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Liu X, Lin L, Sinding MHS, Bertola LD, Hanghøj K, Quinn L, Garcia-Erill G, Rasmussen MS, Schubert M, Pečnerová P, Balboa RF, Li Z, Heaton MP, Smith TPL, Pinto RR, Wang X, Kuja J, Brüniche-Olsen A, Meisner J, Santander CG, Ogutu JO, Masembe C, da Fonseca RR, Muwanika V, Siegismund HR, Albrechtsen A, Moltke I, Heller R. Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations. Nat Commun 2024; 15:2921. [PMID: 38609362 PMCID: PMC11014984 DOI: 10.1038/s41467-024-47015-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024] Open
Abstract
The blue wildebeest (Connochaetes taurinus) is a keystone species in savanna ecosystems from southern to eastern Africa, and is well known for its spectacular migrations and locally extreme abundance. In contrast, the black wildebeest (C. gnou) is endemic to southern Africa, barely escaped extinction in the 1900s and is feared to be in danger of genetic swamping from the blue wildebeest. Despite the ecological importance of the wildebeest, there is a lack of understanding of how its unique migratory ecology has affected its gene flow, genetic structure and phylogeography. Here, we analyze whole genomes from 121 blue and 22 black wildebeest across the genus' range. We find discrete genetic structure consistent with the morphologically defined subspecies. Unexpectedly, our analyses reveal no signs of recent interspecific admixture, but rather a late Pleistocene introgression of black wildebeest into the southern blue wildebeest populations. Finally, we find that migratory blue wildebeest populations exhibit a combination of long-range panmixia, higher genetic diversity and lower inbreeding levels compared to neighboring populations whose migration has recently been disrupted. These findings provide crucial insights into the evolutionary history of the wildebeest, and tangible genetic evidence for the negative effects of anthropogenic activities on highly migratory ungulates.
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Affiliation(s)
- Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA
| | - Timothy P L Smith
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA
| | - Rui Resende Pinto
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research-University of Porto, Porto, Portugal
- Section for Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Jonas Meisner
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Copenhagen Research Centre for Mental Health, Copenhagen University Hospital, Copenhagen, Denmark
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Joseph O Ogutu
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Rute R da Fonseca
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research-University of Porto, Porto, Portugal
- Section for Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vincent Muwanika
- Department of Environmental Management, Makerere University, PO Box 7062, Kampala, Uganda
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Spinard E, Wade A, Unger H, Robert N, Mayega FJ, Sreenu VB, Da Silva Filpe A, Mair D, Borca MV, Gladue DP, Masembe C. Near-complete genome sequences of multiple genotype 1 African swine fever virus isolates from 2016 to 2018 in Cameroon. Microbiol Resour Announc 2024; 13:e0097823. [PMID: 38477459 PMCID: PMC11008206 DOI: 10.1128/mra.00978-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
African swine fever virus has been endemic in Cameroon since 1982. Here, we announce the sequences of Cameroon/2016/C1, Cameroon/2016/C5, Cameroon/2017/C-A2, Cameroon/2018/C02, and Cameroon/2018/CF3, five genotype 1 African swine fever virus genomes collected from domestic pigs between 2016 and 2018.
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Affiliation(s)
- Edward Spinard
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, New York, USA
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Unit Name, Manhattan, Kansas, USA
| | - Abel Wade
- National Veterinary Laboratory (LANAVET), Garoua, Cameroon
| | - Hermann Unger
- Animal Production and Health Section, Joint FAO/IAEA Division for Nuclear Applications in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria
| | - Nenkam Robert
- Laboratoire National Veterinaire (LANAVET), Garoua, Cameroon
| | | | | | - Ana Da Silva Filpe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Daniel Mair
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Manuel V. Borca
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, New York, USA
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Unit Name, Manhattan, Kansas, USA
| | - Douglas P. Gladue
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, New York, USA
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Unit Name, Manhattan, Kansas, USA
| | - Charles Masembe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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Bertola LD, Quinn L, Hanghøj K, Garcia-Erill G, Rasmussen MS, Balboa RF, Meisner J, Bøggild T, Wang X, Lin L, Nursyifa C, Liu X, Li Z, Chege M, Moodley Y, Brüniche-Olsen A, Kuja J, Schubert M, Agaba M, Santander CG, Sinding MHS, Muwanika V, Masembe C, Siegismund HR, Moltke I, Albrechtsen A, Heller R. Giraffe lineages are shaped by major ancient admixture events. Curr Biol 2024; 34:1576-1586.e5. [PMID: 38479386 DOI: 10.1016/j.cub.2024.02.051] [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: 06/11/2023] [Revised: 09/29/2023] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
Strong genetic structure has prompted discussion regarding giraffe taxonomy,1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa).4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations.
