a general group of unclassified viruses were categorized. The top three discovered novel mosquito-associated viruses belonged to families Flaviviridae (n=32), Rhabdoviridae (n=16), and Peribunyaviridae (n=14). Also, 67 unclassified viruses were reported. Majority of these novel viruses were identified from Culex spp, Anopheles spp, Aedes spp, and Mansonia spp mosquitoes, respectively. Notably, the number of these discovered novels is not representative of intercontinental virus diversity but rather is influenced by the number of studies done in the study period. Some of these newly discovered mosquito-associated viruses have medical significance, either directly or indirectly. For instance, in the study period, 14 novel mosquito-borne viruses that infect mammalian cells in vitro were reported. These viruses pose a danger to the global health security on emerging viral diseases. On the other hand, some of the newly discovered insect specific viruses described herein have potential application as future biocontrol and vaccine agents against known pathogenic arboviruses. Overall, this review outlines the crucial role played by mosquitoes as viral vectors in the global virosphere.
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Affiliation(s)
- Evans Atoni
- Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lu Zhao
- Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Samuel Karungu
- Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Vincent Obanda
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | | | - Han Xia
- Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zhiming Yuan
- Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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19
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Karungu S, Atoni E, Ogalo J, Mwaliko C, Agwanda B, Yuan Z, Hu X. Mosquitoes of Etiological Concern in Kenya and Possible Control Strategies. Insects 2019; 10:E173. [PMID: 31208124 PMCID: PMC6627689 DOI: 10.3390/insects10060173] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 12/21/2022]
Abstract
Kenya is among the most affected tropical countries with pathogen transmitting Culicidae vectors. For decades, insect vectors have contributed to the emergence and distribution of viral and parasitic pathogens. Outbreaks and diseases have a great impact on a country's economy, as resources that would otherwise be used for developmental projects are redirected to curb hospitalization cases and manage outbreaks. Infected invasive mosquito species have been shown to increasingly cross both local and global boarders due to the presence of increased environmental changes, trade, and tourism. In Kenya, there have been several mosquito-borne disease outbreaks such as the recent outbreaks along the coast of Kenya, involving chikungunya and dengue. This certainly calls for the implementation of strategies aimed at strengthening integrated vector management programs. In this review, we look at mosquitoes of public health concern in Kenya, while highlighting the pathogens they have been linked with over the years and across various regions. In addition, the major strategies that have previously been used in mosquito control and what more could be done to reduce or combat the menace caused by these hematophagous vectors are presented.
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Affiliation(s)
- Samuel Karungu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Evans Atoni
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Joseph Ogalo
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Caroline Mwaliko
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Bernard Agwanda
- Mammalogy Section, National Museum of Kenya, P.O. Box 40658, Nairobi 00100, Kenya.
| | - Zhiming Yuan
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Xiaomin Hu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
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20
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Ommeh S, Zhang W, Zohaib A, Chen J, Zhang H, Hu B, Ge XY, Yang XL, Masika M, Obanda V, Luo Y, Li S, Waruhiu C, Li B, Zhu Y, Ouma D, Odendo V, Wang LF, Anderson DE, Lichoti J, Mungube E, Gakuya F, Zhou P, Ngeiywa KJ, Yan B, Agwanda B, Shi ZL. Genetic Evidence of Middle East Respiratory Syndrome Coronavirus (MERS-Cov) and Widespread Seroprevalence among Camels in Kenya. Virol Sin 2018; 33:484-492. [PMID: 30570714 PMCID: PMC6335226 DOI: 10.1007/s12250-018-0076-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/27/2018] [Indexed: 11/25/2022] Open
Abstract
We describe the first genome isolation of Middle East respiratory syndrome coronavirus (MERS-CoV) in Kenya. This fatal zoonotic pathogen was first described in the Kingdom of Saudi Arabia in 2012. Epidemiological and molecular evidence revealed zoonotic transmission from camels to humans and between humans. Currently, MERS-CoV is classified by the WHO as having high pandemic potential requiring greater surveillance. Previous studies of MERS-CoV in Kenya mainly focused on site-specific and archived camel and human serum samples for antibodies. We conducted active nationwide cross-sectional surveillance of camels and humans in Kenya, targeting both nasal swabs and plasma samples from 1,163 camels and 486 humans collected from January 2016 to June 2018. A total of 792 camel plasma samples were positive by ELISA. Seroprevalence increased with age, and the highest prevalence was observed in adult camels (82.37%, 95% confidence interval (CI) 79.50–84.91). More female camels were significantly seropositive (74.28%, 95% CI 71.14–77.19) than male camels (P < 0.001) (53.74%, 95% CI 48.48–58.90). Only 11 camel nasal swabs were positive for MERS-CoV by reverse transcription-quantitative PCR. Phylogenetic analysis of whole genome sequences showed that Kenyan MERS-CoV clustered within sub-clade C2, which is associated with the African clade, but did not contain signature deletions of orf4b in African viruses. None of the human plasma screened contained neutralizing antibodies against MERS-CoV. This study confirms the geographically widespread occurrence of MERS-CoV in Kenyan camels. Further one-health surveillance approaches in camels, wildlife, and human populations are needed.
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Affiliation(s)
- Sheila Ommeh
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, 62000-00200, Kenya
| | - Wei Zhang
- CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Ali Zohaib
- CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jing Chen
- CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Huajun Zhang
- CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Ben Hu
- CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xing-Yi Ge
- College of Biology, Hunan University, Changsha, 410006, China
| | - Xing-Lou Yang
- CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Moses Masika
- Department of Medical Microbiology, University of Nairobi, Nairobi, 30197-00100, Kenya
| | - Vincent Obanda
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, 40241-00100, Kenya
| | - Yun Luo
- CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Shan Li
- CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Cecilia Waruhiu
- CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Bei Li
- CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yan Zhu
- CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Desterio Ouma
- Veterinary Research Institute, Kenya Agriculture and Livestock Research Organization, Nairobi, 57811-00200, Kenya
| | - Vincent Odendo
- Veterinary Research Institute, Kenya Agriculture and Livestock Research Organization, Nairobi, 57811-00200, Kenya
| | - Lin-Fa Wang
- Veterinary Services Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Danielle E Anderson
- Veterinary Services Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Jacqueline Lichoti
- Directorate of Veterinary Services, State Department of Livestock, Ministry of Agriculture, Livestock Fisheries and Irrigation, Nairobi, 34188-00100, Kenya
| | - Erick Mungube
- Veterinary Research Institute, Kenya Agriculture and Livestock Research Organization, Nairobi, 57811-00200, Kenya
| | - Francis Gakuya
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, 40241-00100, Kenya
| | - Peng Zhou
- CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Kisa-Juma Ngeiywa
- Directorate of Veterinary Services, State Department of Livestock, Ministry of Agriculture, Livestock Fisheries and Irrigation, Nairobi, 34188-00100, Kenya.,Kenya Camel Association, Nairobi, 30095-00100, Kenya
| | - Bing Yan
- CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi, 40658-00100, Kenya.