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Affiliation(s)
- Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Meisner
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Bøggild
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Casia Nursyifa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mumbi Chege
- Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands; Wildlife Research and Training Institute, Naivasha, Kenya
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa
| | | | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Morris Agaba
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Nelson Mandela Road, Arusha, Tanzania
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Vincent Muwanika
- College of Agricultural and Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, P O. Box 7062, Kampala, Uganda
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Etiang P, Atim SA, Nkamwesiga J, Nalumenya D, Byaruhanga C, Odongo S, Vudriko P, Ademun AR, Biryomumaisho S, Erume J, Masembe C, Thomson EC, Muhanguzi D, Tweyongyere R. Identification and distribution of Rhipicephalus microplus in selected high-cattle density districts in Uganda: signaling future demand for novel tick control approaches. BMC Vet Res 2024; 20:119. [PMID: 38528496 DOI: 10.1186/s12917-024-03979-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/15/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Rhipicephalus (Boophilus) microplus (Canestrini, 1888), the Asian blue tick, is a highly invasive and adaptable ectoparasite. This tick species has successfully established itself in most regions of the world, with movement of cattle being a major driver for its spread. In the recent past, R. microplus ticks have been reported in three districts of Uganda. Information on its spread and distribution are vital in deepening our understanding of the ecological scenarios that lead to tick persistence and in the formulation of control strategies. This is especially important in the cattle-dense districts. METHODS We randomly collected tick specimens from 1,461cattle spread across seven cattle dense districts located in the Central, Karamoja and West Nile regions of Uganda from January to September 2020. The ticks were identified using standard morpho-taxonomic keys and the R. microplus tick species identities were confirmed by sequencing of the ITS2 region, 12S rRNA and 16S rRNA genes and phylogenetic analyses. RESULTS Adult ticks (n = 13,019) were collected from 1,461 cattle. Seventeen tick species were identified based on morpho-taxonomic keys and the majority (47.4%; n=6184) of these were R. appendiculatus. In total, 257 R. microplus ticks were found infesting cattle in 18 study sites in the districts of Amudat, Kaabong, Napak (Karamoja region) and Arua (West Nile region). The identity of R. microplus was confirmed using molecular technics. No R. microplus tick was recorded in the districts of Lyantonde and Nakaseke (Central region). Arua district accounted for 82.1% (n=211) of the R. microplus ticks recorded followed by Napak district at 16.3% (n=42), while Amudat and Kaabong districts accounted for 1.5% (n=4). Rhipicephalus microplus and R. decoloratus co-existed in 6 of the 13 study sites in Arua district, while in another 6 study sites, no R. decoloratus was recorded. In the Karamoja region districts R. decoloratus co-existed with R.microplus. Of the total 618 ticks belonging to four species of the subgenus Boophilus recorded in this study, R. decoloratus accounted for 50.04% (n=334), followed by R. microplus at 41.58% (n=257), R. geigyi at 2.75% (n=17) and R. annulatus at 1.61% (n=10). In the districts of Amudat, Kaabong and Napak, R. decoloratus was more dominant (76.1%; n=179) of the three Rhipicephalus (Boophilus) tick species recorded, followed by R. microplus (19.5%; n=46) and R. geigyi (4.2%; n=10). Contrariwise, R. microplus was more dominant (84%; n=211) in Arua district followed by R. decoloratus (10.7%; n=27), R. annulatus (3.9%; n=10) and R. geigyi (1.1%; n=3). Phylogenetic analyses of the ITS2 region, 12S rRNA and 16S rRNA genes revealed subgrouping of the obtained sequences with the previously published R. microplus sequences from other parts of the world. CONCLUSION Rhipicephalus microplus ticks were found infesting cattle in four districts of Uganda. The inability to find R. decoloratus, an indigenous tick, from six sites in the district of Arua is suggestive of its replacement by R. microplus. Rhipicephalus microplus negatively affects livestock production, and therefore, there is a need to determine its distribution and to deepen the understanding of the ecological factors that lead to its spread and persistence in an area.
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Affiliation(s)
- Patrick Etiang
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P.O. Box 7062, Kampala, Uganda
- Faculty of Agriculture and Animal Sciences, Busitema University, P.O. Box 236, Tororo, Uganda
| | - Stella A Atim
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P.O. Box 7062, Kampala, Uganda
- Ministry of Agriculture, Animal Industry and Fisheries, P.O. Box 102, Entebbe, Uganda
| | - Joseph Nkamwesiga
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P.O. Box 7062, Kampala, Uganda
| | - David Nalumenya
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Charles Byaruhanga
- National Agricultural Research Organization, P.O. Box 259, Entebbe, Uganda
- Vectors and Vector-Borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, 0110, South Africa
| | - Steven Odongo
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Patrick Vudriko
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Anna Rose Ademun
- Ministry of Agriculture, Animal Industry and Fisheries, P.O. Box 102, Entebbe, Uganda
| | - Savino Biryomumaisho
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Joseph Erume
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences (CONAS), Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Dennis Muhanguzi
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Robert Tweyongyere
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P.O. Box 7062, Kampala, Uganda.
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Yussif I, Kugonza DR, Masembe C. Uganda chicken genetic resources: II. genetic diversity and population demographic history inferred from mitochondrial DNA D-loop sequences. Front Genet 2024; 15:1325569. [PMID: 38516375 PMCID: PMC10955702 DOI: 10.3389/fgene.2024.1325569] [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: 10/21/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
The genetic diversity of indigenous chickens, which comprise over 80% of the chicken resources in Uganda, is largely not well-characterized for their genetic contribution. This study assessed the genetic diversity and population structure of the indigenous chicken population in Uganda to serve as an essential component for improvement and conservation strategies. A set of 344 mitochondrial DNA (mtDNA) D-loop sequences among 12 Ugandan chicken populations was evaluated. Twenty-eight polymorphic sites, accounting for 4.26% of the total analyzed loci of 658 bp, defined 32 haplotypes. The haplotype diversity (Hd) was 0.437, with a nucleotide diversity (π) of 0.0169, while the average number of nucleotide differences (k) was 0.576, indicating a population that is moderately genetically diverse. Analysis of molecular variance found 98.39% (ρ < 0.01) of the total sequence variation among the chicken haplotypes within populations, 1.08% (ρ < 0.05) among populations, and 0.75% (ρ > 0.05) among populations within regions. This revealed subtle genetic differentiation among the populations, which appeared to be influenced by population fragmentation, probably due to neutral mutation, random genetic drift, and/or balancing selection. All the haplotypes showed affinity exclusively to the haplogroup-E mtDNA phylogeny, with haplotype UGA01 signaling an ancestral haplotype in Uganda. Neutrality tests Tajima's D (-2.320) and Fu's Fs (-51.369), augmented with mismatch distribution to measure signatures of recent historical demographic events, supported a population expansion across the chicken populations. The results show one matrilineal ancestry of Ugandan chickens from a lineage widespread throughout the world that began in the Indian subcontinent. The lack of phylogeographic signals is consistent with recent expansion events with extensive within-country genetic intermixing among haplotypes. Thus, the findings in this study hold the potential to guide conservation strategies and breeding programs in Uganda, given that higher genetic diversity comes from within the chicken population.