| | - Zheng-Li Shi
- CAS Key Laboratory for Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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21
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Young HS, McCauley DJ, Dirzo R, Nunn CL, Campana MG, Agwanda B, Otarola-Castillo ER, Castillo ER, Pringle RM, Veblen KE, Salkeld DJ, Stewardson K, Fleischer R, Lambin EF, Palmer TM, Helgen KM. Interacting effects of land use and climate on rodent-borne pathogens in central Kenya. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0116. [PMID: 28438909 PMCID: PMC5413868 DOI: 10.1098/rstb.2016.0116] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2016] [Indexed: 12/13/2022] Open
Abstract
Understanding the effects of anthropogenic disturbance on zoonotic disease risk is both a critical conservation objective and a public health priority. Here, we evaluate the effects of multiple forms of anthropogenic disturbance across a precipitation gradient on the abundance of pathogen-infected small mammal hosts in a multi-host, multi-pathogen system in central Kenya. Our results suggest that conversion to cropland and wildlife loss alone drive systematic increases in rodent-borne pathogen prevalence, but that pastoral conversion has no such systematic effects. The effects are most likely explained both by changes in total small mammal abundance, and by changes in relative abundance of a few high-competence species, although changes in vector assemblages may also be involved. Several pathogens responded to interactions between disturbance type and climatic conditions, suggesting the potential for synergistic effects of anthropogenic disturbance and climate change on the distribution of disease risk. Overall, these results indicate that conservation can be an effective tool for reducing abundance of rodent-borne pathogens in some contexts (e.g. wildlife loss alone); however, given the strong variation in effects across disturbance types, pathogen taxa and environmental conditions, the use of conservation as public health interventions will need to be carefully tailored to specific pathogens and human contexts. This article is part of the themed issue ‘Conservation, biodiversity and infectious disease: scientific evidence and policy implications’.
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Affiliation(s)
- Hillary S Young
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA .,Mpala Research Centre, Box 555, Nanyuki, Kenya
| | - Douglas J McCauley
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA.,Mpala Research Centre, Box 555, Nanyuki, Kenya
| | - Rodolfo Dirzo
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Charles L Nunn
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Duke Global Health Institute, Duke University, Durham, NC 27710, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | | | | | - Eric R Castillo
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Robert M Pringle
- Mpala Research Centre, Box 555, Nanyuki, Kenya.,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Kari E Veblen
- Mpala Research Centre, Box 555, Nanyuki, Kenya.,Department of Wildland Resources and Ecology Center, Utah State University, Logan, UT 84322, USA
| | - Daniel J Salkeld
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kristin Stewardson
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | - Robert Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | - Eric F Lambin
- Department of Earth System Science and Woods Institute for the Environment, Stanford University, Stanford, CA 94305, USA
| | - Todd M Palmer
- Mpala Research Centre, Box 555, Nanyuki, Kenya.,Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Kristofer M Helgen
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
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22
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Wainaina M, Bett B, Ontiri E, Picozzi K, Agwanda B, Strand T, Grace D, Lundkvist Å, Lindahl J. Leptospira bacteria detected in rodents in Tana River and Garissa counties of Kenya. Infect Ecol Epidemiol 2018. [DOI: 10.1080/20008686.2018.1547093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Martin Wainaina
- International Livestock Research Institute, Nairobi, Kenya
- The University of Edinburgh, Edinburgh, UK
| | - Bernard Bett
- International Livestock Research Institute, Nairobi, Kenya
| | - Enoch Ontiri
- International Livestock Research Institute, Nairobi, Kenya
| | | | | | - Tanja Strand
- Zoonosis Science Center, Uppsala University, Uppsala, Sweden
- Swedish University of Agriculture, Uppsala, Sweden
| | - Delia Grace
- International Livestock Research Institute, Nairobi, Kenya
| | - Åke Lundkvist
- Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Johanna Lindahl
- International Livestock Research Institute, Nairobi, Kenya
- Zoonosis Science Center, Uppsala University, Uppsala, Sweden
- Swedish University of Agriculture, Uppsala, Sweden
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23
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Weinstein S, Titcomb G, Agwanda B, Riginos C, Young H. Parasite responses to large mammal loss in an African savanna. Ecology 2017; 98:1839-1848. [PMID: 28403506 DOI: 10.1002/ecy.1858] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 03/01/2017] [Accepted: 04/05/2017] [Indexed: 11/11/2022]
Abstract
Biodiversity loss can alter disease transmission; however, the magnitude and direction of these effects vary widely across ecosystems, scales, and pathogens. Here we experimentally examine the effects of one of the most globally pervasive patterns of biodiversity decline, the selective loss of large wildlife, on infection probability, intensity and population size of a group of common rodent-borne parasites - macroparasitic helminths. Consistent with previous work on vector-borne pathogens, we found that large wildlife removal causes strong and systematic increases of rodent-borne parasites, largely due to increases in rodent density, as rodents are released from competition with larger herbivores. Although we predicted that increased host density would also increase per capita infection among all directly transmitted parasites, this additional amplification occurred for only two of three examined parasites. Furthermore, the actual effects of large mammal loss on per capita infection were mediated by the complex suite of abiotic and biotic factors that regulate parasite transmission. Thus, while these results strongly suggest that large wildlife loss will cause systematic increases in rodent parasite populations, they also underscore the difficulty of making more specific predictions for a given parasite based on simple attributes such as transmission mode or life history strategy. Instead, detailed information on the ecology of each parasite species would be necessary to make more accurate predictions of how biodiversity loss will affect infection.
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Affiliation(s)
- Sara Weinstein
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Georgia Titcomb
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California, USA.,Mpala Research Centre, Nanyuki, Kenya
| | - Bernard Agwanda
- Zoology Department, Mammalogy Section, National Museums Kenya, Nairobi, Kenya
| | - Corinna Riginos
- Mpala Research Centre, Nanyuki, Kenya.,Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming, USA
| | - Hillary Young
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California, USA.,Mpala Research Centre, Nanyuki, Kenya
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24
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Guerra AS, Eckerlin RP, Dowling APG, Durden LA, Robbins RG, Dittmar K, Helgen KM, Agwanda B, Allan BF, Hedlund T, Young HS. Host-Parasite Associations in Small Mammal Communities in Semiarid Savanna Ecosystems of East Africa. J Med Entomol 2016; 53:851-860. [PMID: 27113102 DOI: 10.1093/jme/tjw048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/22/2016] [Indexed: 06/05/2023]
Abstract
Despite the established importance of rodents as reservoirs of vector-borne zoonoses in East Africa, there is relatively limited information regarding the infestation parameters and host associations of ectoparasites that vector many such pathogens among small mammals in this region. Between 2009 and 2013, small mammals were live-trapped in the semiarid savanna of Kenya. A subset of these individual hosts, including 20 distinct host taxa, was examined for ectoparasites, which were identified to species. Species of fleas, ticks, mites, and sucking lice were recorded. Based on these data, we calculated host-specific infestation parameters, documented host preferences among ectoparasites, conducted a rarefaction analysis and extrapolation to determine if ectoparasites were adequately sampled, and assessed nestedness for fleas to understand how pathogens might spread in this system. We found that the flea community structure was significantly nested. Understanding the ectoparasite network structure may have significant human relevance, as at least seven of the ectoparasite species collected are known vectors of pathogens of medical importance in the region, including Yersinia pestis, Rickettsia spp., and Theileria parva, the causative agents of plague, spotted fevers and other rickettsial illnesses in humans, and theileriosis, respectively.
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Affiliation(s)
- Ana Sofia Guerra
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA (; ),
| | - Ralph P Eckerlin
- Natural Sciences Division, Northern Virginia Community College, Annandale, VA
| | | | - Lance A Durden
- Department of Biology, Georgia Southern University, Statesboro, GA
| | - Richard G Robbins
- Armed Forces Pest Management Board, Office of the Assistant Secretary of Defense for Energy, Installations and Environment, Silver Spring, MD
| | | | - Kristofer M Helgen
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC
| | - Bernard Agwanda
- Mammal Section, National Museums of Kenya, Nairobi, Kenya , and
| | - Brian F Allan
- Department of Entomology, University of Illinois Urbana-Champaign, Urbana, IL (; )
| | - Tyler Hedlund
- Department of Entomology, University of Illinois Urbana-Champaign, Urbana, IL (; )
| | - Hillary S Young
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA (; )
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25
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Mortlock M, Kuzmin IV, Weyer J, Gilbert AT, Agwanda B, Rupprecht CE, Nel LH, Kearney T, Malekani JM, Markotter W. Novel Paramyxoviruses in Bats from Sub-Saharan Africa, 2007-2012. Emerg Infect Dis 2016; 21:1840-3. [PMID: 26402433 PMCID: PMC4593419 DOI: 10.3201/eid2110.140368] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
As part of a larger survey for detection of pathogens among wildlife in sub-Saharan Africa conducted during 2007–2012, multiple diverse paramyxovirus sequences were detected in renal tissues of bats. Phylogenetic analysis supports the presence of at least 2 major viral lineages and suggests that paramyxoviruses are strongly associated with several bat genera.
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26
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Campana MG, Hawkins MTR, Henson LH, Stewardson K, Young HS, Card LR, Lock J, Agwanda B, Brinkerhoff J, Gaff HD, Helgen KM, Maldonado JE, McShea WJ, Fleischer RC. Simultaneous identification of host, ectoparasite and pathogen DNA via in-solution capture. Mol Ecol Resour 2016; 16:1224-39. [DOI: 10.1111/1755-0998.12524] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 01/08/2016] [Accepted: 01/19/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Michael G. Campana
- Center for Conservation and Evolutionary Genetics; Smithsonian Conservation Biology Institute; 3001 Connecticut Avenue NW Washington DC 20008 USA
| | - Melissa T. R. Hawkins
- Center for Conservation and Evolutionary Genetics; Smithsonian Conservation Biology Institute; 3001 Connecticut Avenue NW Washington DC 20008 USA
- Division of Mammals; National Museum of Natural History; Smithsonian Institution; MRC 108, P.O. Box 37012 Washington DC 20013-7012 USA
| | - Lauren H. Henson
- Center for Conservation and Evolutionary Genetics; Smithsonian Conservation Biology Institute; 3001 Connecticut Avenue NW Washington DC 20008 USA
| | - Kristin Stewardson
- Center for Conservation and Evolutionary Genetics; Smithsonian Conservation Biology Institute; 3001 Connecticut Avenue NW Washington DC 20008 USA
| | - Hillary S. Young
- Department of Ecology, Evolution and Marine Biology; University of California Santa Barbara; Santa Barbara CA 93106 USA
| | - Leah R. Card
- Smithsonian Conservation Biology Institute; National Zoological Park; 1500 Remount Rd. Front Royal VA 22630 USA
| | - Justin Lock
- Center for Conservation and Evolutionary Genetics; Smithsonian Conservation Biology Institute; 3001 Connecticut Avenue NW Washington DC 20008 USA
| | | | - Jory Brinkerhoff
- Department of Biology; B322 Gottwald Center for the Sciences; University of Richmond; 28 Westhampton Way Richmond VA 23173 USA
| | - Holly D. Gaff
- Department of Biological Sciences; Old Dominion University; Norfolk VA 23529 USA
| | - Kristofer M. Helgen
- Division of Mammals; National Museum of Natural History; Smithsonian Institution; MRC 108, P.O. Box 37012 Washington DC 20013-7012 USA
| | - Jesús E. Maldonado
- Center for Conservation and Evolutionary Genetics; Smithsonian Conservation Biology Institute; 3001 Connecticut Avenue NW Washington DC 20008 USA
- Division of Mammals; National Museum of Natural History; Smithsonian Institution; MRC 108, P.O. Box 37012 Washington DC 20013-7012 USA
| | - William J. McShea
- Smithsonian Conservation Biology Institute; National Zoological Park; 1500 Remount Rd. Front Royal VA 22630 USA
| | - Robert C. Fleischer
- Center for Conservation and Evolutionary Genetics; Smithsonian Conservation Biology Institute; 3001 Connecticut Avenue NW Washington DC 20008 USA
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27
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Eisenring M, Beck J, Agwanda B, Kioko E, Curran M. Effects of habitat age and disturbance intensity on the biodiversity of three trophic levels in Central Kenya. Afr J Ecol 2016. [DOI: 10.1111/aje.12292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Michael Eisenring
- Department of Environmental Systems Science; Ecosystem Management; Institute of Terrestrial Ecosystems; ETH Zurich; Universitätstrasse 16 8092 Zurich Switzerland