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Affiliation(s)
- Illyass Yussif
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - Donald Rugira Kugonza
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - Charles Masembe
- College of Natural Resources, Makerere University, Kampala, Uganda
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Balboa RF, Bertola LD, Brüniche-Olsen A, Rasmussen MS, Liu X, Besnard G, Salmona J, Santander CG, He S, Zinner D, Pedrono M, Muwanika V, Masembe C, Schubert M, Kuja J, Quinn L, Garcia-Erill G, Stæger FF, Rakotoarivony R, Henrique M, Lin L, Wang X, Heaton MP, Smith TPL, Hanghøj K, Sinding MHS, Atickem A, Chikhi L, Roos C, Gaubert P, Siegismund HR, Moltke I, Albrechtsen A, Heller R. African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival. Nat Commun 2024; 15:172. [PMID: 38172616 PMCID: PMC10764920 DOI: 10.1038/s41467-023-44105-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1000-5000 years ago, concurrent with human arrival in Madagascar. These results shed light on the evolutionary history of an iconic and widespread African mammal and provide insight into the longstanding biogeographic puzzle surrounding the bushpig's presence in Madagascar.
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Affiliation(s)
- Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Guillaume Besnard
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Jordi Salmona
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shixu He
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Dietmar Zinner
- Cognitive Ecology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
- Leibniz Science Campus Primate Cognition, 37077, Göttingen, Germany
| | - Miguel Pedrono
- UMR ASTRE, CIRAD, Campus International de Baillarguet, Montpellier, France
| | - Vincent Muwanika
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Mikkel Schubert
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Anagaw Atickem
- Department of Zoological Sciences, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - Lounès Chikhi
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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7
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Robledo D, Ogwang J, Byakora E, Schulze JN, Benda KK, Fraslin C, Salisbury S, Solimo M, Mayega JF, Peter B, Masembe C, Houston R, Mukiibi R. Genetic diversity and population structure of farmed and wild Nile tilapia (Oreochromis niloticus) in Uganda: The potential for aquaculture selection and breeding programs. Genomics 2024; 116:110781. [PMID: 38182036 DOI: 10.1016/j.ygeno.2024.110781] [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: 09/15/2023] [Revised: 12/17/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
Nile tilapia is one of the most important aquaculture species globally, providing high-quality animal protein for human nutrition and a source of income to sustain the livelihoods of many people in low- and middle-income countries. This species is native to Africa and nowadays farmed throughout the world. However, the genetic makeup of its native populations remains poorly characterized. Additionally, there has been important introgression and movement of farmed (as well as wild) strains connected to tilapia aquaculture in Africa, yet the relationship between wild and farmed populations is unknown in most of the continent. Genetic characterization of the species in Africa has the potential to support the conservation of the species as well as supporting selective breeding to improve the indigenous strains for sustainable and profitable aquaculture production. In the current study, a total of 382 fish were used to investigate the genetic structure, diversity, and ancestry within and between Ugandan Nile tilapia populations from three major lakes including Lake Albert (L. Albert), Lake Kyoga (L. Kyoga) and Lake Victoria (L. Victoria), and 10 hatchery farms located in the catchment regions of these lakes. Our results showed clear genetic structure of the fish sourced from the lakes, with L. Kyoga and L. Albert populations showing higher genetic similarity. We also observed noticeable genetic structure among farmed populations, with most of them being genetically similar to L. Albert and L. Kyoga fish. Admixture results showed a higher (2.55-52.75%) contribution of L. Albert / L. Kyoga stocks to Uganda's farmed fish than the stock from L. Victoria (2.12-28.02%). We observed relatively high genetic diversity across both wild and farmed populations, but some farms had sizable numbers of highly inbred fish, raising concerns about management practices. In addition, we identified a genomic region on chromosome 5, harbouring the key innate immune gene BPI and the key growth gene GHRH, putatively under selection in the Ugandan Nile tilapia population. This region overlaps with the genomic region previously identified to be associated with growth rate in farmed Nile tilapia.
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Affiliation(s)
- Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Joel Ogwang
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB), P.O. Box 183, Nsamizi Road, Entebbe, Uganda
| | - Ezra Byakora
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB), P.O. Box 183, Nsamizi Road, Entebbe, Uganda
| | - Jennifer Nascimento Schulze
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK; Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, Kiel 24105, Germany
| | - Katali Kirungi Benda
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB), P.O. Box 183, Nsamizi Road, Entebbe, Uganda
| | - Clemence Fraslin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Sarah Salisbury
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Moses Solimo
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB), P.O. Box 183, Nsamizi Road, Entebbe, Uganda
| | - Johnson Francis Mayega
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, P.O. Box, 7062, Kampala, Uganda
| | - Beine Peter
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB), P.O. Box 183, Nsamizi Road, Entebbe, Uganda
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, P.O. Box, 7062, Kampala, Uganda
| | - Ross Houston
- Benchmark Genetics, 1 Pioneer Building, Edinburgh Technopole, Penicuik EH26 0GB, United Kingdom
| | - Robert Mukiibi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK.
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8
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Dinhobl M, Spinard E, Tesler N, Birtley H, Signore A, Ambagala A, Masembe C, Borca MV, Gladue DP. Reclassification of ASFV into 7 Biotypes Using Unsupervised Machine Learning. Viruses 2023; 16:67. [PMID: 38257767 PMCID: PMC10819123 DOI: 10.3390/v16010067] [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: 12/05/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
In 2007, an outbreak of African swine fever (ASF), a deadly disease of domestic swine and wild boar caused by the African swine fever virus (ASFV), occurred in Georgia and has since spread globally. Historically, ASFV was classified into 25 different genotypes. However, a newly proposed system recategorized all ASFV isolates into 6 genotypes exclusively using the predicted protein sequences of p72. However, ASFV has a large genome that encodes between 150-200 genes, and classifications using a single gene are insufficient and misleading, as strains encoding an identical p72 often have significant mutations in other areas of the genome. We present here a new classification of ASFV based on comparisons performed considering the entire encoded proteome. A curated database consisting of the protein sequences predicted to be encoded by 220 reannotated ASFV genomes was analyzed for similarity between homologous protein sequences. Weights were applied to the protein identity matrices and averaged to generate a genome-genome identity matrix that was then analyzed by an unsupervised machine learning algorithm, DBSCAN, to separate the genomes into distinct clusters. We conclude that all available ASFV genomes can be classified into 7 distinct biotypes.
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Affiliation(s)
- Mark Dinhobl
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, NY 11957, USA; (M.D.); (E.S.); (N.T.); (H.B.)
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.S.); (A.A.); (C.M.)
| | - Edward Spinard
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, NY 11957, USA; (M.D.); (E.S.); (N.T.); (H.B.)
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.S.); (A.A.); (C.M.)
| | - Nicolas Tesler
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, NY 11957, USA; (M.D.); (E.S.); (N.T.); (H.B.)
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Hillary Birtley
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, NY 11957, USA; (M.D.); (E.S.); (N.T.); (H.B.)
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Anthony Signore
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.S.); (A.A.); (C.M.)
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Aruna Ambagala
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.S.); (A.A.); (C.M.)
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Charles Masembe
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.S.); (A.A.); (C.M.)
- Department of Zoology, Entomology and Fisheries Sciences, School of Biosciences, College of Natural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Manuel V. Borca
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, NY 11957, USA; (M.D.); (E.S.); (N.T.); (H.B.)
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.S.); (A.A.); (C.M.)
| | - Douglas P. Gladue
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, NY 11957, USA; (M.D.); (E.S.); (N.T.); (H.B.)
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.S.); (A.A.); (C.M.)
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Lukindu M, Mukwaya LG, Masembe C, Birungi J. Behavioral Changes of Some Arboviral Vectors in Zika Forest: A Concern for Emerging and Re-Emerging Diseases in Uganda. Vector Borne Zoonotic Dis 2023; 23:653-661. [PMID: 37669008 DOI: 10.1089/vbz.2023.0026] [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] [Indexed: 09/06/2023] Open
Abstract
Background: The increasing reports on emerging/re-emerging arboviral disease outbreaks or epidemics in Sub-Saharan Africa have been impacted by factors, including the changing climate plus human activities that have resulted in land cover changes. These factors influence the prevalence, incidence, behavior, and distribution of vectors and vector-borne diseases. In this study, we assessed the potential effect of land cover changes on the distribution and oviposition behavior of some arboviral vectors in Zika forest, Uganda, which has decreased by an estimated 7 hectares since 1952 due to an increase in anthropogenic activities in the forest and its periphery. Materials and Methods: Immature mosquitoes were collected using bamboo pots and placed at various levels of a steel tower in the forest and at different intervals from the forest periphery to areas among human dwellings. Collections were conducted for 20 months. Results and Conclusion: Inside the forest, 22,280 mosquitoes were collected belonging to four arboviral vectors: Aedes aegypti, Aedes africanus, Aedes apicoargenteus, and Aedes cumminsii. When compared with similar studies conducted in the forest in 1964, there was a change from a sylvatic to a tendency of peridomestic behavior in A. africanus, which was now collected among human dwellings. There was an unexpected change in the distribution of A. aegypti, which was not only collected outside the forest as in previous reports but also collected in the forest. Conversely, A. cumminsii originally collected in the forest expanded its ranges with collections outside the forest in this study. Aedes simpsoni maintained its distribution range outside the forest among agricultural sites. We suspect that land cover changes were favorable to most of the arboviral vectors hence enhancing their proliferation and habitat range. This potentially increases the transmission of arboviral diseases in the area, hence impacting the epidemiology of emerging/remerging diseases in Uganda.