| | - Jan Beck
- Department of Environmental Science (Biogeography); University of Basel; St. Johanns-Vorstadt 10 4056 Basel Switzerland
- Museum of Natural History, University of Colorado; University of Colorado; 265 UCB Boulder CO 80309 U.S.A
| | - Bernard Agwanda
- Zoology Department; Mammalogy Section; National Museums of Kenya; Museum Hill P.O. BOX 40658 Nairobi Kenya
| | - Esther Kioko
- Zoology Department; Invertebrate Zoology Section; National Museums of Kenya; Museum Hill P.O. BOX 40658 Nairobi Kenya
| | - Michael Curran
- Institute of Environmental Engineering; Chair of Ecological Systems Design; ETH Zurich; HPZ E33 John-von-Neumann-Weg 9 8093 Zurich Switzerland
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28
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Demos TC, Kerbis Peterhans JC, Joseph TA, Robinson JD, Agwanda B, Hickerson MJ. Comparative Population Genomics of African Montane Forest Mammals Support Population Persistence across a Climatic Gradient and Quaternary Climatic Cycles. PLoS One 2015; 10:e0131800. [PMID: 26394036 PMCID: PMC4578943 DOI: 10.1371/journal.pone.0131800] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 06/07/2015] [Indexed: 12/03/2022] Open
Abstract
The Eastern Afromontane biodiversity hotspot (EABH) has the highest concentration of biodiversity in tropical Africa, yet few studies have investigated recent historical diversification processes in EABH lineages. Herein, we analyze restriction-site associated DNA-sequences (RAD-Seq) to study recent historical processes in co-distributed mouse (Hylomyscus) and shrew (Sylvisorex) species complexes, with an aim to better determine how historical paleoenvironmental processes might have contributed to the EABH’s high diversity. We analyzed complete SNP matrices of > 50,000 RAD loci to delineate populations, reconstruct the history of isolation and admixture, and discover geographic patterns of genetic partitioning. These analyses demonstrate that persistently unsuitable habitat may have isolated multiple populations distributed across montane habitat islands in the Itombwe Massif and Albertine Rift to the west as well as Mt Elgon and Kenyan Highlands to the east. We detected low genetic diversity in Kenyan Highland populations of both genera, consistent with smaller historical population sizes in this region. We additionally tested predictions that Albertine Rift populations are older and more persistently isolated compared to the Kenyan Highlands. Phylogenetic analyses support greater historical isolation among Albertine Rift populations of both shrews and mice compared to the Kenyan Highlands and suggest that there are genetically isolated populations from both focal genera in the Itombwe Massif, Democratic Republic of Congo. The Albertine Rift ecoregion has the highest mammalian tropical forest species richness per unit area on earth. Our results clearly support accelerating efforts to conserve this diversity.
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Affiliation(s)
- Terrence C. Demos
- Biology Department, City College of New York, City University of New York, New York, New York, 10031, United States of America
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, New York, New York, 10016, United States of America
- Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, 60605, United States of America
- * E-mail:
| | - Julian C. Kerbis Peterhans
- Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, 60605, United States of America
- College of Professional Studies, Roosevelt University, Chicago, Illinois, 60605, United States of America
| | - Tyler A. Joseph
- Biology Department, City College of New York, City University of New York, New York, New York, 10031, United States of America
| | - John D. Robinson
- Biology Department, City College of New York, City University of New York, New York, New York, 10031, United States of America
- South Carolina Department of Natural Resources, Charleston, South Carolina, 29412, United States of America
| | - Bernard Agwanda
- Mammalogy Section, National Museums of Kenya, Nairobi, 00100, Kenya
| | - Michael J. Hickerson
- Biology Department, City College of New York, City University of New York, New York, New York, 10031, United States of America
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, New York, New York, 10016, United States of America
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York 10024, United States of America
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29
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Halliday JEB, Knobel DL, Agwanda B, Bai Y, Breiman RF, Cleaveland S, Njenga MK, Kosoy M. Prevalence and diversity of small mammal-associated Bartonella species in rural and urban Kenya. PLoS Negl Trop Dis 2015; 9:e0003608. [PMID: 25781015 PMCID: PMC4362764 DOI: 10.1371/journal.pntd.0003608] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 02/08/2015] [Indexed: 11/22/2022] Open
Abstract
Several rodent-associated Bartonella species are human pathogens but little is known about their epidemiology. We trapped rodents and shrews around human habitations at two sites in Kenya (rural Asembo and urban Kibera) to determine the prevalence of Bartonella infection. Bartonella were detected by culture in five of seven host species. In Kibera, 60% of Rattus rattus were positive, as compared to 13% in Asembo. Bartonella were also detected in C. olivieri (7%), Lemniscomys striatus (50%), Mastomys natalensis (43%) and R. norvegicus (50%). Partial sequencing of the citrate synthase (gltA) gene of isolates showed that Kibera strains were similar to reference isolates from Rattus trapped in Asia, America, and Europe, but that most strains from Asembo were less similar. Host species and trapping location were associated with differences in infection status but there was no evidence of associations between host age or sex and infection status. Acute febrile illness occurs at high incidence in both Asembo and Kibera but the etiology of many of these illnesses is unknown. Bartonella similar to known human pathogens were detected in small mammals at both sites and investigation of the ecological determinants of host infection status and of the public health significance of Bartonella infections at these locations is warranted. Bartonella are bacteria that infect many different mammal species and can cause illness in people. Several Bartonella species carried by rodents cause disease in humans but little is known about their distribution or the importance of bartonellosis as a cause of human illness. Data from Africa are particularly scarce. This study involved trapping of rodents and other small mammals at two sites in Kenya: Asembo, a rural area in Western Kenya, and Kibera, an informal urban settlement in Nairobi. Blood samples were collected from trapped animals to detect and characterize the types of Bartonella carried. At the Kibera site over half of the trapped rats were infected with Bartonella very similar to human pathogenic strains isolated from rats from other global regions. In Asembo, Bartonella were detected in four of the five animal species trapped and these Bartonella were less similar to previously identified isolates. All of the small mammals included in this study were trapped in or around human habitations. The data from this study show that Bartonella that can cause human illness are carried by the small mammals at these two sites and indicate that the public health impacts of human bartonellosis should be investigated.