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Affiliation(s)
- Martin Lukindu
- Department of Entomology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Louis G Mukwaya
- Department of Entomology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Science, College of Natural Sciences School, Makerere University, Kampala, Uganda
| | - Josephine Birungi
- Department of Entomology, Uganda Virus Research Institute, Entebbe, Uganda
- International Livestock Research Institute, Nairobi, Kenya
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10
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Aliro T, Odongo W, Ståhl K, Dione MM, Okello DM, Masembe C, Chenais E. Actions and perceived impact of African swine fever control measures along the smallholder pig value chain in Uganda. Trop Anim Health Prod 2023; 55:410. [PMID: 37987884 PMCID: PMC10663180 DOI: 10.1007/s11250-023-03828-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023]
Abstract
Pig production in Uganda is constrained by African swine fever (ASF) which is endemic in the country. Current measures taken by the Government of Uganda in controlling ASF outbreaks include trade and livestock movement restrictions, called "quarantine." Little is known about the actions of, and impact of value chain actors in response to ASF quarantines. This study describes actions that different stakeholders in the smallholder pig value chain took, and the perceived economic impact, during ASF quarantines. Data was collected in ten focus group discussions (FGD) using participatory epidemiology tools and two key informants' (KIs) interviews with District Veterinary Officers (DVOs) of Kisoro and Moyo districts in Uganda. The results show that during ASF quarantine, pig value chain actors shifted their activities from formal places such as livestock markets, slaughter slabs, pork butcheries and pork joints to informal places such as farmers' homesteads. Farmers were perceived the most economically affected stakeholder group with forgone income due to unsold pigs, costs for implementing biosecurity measures and extra costs for feeding unsold pigs being the major perceived causes of the losses. The continued trade in pigs and pig products in informal marketplaces suggests that quarantine might not be effective for hindering activities that might spread ASF in these settings. The perceived economic losses provide an insight into the negative economic impact of the quarantine for the different stakeholders.
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Affiliation(s)
- Tonny Aliro
- Faculty of Agriculture and Environment, Gulu University, P. O. Box 166, Gulu, Uganda.
| | - Walter Odongo
- Faculty of Agriculture and Environment, Gulu University, P. O. Box 166, Gulu, Uganda
| | - Karl Ståhl
- Department of Disease Control and Epidemiology, National Veterinary Institute, Uppsala, Sweden
| | - Michel Mainack Dione
- International Livestock Research Institute (ILRI), P. O. Box 30709, Nairobi, Kenya
| | - Daniel Micheal Okello
- Faculty of Agriculture and Environment, Gulu University, P. O. Box 166, Gulu, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Erika Chenais
- Department of Disease Control and Epidemiology, National Veterinary Institute, Uppsala, Sweden
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11
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Spinard E, Dinhobl M, Tesler N, Birtley H, Signore AV, Ambagala A, Masembe C, Borca MV, Gladue DP. A Re-Evaluation of African Swine Fever Genotypes Based on p72 Sequences Reveals the Existence of Only Six Distinct p72 Groups. Viruses 2023; 15:2246. [PMID: 38005923 PMCID: PMC10675559 DOI: 10.3390/v15112246] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The African swine fever virus (ASFV) is currently causing a world-wide pandemic of a highly lethal disease in domestic swine and wild boar. Currently, recombinant ASF live-attenuated vaccines based on a genotype II virus strain are commercially available in Vietnam. With 25 reported ASFV genotypes in the literature, it is important to understand the molecular basis and usefulness of ASFV genotyping, as well as the true significance of genotypes in the epidemiology, transmission, evolution, control, and prevention of ASFV. Historically, genotyping of ASFV was used for the epidemiological tracking of the disease and was based on the analysis of small fragments that represent less than 1% of the viral genome. The predominant method for genotyping ASFV relies on the sequencing of a fragment within the gene encoding the structural p72 protein. Genotype assignment has been accomplished through automated phylogenetic trees or by comparing the target sequence to the most closely related genotyped p72 gene. To evaluate its appropriateness for the classification of genotypes by p72, we reanalyzed all available genomic data for ASFV. We conclude that the majority of p72-based genotypes, when initially created, were neither identified under any specific methodological criteria nor correctly compared with the already existing ASFV genotypes. Based on our analysis of the p72 protein sequences, we propose that the current twenty-five genotypes, created exclusively based on the p72 sequence, should be reduced to only six genotypes. To help differentiate between the new and old genotype classification systems, we propose that Arabic numerals (1, 2, 8, 9, 15, and 23) be used instead of the previously used Roman numerals. Furthermore, we discuss the usefulness of genotyping ASFV isolates based only on the p72 gene sequence.
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Affiliation(s)
- Edward Spinard
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Foreign Animal Disease Research Unit, Orient, NY 11957, USA; (E.S.); (M.D.); (N.T.); (H.B.)
- National Bio and Agro-Defense Facility, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.V.S.); (A.A.); (C.M.)
| | - Mark Dinhobl
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Foreign Animal Disease Research Unit, Orient, NY 11957, USA; (E.S.); (M.D.); (N.T.); (H.B.)
- National Bio and Agro-Defense Facility, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.V.S.); (A.A.); (C.M.)
| | - Nicolas Tesler
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Foreign Animal Disease Research Unit, Orient, NY 11957, USA; (E.S.); (M.D.); (N.T.); (H.B.)
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Hillary Birtley
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Foreign Animal Disease Research Unit, Orient, NY 11957, USA; (E.S.); (M.D.); (N.T.); (H.B.)
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Anthony V. Signore
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.V.S.); (A.A.); (C.M.)
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Aruna Ambagala
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.V.S.); (A.A.); (C.M.)
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Charles Masembe
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.V.S.); (A.A.); (C.M.)
- College of Natural Resources (CoNAS), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Manuel V. Borca
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Foreign Animal Disease Research Unit, Orient, NY 11957, USA; (E.S.); (M.D.); (N.T.); (H.B.)
- National Bio and Agro-Defense Facility, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.V.S.); (A.A.); (C.M.)
| | - Douglas P. Gladue
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Foreign Animal Disease Research Unit, Orient, NY 11957, USA; (E.S.); (M.D.); (N.T.); (H.B.)
- National Bio and Agro-Defense Facility, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.V.S.); (A.A.); (C.M.)