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Affiliation(s)
- Jo E. B. Halliday
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
| | - Darryn L. Knobel
- Center for Conservation Medicine and Ecosystem Health, Ross University School of Veterinary Medicine, Basseterre, St. Kitts
| | | | - Ying Bai
- Centers for Disease Control and Prevention, Division of Vector-Borne Diseases, Fort Collins, Colorado, United States of America
| | - Robert F. Breiman
- Division of Global Health Protection, Atlanta, Georgia, United States of America
- Emory Global Health Institute, Emory University, Atlanta, Georgia, United States of America
| | - Sarah Cleaveland
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - M. Kariuki Njenga
- Kenya Medical Research Institute/CDC Public Health and Research Collaboration, Kisumu and Nairobi, Kenya
- Global Disease Detection Division, CDC-Kenya, Nairobi, Kenya
| | - Michael Kosoy
- Centers for Disease Control and Prevention, Division of Vector-Borne Diseases, Fort Collins, Colorado, United States of America
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Young HS, McCauley DJ, Dirzo R, Goheen JR, Agwanda B, Brook C, Otarola-Castillo E, Ferguson AW, Kinyua SN, McDonough MM, Palmer TM, Pringle RM, Young TP, Helgen KM. Context-dependent effects of large-wildlife declines on small-mammal communities in central Kenya. Ecol Appl 2015; 25:348-60. [PMID: 26263659 DOI: 10.1890/14-0995.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Many species of large wildlife have declined drastically worldwide. These reductions often lead to profound shifts in the ecology of entire communities and ecosystems. However, the effects of these large-wildlife declines on other taxa likely hinge upon both underlying abiotic properties of these systems and on the types of secondary anthropogenic changes associated with wildlife loss, making impacts difficult to predict. To better understand how these important contextual factors determine the consequences of large-wildlife declines on other animals in a community, we examined the effects of three common forms of large-wildlife loss (removal without replacement [using fences], removal followed by replacement with domestic stock, and removal accompanied by crop agricultural use) on small-mammal abundance, diversity, and community composition, in landscapes that varied in several abiotic attributes (rainfall, soil fertility, land-use intensity) in central Kenya. We found that small-mammal communities were indeed heavily impacted by all forms of large-wildlife decline, showing, on average: (1) higher densities, (2) lower species richness per site, and (3) different species assemblages in sites from which large wildlife were removed. However, the nature and magnitude of these effects were strongly context dependent. Rainfall, type of land-use change, and the interaction of these two factors were key predictors of both the magnitude and type of responses of small mammals. The strongest effects, particularly abundance responses, tended to be observed in low-rainfall areas. Whereas isolated wildlife removal primarily led to increased small-mammal abundance, wildlife removal associated with secondary uses (agriculture, domestic stock) had much more variable effects on abundance and stronger impacts on diversity and composition. Collectively, these results (1) highlight the importance of context in determining the impacts of large-wildlife decline on small-mammal communities, (2) emphasize the challenges in extrapolating results from controlled experimental studies to predict the effects of wildlife declines that are accompanied by secondary land-uses, and (3) suggest that, because of the context-dependent nature of the responses to large-wildlife decline, large-wildlife status alone cannot be reliably used to predict small-mammal community changes.
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31
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Young HS, Dirzo R, McCauley DJ, Agwanda B, Cattaneo L, Dittmar K, Eckerlin RP, Fleischer RC, Helgen LE, Hintz A, Montinieri J, Zhao S, Helgen KM. Drivers of Intensity and Prevalence of Flea Parasitism on Small Mammals in East African Savanna Ecosystems. J Parasitol 2015; 101:327-35. [PMID: 25634599 DOI: 10.1645/14-684.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The relative importance of environmental factors and host factors in explaining variation in prevalence and intensity of flea parasitism in small mammal communities is poorly established. We examined these relationships in an East African savanna landscape, considering multiple host levels: across individuals within a local population, across populations within species, and across species within a landscape. We sampled fleas from 2,672 small mammals of 27 species. This included a total of 8,283 fleas, with 5 genera and 12 species identified. Across individual hosts within a site, both rodent body mass and season affected total intensity of flea infestation, although the explanatory power of these factors was generally modest (<10%). Across host populations in the landscape, we found consistently positive effects of host density and negative effects of vegetation cover on the intensity of flea infestation. Other factors explored (host diversity, annual rainfall, anthropogenic disturbance, and soil properties) tended to have lower and less consistent explanatory power. Across host species in the landscape, we found that host body mass was strongly positively correlated with both prevalence and intensity of flea parasitism, while average robustness of a host species to disturbance was not correlated with flea parasitism. Cumulatively, these results provide insight into the intricate roles of both host and environmental factors in explaining complex patterns of flea parasitism across landscape mosaics.
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Affiliation(s)
- Hillary S Young
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California 93106
| | | | - Douglas J McCauley
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California 93106
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32
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Conrardy C, Tao Y, Kuzmin IV, Niezgoda M, Agwanda B, Breiman RF, Anderson LJ, Rupprecht CE, Tong S. Molecular detection of adenoviruses, rhabdoviruses, and paramyxoviruses in bats from Kenya. Am J Trop Med Hyg 2014; 91:258-266. [PMID: 24865685 PMCID: PMC4125246 DOI: 10.4269/ajtmh.13-0664] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We screened 217 bats of at least 20 species from 17 locations in Kenya during July and August of 2006 for the presence of adenovirus, rhabdovirus, and paramyxovirus nucleic acids using generic reverse transcription polymerase chain reaction (RT-PCR) and PCR assays. Of 217 bat fecal swabs examined, 4 bats were adenovirus DNA-positive, 11 bats were paramyxovirus RNA-positive, and 2 bats were rhabdovirus RNA-positive. Three bats were coinfected by two different viruses. By sequence comparison and phylogenetic analysis, the Kenya bat paramyxoviruses and rhabdoviruses from this study may represent novel viral lineages within their respective families; the Kenya bat adenoviruses could not be confirmed as novel, because the same region sequences from other known bat adenovirus genomes for comparison were lacking. Our study adds to previous evidence that bats carry diverse, potentially zoonotic viruses and may be coinfected with more than one virus.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Suxiang Tong
- *Address correspondence to Suxiang Tong, Centers for Disease Control and Prevention, 1600 Clifton Road, MS G18, Atlanta, GA 30333. E-mail:
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33
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Demos TC, Agwanda B, Hickerson MJ. Integrative taxonomy within theHylomyscus denniaecomplex (Rodentia: Muridae) and a new species from Kenya. J Mammal 2014. [DOI: 10.1644/13-mamm-a-268] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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34
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Demos TC, Kerbis Peterhans JC, Agwanda B, Hickerson MJ. Uncovering cryptic diversity and refugial persistence among small mammal lineages across the Eastern Afromontane biodiversity hotspot. Mol Phylogenet Evol 2014; 71:41-54. [DOI: 10.1016/j.ympev.2013.10.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 10/11/2013] [Accepted: 10/17/2013] [Indexed: 01/04/2023]
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35
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Halliday JEB, Knobel DL, Allan KJ, de C. Bronsvoort BM, Handel I, Agwanda B, Cutler SJ, Olack B, Ahmed A, Hartskeerl RA, Njenga MK, Cleaveland S, Breiman RF. Urban leptospirosis in Africa: a cross-sectional survey of Leptospira infection in rodents in the Kibera urban settlement, Nairobi, Kenya. Am J Trop Med Hyg 2013; 89:1095-1102. [PMID: 24080637 PMCID: PMC3854886 DOI: 10.4269/ajtmh.13-0415] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Leptospirosis is a widespread but under-reported cause of morbidity and mortality. Global re-emergence of leptospirosis has been associated with the growth of informal urban settlements in which rodents are thought to be important reservoir hosts. Understanding the multi-host epidemiology of leptospirosis is essential to control and prevent disease. A cross-sectional survey of rodents in the Kibera settlement in Nairobi, Kenya was conducted in September–October 2008 to demonstrate the presence of pathogenic leptospires. A real-time quantitative polymerase chain reaction showed that 41 (18.3%) of 224 rodents carried pathogenic leptospires in their kidneys, and sequence data identified Leptospira interrogans and L. kirschneri in this population. Rodents of the genus Mus (37 of 185) were significantly more likely to be positive than those of the genus Rattus (4 of 39; odds ratio = 15.03). Questionnaire data showed frequent contact between humans and rodents in Kibera. This study emphasizes the need to quantify the public health impacts of this neglected disease at this and other urban sites in Africa.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Sarah Cleaveland
- *Address correspondence to Sarah Cleaveland, Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G11 8QQ, United Kingdom. E-mail:
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36
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Kading RC, Gilbert AT, Mossel EC, Crabtree MB, Kuzmin IV, Niezgoda M, Agwanda B, Markotter W, Weil MR, Montgomery JM, Rupprecht CE, Miller BR. Isolation and molecular characterization of Fikirini rhabdovirus, a novel virus from a Kenyan bat. J Gen Virol 2013; 94:2393-2398. [PMID: 23939976 DOI: 10.1099/vir.0.053983-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Zoonotic and vector-borne pathogens have comprised a significant component of emerging human infections in recent decades, and bats are increasingly recognized as reservoirs for many of these disease agents. To identify novel pathogens associated with bats, we screened tissues of bats collected in Kenya. Virus isolates were identified by next generation sequencing of viral nucleic acid preparations from the infected cell culture supernatant and characterized. Here we report the identification of Fikirini rhabdovirus, a novel rhabdovirus isolated from a bat, Hipposideros vittatus, captured along the Kenyan coast.
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Affiliation(s)
- Rebekah C Kading
- Centers for Disease Control and Prevention, Division of Vector-borne Diseases, Arbovirus Diseases Branch, Fort Collins, CO, USA
| | - Amy T Gilbert
- Centers for Disease Control and Prevention, Division of High Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, Atlanta, GA, USA
| | - Eric C Mossel
- Centers for Disease Control and Prevention, Division of Vector-borne Diseases, Arbovirus Diseases Branch, Fort Collins, CO, USA
| | - Mary B Crabtree
- Centers for Disease Control and Prevention, Division of Vector-borne Diseases, Arbovirus Diseases Branch, Fort Collins, CO, USA
| | - Ivan V Kuzmin
- Centers for Disease Control and Prevention, Division of High Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, Atlanta, GA, USA
| | - Michael Niezgoda
- Centers for Disease Control and Prevention, Division of High Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, Atlanta, GA, USA
| | | | - Wanda Markotter
- University of Pretoria, Department of Microbiology and Plant Pathology, Pretoria, South Africa
| | - M Ryan Weil
- Centers for Disease Control and Prevention, Office of Infectious Disease, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA, USA.,SRA International, Atlanta, GA, USA
| | - Joel M Montgomery
- Centers for Disease Control and Prevention, Global Disease Detection Program, Nairobi, Kenya
| | - Charles E Rupprecht
- Centers for Disease Control and Prevention, Division of High Consequence Pathogens and Pathology, Poxvirus and Rabies Branch, Atlanta, GA, USA
| | - Barry R Miller
- Centers for Disease Control and Prevention, Division of Vector-borne Diseases, Arbovirus Diseases Branch, Fort Collins, CO, USA
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Haus T, Akom E, Agwanda B, Hofreiter M, Roos C, Zinner D. Mitochondrial diversity and distribution of African green monkeys (chlorocebus gray, 1870). Am J Primatol 2013; 75:350-60. [PMID: 23307319 PMCID: PMC3613741 DOI: 10.1002/ajp.22113] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Revised: 10/19/2012] [Accepted: 11/23/2012] [Indexed: 11/21/2022]
Abstract
African green monkeys (Chlorocebus) represent a widely distributed and morphologically diverse primate genus in sub-Saharan Africa. Little attention has been paid to their genetic diversity and phylogeny. Based on morphological data, six species are currently recognized, but their taxonomy remains disputed. Here, we aim to characterize the mitochondrial (mt) DNA diversity, biogeography and phylogeny of African green monkeys. We analyzed the complete mitochondrial cytochrome b gene of 126 samples using feces from wild individuals and material from zoo and museum specimens with clear geographical provenance, including several type specimens. We found evidence for nine major mtDNA clades that reflect geographic distributions rather than taxa, implying that the mtDNA diversity of African green monkeys does not conform to existing taxonomic classifications. Phylogenetic relationships among clades could not be resolved suggesting a rapid early divergence of lineages. Several discordances between mtDNA and phenotype indicate that hybridization may have occurred in contact zones among species, including the threatened Bale monkey (Chlorocebus djamdjamensis). Our results provide both valuable data on African green monkeys' genetic diversity and evolution and a basis for further molecular studies on this genus.