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12
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Masembe C, Benda KK, Opoola O, Francis MJ, Ndinawe RP, Beine P, Mukiibi R. A case of forensic genomics in Uganda reveals animal ownership and low exotic genetic introgression in indigenous cattle. Vet Med Sci 2023; 9:2844-2851. [PMID: 37725326 PMCID: PMC10650367 DOI: 10.1002/vms3.1272] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND The cattle industry contributes to Uganda's agricultural output. It faces challenges that include theft and parentage ascertainment. These challenges can benefit from recent molecular genomics and bioinformatics technologies. OBJECTIVES We employed genomic analyses to establish potential ownership of a group of nine cattle that were being claimed by two farmers in Uganda. We investigated the genetic relationship of Ugandan cattle with regional indigenous breeds as well as exotic breeds that are currently present in Uganda. In addition, we investigated regions that are likely to be under selection in the Ugandan cattle. METHODS Hair samples were collected from seven and two animals from farmers A and B, respectively. They were genotyped for 53,218 Single Nucleotide Polymorphism markers. To establish genetic relationships between the sampled animals, we performed genomic analyses including, principal component analysis (PCA), hierarchical clustering analysis and identity by state/descent. We also performed admixture and runs of homozygosity analyses to assess the ancestry composition and identify regions potentially under selection in Ugandan cattle, respectively. RESULTS The seven animals from Farmer A were genetically close to each other but showed minimal relationship with the disputed animals. The two animals from Farmer B were genetically distant from each other but showed greater similarity to four of the disputed animals. Four of the disputed animals showed great dissimilarity from the animals of both farmers. Comparison of these with the reference breeds revealed minimal European exotic genetic introgression into these animals, but rather high similarity to the Sheko. Results also revealed high homozygosity in the major histocompatibility complex regions. CONCLUSIONS Our results demonstrate the use of currently available genomic tools to empirically establish the ownership of cattle; these could be scaled up as a resourceful and viable tool that could be employed to support conflict resolution where reliable livestock identification is unavailable.
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Affiliation(s)
- Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural SciencesMakerere UniversityKampalaUganda
| | - Kirungi Katali Benda
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural SciencesMakerere UniversityKampalaUganda
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB)EntebbeUganda
| | - Oluyinka Opoola
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUK
- Centre for Tropical Livestock Genetics and Health (CTLGH)University of EdinburghEdinburghUK
| | - Mayega Johnson Francis
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural SciencesMakerere UniversityKampalaUganda
| | - Ruth Pamela Ndinawe
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB)EntebbeUganda
| | - Peter Beine
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB)EntebbeUganda
| | - Robert Mukiibi
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUK
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Ambagala A, Goonewardene K, Lamboo L, Goolia M, Erdelyan C, Fisher M, Handel K, Lung O, Blome S, King J, Forth JH, Calvelage S, Spinard E, Gladue DP, Masembe C, Adedeji AJ, Olubade T, Maurice NA, Ularamu HG, Luka PD. Characterization of a Novel African Swine Fever Virus p72 Genotype II from Nigeria. Viruses 2023; 15:v15040915. [PMID: 37112895 PMCID: PMC10146018 DOI: 10.3390/v15040915] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/22/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
African swine fever (ASF) is a high-consequence transboundary hemorrhagic fever of swine. It continues to spread across the globe causing socio-economic issues and threatening food security and biodiversity. In 2020, Nigeria reported a major ASF outbreak, killing close to half a million pigs. Based on the partial sequences of the genes B646L (p72) and E183L (p54), the virus responsible for the outbreak was identified as an African swine fever virus (ASFV) p72 genotype II. Here, we report further characterization of ASFV RV502, one of the isolates obtained during the outbreak. The whole genome sequence of this virus revealed a deletion of 6535 bp between the nucleotide positions 11,760–18,295 of the genome, and an apparent reverse complement duplication of the 5′ end of the genome at the 3′ end. Phylogenetically, ASFV RV502 clustered together with ASFV MAL/19/Karonga and ASFV Tanzania/Rukwa/2017/1 suggesting that the virus responsible for the 2020 outbreak in Nigeria has a South-eastern African origin.
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Affiliation(s)
- Aruna Ambagala
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Kalhari Goonewardene
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Lindsey Lamboo
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Melissa Goolia
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Cassidy Erdelyan
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Mathew Fisher
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Katherine Handel
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Oliver Lung
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Sandra Blome
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald, Germany
| | - Jacqueline King
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald, Germany
| | - Jan Hendrik Forth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald, Germany
| | - Sten Calvelage
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald, Germany
| | - Edward Spinard
- Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, NY 11944, USA
| | - Douglas P. Gladue
- Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, NY 11944, USA
| | - Charles Masembe
- College of Natural Resources (CoNAS), Makerere University, Kampala P.O Box 7062, Uganda
| | | | - Toyin Olubade
- National Veterinary Research Institute, Vom 930103, Nigeria
| | | | | | - Pam D. Luka
- National Veterinary Research Institute, Vom 930103, Nigeria
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14
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Masembe C, Adedeji AJ, Jambol AR, Weka R, Muwanika V, Luka PD. Diversity and emergence of new variants of African swine fever virus Genotype I circulating in domestic pigs in Nigeria (2016-2018). Vet Med Sci 2023; 9:819-828. [PMID: 36377750 PMCID: PMC10152979 DOI: 10.1002/vms3.988] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND African swine fever (ASF) is the most lethal disease of pigs caused by ASF virus (ASFV) with severe economic implications and threat to the swine industry in endemic countries. Between 2016 and 2018, several ASF outbreaks were reported throughout pig producing states in Nigeria. OBJECTIVES Thereafter, this study was designed to identify the ASFV genotypes responsible for these outbreaks within the study period (2016-2018). METHODS Twenty-two ASFV-positive samples by polymerase chain reaction were selected. The samples were collected during passive surveillance in eight states of Nigeria were characterised using 3 partial genes sequences of the virus namely, p72 capsid protein of the B646L, p54 envelope protein of E183L and the central variable region (CVR) within B602L of ASFV. RESULTS Phylogenetic and sequences analysis based on p72 and p54 revealed ASFV genotype I as the circulating virus. Sequence analysis of the CVR of B602L revealed genetic variations with six ASFV tandem repeat sequence (TRS) variants namely, Tet-15, Tet-20a, Tet-21b, Tet-27, Tet-31 and Tet-34, thus increasing the overall genetic diversity of ASFV in Nigeria. Three of the TRS variants, Tet-21b, Tet-31 and Tet-34, were identified for the first time in Nigeria. The new TRS variants of ASFV genotype I were identified in Enugu, Imo, Plateau and Taraba states, while co-circulation of multiple variants of ASFV genotype I was recorded in Plateau and Benue states. CONCLUSIONS The high genetic diversity, emergence and increasing recovery of new variants of genotype I in Nigeria should be a concern given that ASFV is a relatively stable DNA virus. The epidemiological implications of these findings require further investigation.
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Affiliation(s)
- C Masembe
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - A J Adedeji
- College of Natural Sciences, Makerere University, Kampala, Uganda
- Biotechnology Division, National Veterinary Research Institute, Vom, Nigeria
| | - A R Jambol
- College of Natural Sciences, Makerere University, Kampala, Uganda
- Biotechnology Division, National Veterinary Research Institute, Vom, Nigeria
| | - R Weka
- Biotechnology Division, National Veterinary Research Institute, Vom, Nigeria
| | - V Muwanika
- College of Agricultural & Environmental Sciences, Makerere University, Kampala, Uganda
| | - P D Luka
- Biotechnology Division, National Veterinary Research Institute, Vom, Nigeria
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Atim SA, Niebel M, Ashraf S, Vudriko P, Odongo S, Balinandi S, Aber P, Bameka R, Ademun AR, Masembe C, Tweyongyere R, Thomson EC. Prevalence of Crimean-Congo haemorrhagic fever in livestock following a confirmed human case in Lyantonde district, Uganda. Parasit Vectors 2023; 16:7. [PMID: 36611216 PMCID: PMC9824997 DOI: 10.1186/s13071-022-05588-x] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/13/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Crimean-Congo haemorrhagic fever (CCHF) is a tick-borne viral infection, characterized by haemorrhagic fever in humans and transient asymptomatic infection in animals. It is an emerging human health threat causing sporadic outbreaks in Uganda. We conducted a detailed outbreak investigation in the animal population following the death from CCHF of a 42-year-old male cattle trader in Lyantonde district, Uganda. This was to ascertain the extent of CCHF virus (CCHFV) circulation among cattle and goats and to identify affected farms and ongoing increased environmental risk for future human infections. METHODS We collected blood and tick samples from 117 cattle and 93 goats, and tested these for anti-CCHFV antibodies and antigen using an enzyme-linked immunosorbent assay (ELISA), quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and target enrichment next generation sequencing. RESULTS CCHFV-specific IgG antibodies were detected in 110/117 (94.0%) cattle and 83/93 (89.3%) goats. Animal seropositivity was independently associated with female animals (AOR = 9.42, P = 0.002), and animals reared under a pastoral animal production system (AOR = 6.02, P = 0.019] were more likely to be seropositive than tethered or communally grazed animals. CCHFV was detected by sequencing in Rhipicephalus appendiculatus ticks but not in domestic animals. CONCLUSION This investigation demonstrated very high seroprevalence of CCHFV antibodies in both cattle and goats in farms associated with a human case of CCHF in Lyantonde. Therefore, building surveillance programs for CCHF around farms in this area and the Ugandan cattle corridor is indicated, in order to identify opportunities for case prevention and control.
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Affiliation(s)
- Stella A Atim
- College of Veterinary Medicine, Animal Resources and Biosecurity (CoVAB), Makerere University, Kampala, Uganda
- Centre of Virus Research (CVR), University of Glasgow, Glasgow, UK
- Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda
| | - Marc Niebel
- Centre of Virus Research (CVR), University of Glasgow, Glasgow, UK
| | - Shirin Ashraf
- Centre of Virus Research (CVR), University of Glasgow, Glasgow, UK
| | - Patrick Vudriko
- College of Veterinary Medicine, Animal Resources and Biosecurity (CoVAB), Makerere University, Kampala, Uganda
| | - Steven Odongo
- College of Veterinary Medicine, Animal Resources and Biosecurity (CoVAB), Makerere University, Kampala, Uganda
| | - Stephen Balinandi
- Department of Emerging, Re-Emerging and Arbovirus Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Peace Aber
- Case Western Research Collaboration, Makerere University, Kampala, Uganda
| | - Ronald Bameka
- Lyantonde District Local Government, Lyantonde, Uganda
| | - Anna R Ademun
- Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda
| | - Charles Masembe
- College of Natural Resources (CoNAS), Makerere University, Kampala, Uganda
| | - Robert Tweyongyere
- College of Veterinary Medicine, Animal Resources and Biosecurity (CoVAB), Makerere University, Kampala, Uganda
| | - Emma C Thomson
- Centre of Virus Research (CVR), University of Glasgow, Glasgow, UK.
- MRC-University of Glasgow Centre for Virus Research, Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK.