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Affiliation(s)
- Tanja Haus
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, Goettingen, Germany.
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Tao Y, Shi M, Conrardy C, Kuzmin IV, Recuenco S, Agwanda B, Alvarez DA, Ellison JA, Gilbert AT, Moran D, Niezgoda M, Lindblade KA, Holmes EC, Breiman RF, Rupprecht CE, Tong S. Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae. J Gen Virol 2013; 94:738-748. [PMID: 23239573 PMCID: PMC7346582 DOI: 10.1099/vir.0.047928-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/09/2012] [Indexed: 12/18/2022] Open
Abstract
Polyomaviruses (PyVs) have been identified in a wide range of avian and mammalian species. However, little is known about their occurrence, genetic diversity and evolutionary history in bats, even though bats are important reservoirs for many emerging viral pathogens. This study screened 380 specimens from 35 bat species from Kenya and Guatemala for the presence of PyVs by semi-nested pan-PyV PCR assays. PyV DNA was detected in 24 of the 380 bat specimens. Phylogenetic analysis revealed that the bat PyV sequences formed 12 distinct lineages. Full-genome sequences were obtained for seven representative lineages and possessed similar genomic features to known PyVs. Strikingly, this evolutionary analysis revealed that the bat PyVs were paraphyletic, suggestive of multiple species jumps between bats and other mammalian species, such that the theory of virus-host co-divergence for mammalian PyVs as a whole could be rejected. In addition, evidence was found for strong heterogeneity in evolutionary rate and potential recombination in a number of PyV complete genomes, which complicates both phylogenetic analysis and virus classification. In summary, this study revealed that bats are important reservoirs of PyVs and that these viruses have a complex evolutionary history.
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Affiliation(s)
- Ying Tao
- Division of Viral Diseases, Centers for Disease Control and
Prevention, Atlanta, GA 30333, USA
| | - Mang Shi
- Sydney Emerging Infections and Biosecurity Institute, School of
Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW
2006, Australia
| | - Christina Conrardy
- Division of Viral Diseases, Centers for Disease Control and
Prevention, Atlanta, GA 30333, USA
| | - Ivan V. Kuzmin
- Division of High Consequence Pathogens and Pathology, Centers for
Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Sergio Recuenco
- Division of High Consequence Pathogens and Pathology, Centers for
Disease Control and Prevention, Atlanta, GA 30333, USA
| | | | - Danilo A. Alvarez
- Center for Health Studies, Universidad del Valle de Guatemala,
Guatemala City, Guatemala
| | - James A. Ellison
- Division of High Consequence Pathogens and Pathology, Centers for
Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Amy T. Gilbert
- Division of High Consequence Pathogens and Pathology, Centers for
Disease Control and Prevention, Atlanta, GA 30333, USA
| | - David Moran
- Center for Health Studies, Universidad del Valle de Guatemala,
Guatemala City, Guatemala
| | - Michael Niezgoda
- Division of High Consequence Pathogens and Pathology, Centers for
Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Kim A. Lindblade
- Centers for Disease Control and Prevention Central America and
Panama, Guatemala
| | - Edward C. Holmes
- Sydney Emerging Infections and Biosecurity Institute, School of
Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW
2006, Australia
- Fogarty International Center, National Institutes of Health,
Bethesda, MD 20892, USA
| | | | - Charles E. Rupprecht
- Division of High Consequence Pathogens and Pathology, Centers for
Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Suxiang Tong
- Division of Viral Diseases, Centers for Disease Control and
Prevention, Atlanta, GA 30333, USA
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Kuzmin IV, Turmelle AS, Agwanda B, Markotter W, Niezgoda M, Breiman RF, Rupprecht CE. Commerson's leaf-nosed bat (Hipposideros commersoni) is the likely reservoir of Shimoni bat virus. Vector Borne Zoonotic Dis 2011; 11:1465-70. [PMID: 21867415 DOI: 10.1089/vbz.2011.0663] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this study we attempted to identify whether Commerson's leaf-nosed bat (Hipposideros commersoni) is the reservoir of Shimoni bat virus (SHIBV), which was isolated from a bat of this species in 2009. An alternative explanation is that the isolation of SHIBV from H. commersoni was a result of spill-over infection from other species, particularly from the Egyptian fruit bats (Rousettus aegyptiacus), which frequently sympatrically roost with H. commersoni and are known as the reservoir of the phylogenetically related Lagos bat virus (LBV). To evaluate these hypotheses, 769 bats of at least 17 species were sampled from 18 locations across Kenya during 2009?2010. Serum samples were subjected to virus neutralization tests against SHIBV and LBV. A limited amount of cross-neutralization between LBV and SHIBV was detected. However, H. commersoni bats demonstrated greater seroprevalence to SHIBV than to LBV, and greater virus-neutralizing titers to SHIBV than to LBV, with a mean difference of 1.16 log(10) (95% confidence intervals [CI]: 0.94-1.40; p<0.001). The opposite pattern was observed for sera of R. aegyptiacus bats, with a mean titer difference of 1.06 log(10) (95% CI: 0.83-1.30; p<0.001). Moreover, the seroprevalence in H. commersoni to SHIBV in the cave where these bats sympatrically roosted with R. aegyptiacus (and where SHIBV was isolated in 2009) was similar to their seroprevalence to SHIBV in a distant cave where no R. aegyptiacus were present (18.9% and 25.0%, respectively). These findings suggest that H. commersoni is the host species of SHIBV. Additional surveillance is needed to better understand the ecology of this virus and the potential risks of infection to humans and other mammalian species.
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Affiliation(s)
- Ivan V Kuzmin
- Rabies Program, Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
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Kingdon J, Agwanda B, Kinnaird M, O'Brien T, Holland C, Gheysens T, Boulet-Audet M, Vollrath F. A poisonous surprise under the coat of the African crested rat. Proc Biol Sci 2011; 279:675-80. [PMID: 21813554 DOI: 10.1098/rspb.2011.1169] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Plant toxins are sequestered by many animals and the toxicity is frequently advertised by aposematic displays to deter potential predators. Such 'unpalatability by appropriation' is common in many invertebrate groups and also found in a few vertebrate groups. However, potentially lethal toxicity by acquisition has so far never been reported for a placental mammal. Here, we describe complex morphological structures and behaviours whereby the African crested rat, Lophiomys imhausi, acquires, dispenses and advertises deterrent toxin. Roots and bark of Acokanthera schimperi (Apocynaceae) trees are gnawed, masticated and slavered onto highly specialized hairs that wick up the compound, to be delivered whenever the animal is bitten or mouthed by a predator. The poison is a cardenolide, closely resembling ouabain, one of the active components in a traditional African arrow poison long celebrated for its power to kill elephants.
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Affiliation(s)
- Jonathan Kingdon
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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Abstract
We report the presence and diversity of Bartonella spp. in bats of 13 insectivorous and frugivorous species collected from various locations across Kenya. Bartonella isolates were obtained from 23 Eidolon helvum, 22 Rousettus aegyptiacus, 4 Coleura afra, 7 Triaenops persicus, 1 Hipposideros commersoni, and 49 Miniopterus spp. bats. Sequence analysis of the citrate synthase gene from the obtained isolates showed a wide assortment of Bartonella strains. Phylogenetically, isolates clustered in specific host bat species. All isolates from R. aegyptiacus, C. afra, and T. persicus bats clustered in separate monophyletic groups. In contrast, E. helvum and Miniopterus spp. bats harbored strains that clustered in several groups. Further investigation is needed to determine whether these agents are responsible for human illnesses in the region.
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Affiliation(s)
- Michael Kosoy
- Centers for Disease Control and Prevention, Fort Collins, Colorado 80521, USA.
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Esona MD, Mijatovic-Rustempasic S, Conrardy C, Tong S, Kuzmin IV, Agwanda B, Breiman RF, Banyai K, Niezgoda M, Rupprecht CE, Gentsch JR, Bowen MD. Reassortant group A rotavirus from straw-colored fruit bat (Eidolon helvum). Emerg Infect Dis 2011; 16:1844-52. [PMID: 21122212 PMCID: PMC3294550 DOI: 10.3201/eid1612.101089] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
TOC summary: Bats may be reservoirs of zoonotic viruses that threaten human health. Bats are known reservoirs of viral zoonoses. We report genetic characterization of a bat rotavirus (Bat/KE4852/07) detected in the feces of a straw-colored fruit bat (Eidolon helvum). Six bat rotavirus genes (viral protein [VP] 2, VP6, VP7, nonstructural protein [NSP] 2, NSP3, and NSP5) shared ancestry with other mammalian rotaviruses but were distantly related. The VP4 gene was nearly identical to that of human P[6] rotavirus strains, and the NSP4 gene was closely related to those of previously described mammalian rotaviruses, including human strains. Analysis of partial sequence of the VP1 gene indicated that it was distinct from cognate genes of other rotaviruses. No sequences were obtained for the VP3 and NSP1 genes of the bat rotavirus. This rotavirus was designated G25-P[6]-I15-R8(provisional)-C8-Mx-Ax-N8-T11-E2-H10. Results suggest that several reassortment events have occurred between human, animal, and bat rotaviruses. Several additional rotavirus strains were detected in bats.
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Affiliation(s)
- Mathew D Esona
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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Kuzmin IV, Mayer AE, Niezgoda M, Markotter W, Agwanda B, Breiman RF, Rupprecht CE. Shimoni bat virus, a new representative of the Lyssavirus genus. Virus Res 2010; 149:197-210. [PMID: 20138934 DOI: 10.1016/j.virusres.2010.01.018] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Revised: 01/30/2010] [Accepted: 01/30/2010] [Indexed: 12/25/2022]
Abstract
During 2009, 616 bats representing at least 22 species were collected from 10 locations throughout Kenya. A new lyssavirus, named Shimoni bat virus (SHIBV), was isolated from the brain of a dead Commerson's leaf-nosed bat (Hipposideros commersoni), found in a cave in the coastal region of Kenya. Genetic distances and phylogenetic reconstructions, implemented for each gene and for the concatenated alignment of all five structural genes (N, P, M, G and L), demonstrated that SHIBV cannot be identified with any of the existing species, but rather should be considered an independent species within phylogroup II of the Lyssavirus genus, most similar to Lagos bat virus (LBV). Antigenic reaction patterns with anti-nucleocapsid monoclonal antibodies corroborated these distinctions. In addition, new data on the diversity of LBV suggests that this species may be subdivided quantitatively into three separate genotypes. However, the identity values alone are not considered sufficient criteria for demarcation of new species within LBV.
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Affiliation(s)
- Ivan V Kuzmin
- Rabies Program, Poxvirus and Rabies Branch, Division of Viral and Rickettsial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA 30333, USA.
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Tong S, Conrardy C, Ruone S, Kuzmin IV, Guo X, Tao Y, Niezgoda M, Haynes L, Agwanda B, Breiman RF, Anderson LJ, Rupprecht CE. Detection of novel SARS-like and other coronaviruses in bats from Kenya. Emerg Infect Dis 2009; 15:482-5. [PMID: 19239771 PMCID: PMC2681120 DOI: 10.3201/eid1503.081013] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Diverse coronaviruses have been identified in bats from several continents but not from Africa. We identified group 1 and 2 coronaviruses in bats in Kenya, including SARS-related coronaviruses. The sequence diversity suggests that bats are well-established reservoirs for and likely sources of coronaviruses for many species, including humans.
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Affiliation(s)
- Suxiang Tong
- Gastroenteritis and Respiratory Virus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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Kuzmin IV, Niezgoda M, Franka R, Agwanda B, Markotter W, Beagley JC, Urazova OY, Breiman RF, Rupprecht CE. Possible emergence of West Caucasian bat virus in Africa. Emerg Infect Dis 2009; 14:1887-9. [PMID: 19046512 PMCID: PMC2634633 DOI: 10.3201/eid1412.080750] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The prevalence of neutralizing antibody against West Caucasian bat virus (WCBV) in Miniopterus bats collected in Kenya ranged from 17% to 26%. Seropositive bats were detected in 4 of 5 locations sampled across the country. These findings provide evidence that WCBV, originally isolated in Europe, may emerge in other continents.
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Affiliation(s)
- Ivan V Kuzmin
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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