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16
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Atim SA, Ashraf S, Belij-Rammerstorfer S, Ademun AR, Vudriko P, Nakayiki T, Niebel M, Shepherd J, Balinandi S, Nakanjako G, Abaasa A, Johnson PC, Odongo S, Esau M, Bahati M, Kaleebu P, Lutwama JJ, Masembe C, Lambe T, Thomson EC, Tweyongyere R. Risk factors for Crimean-Congo Haemorrhagic Fever (CCHF) virus exposure in farming communities in Uganda. J Infect 2022; 85:693-701. [PMID: 36108783 PMCID: PMC9731351 DOI: 10.1016/j.jinf.2022.09.007] [Citation(s) in RCA: 6] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/06/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Crimean-Congo Haemorrhagic Fever (CCHF) is an emerging human-health threat causing sporadic outbreaks in livestock farming communities. However, the full extent and the risks associated with exposure of such communities has not previously been well-described. METHODS We collected blood samples from 800 humans, 666 cattle, 549 goats and 32 dogs in districts within and outside Ugandan cattle corridor in a cross-sectional survey, and tested for CCHFV-specific IgG antibodies using Enzyme-Linked Immunosorbent Assays. Sociodemographic and epidemiological data were recorded using structured questionnaire. Ticks were collected to identify circulating nairoviruses by metagenomic sequencing. RESULTS CCHFV seropositivity was in 221/800 (27·6%) in humans, 612/666 (91·8%) in cattle, 413/549 (75·2%) in goats and 18/32 (56·2%) in dogs. Human seropositivity was associated with livestock farming (AOR=5·68, p<0·0001), age (AOR=2·99, p=0·002) and collecting/eating engorged ticks (AOR=2·13, p=0·004). In animals, seropositivity was higher in cattle versus goats (AOR=2·58, p<0·0001), female sex (AOR=2·13, p=0·002) and heavy tick infestation (>50 ticks: AOR=3·52, p=0·004). CCHFV was identified in multiple tick pools of Rhipicephalus appendiculatus. INTERPRETATION The very high CCHF seropositivity especially among livestock farmers and multiple regional risk factors associated exposures, including collecting/eating engorged ticks previously unrecognised, highlights need for further surveillance and sensitisation and control policies against the disease.
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Affiliation(s)
- Stella A. Atim
- College of Veterinary Medicine, Animal Resources and Biosecurity (CoVAB), Makerere University, Kampala, Uganda,MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom,Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda
| | - Shirin Ashraf
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | - Anna R Ademun
- Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda
| | - Patrick Vudriko
- College of Veterinary Medicine, Animal Resources and Biosecurity (CoVAB), Makerere University, Kampala, Uganda
| | - Teddy Nakayiki
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Marc Niebel
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - James Shepherd
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Stephen Balinandi
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Gladys Nakanjako
- Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda,Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Andrew Abaasa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe Uganda
| | - Paul C.D. Johnson
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Steven Odongo
- College of Veterinary Medicine, Animal Resources and Biosecurity (CoVAB), Makerere University, Kampala, Uganda
| | - Martin Esau
- Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda
| | - Milton Bahati
- Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda
| | - Pontiano Kaleebu
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute, Entebbe, Uganda,MRC/UVRI and LSHTM Uganda Research Unit, Entebbe Uganda
| | - Julius J Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Charles Masembe
- College of Natural Resources (CoNAS), Makerere University, Kampala, Uganda
| | - Teresa Lambe
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Emma C. Thomson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom,London School of Hygiene and Tropical Medicine, London, UK
| | - Robert Tweyongyere
- College of Veterinary Medicine, Animal Resources and Biosecurity (CoVAB), Makerere University, Kampala, Uganda,Corresponding Authors.
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Adedeji AJ, Atai RB, Gyang HE, Gambo P, Habib MA, Weka R, Muwanika VB, Masembe C, Luka PD. Live pig markets are hotspots for spread of African swine fever virus in Nigeria. Transbound Emerg Dis 2022; 69:e1526-e1540. [PMID: 35179830 DOI: 10.1111/tbed.14483] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 01/13/2022] [Revised: 02/08/2022] [Accepted: 02/16/2022] [Indexed: 11/28/2022]
Abstract
Livestock trading through live animal markets are potential pathways for the introduction and spread of economically important pathogens like the African swine fever virus (ASFV) to new areas in several countries. Due to the high demand for live pigs in Nigeria both for restocking and slaughter, live pigs are sold at designated live pig markets (LPM) in the country. This involves movement of pigs over long distances. Despite, reports of ASF outbreaks following restocking of pigs bought from LPMs, there is paucity of information on the role of LPMs in the epidemiology of ASF. In this study, data and pig samples (whole blood, sera, tissue) were collected from 4 selected LPMs in Nigeria (Dawaki, Katsit, Numan & Pandam) between 2019 and 2020. Samples were analysed by polymerase chain reaction (PCR) and Enzyme-linked Immunosorbent Assay (ELISA). Four genes of ASFV positive samples were characterized to identify the circulating genotypes. Results revealed trade activities involving transportation of pigs from these selected markets to 42 major cities and towns in thirteen (13) States of Nigeria. PCR results revealed an overall ASF prevalence of 10.77% (66/613). ASFV was confirmed by PCR in all the selected LPMs with a prevalence rate of 3.13%-23.81%. The phylogeny revealed genotype I and serogroup 4 based on the p72 protein that encodes the B646L gene and the EP402R gene encoding the CD2V. While sequence analysis of CVR of B602L gene revealed 8 tetrameric repeats variants, six of which have never been reported in Nigeria. Analysis of sera samples recorded a seroprevalence of 6.9% (16/217) within the study period. Findings from this study show that LPM are hotspots and channels for transmission and continuous spread of ASFV in Nigeria. Therefore, for ASF to be controlled in Nigeria, disease surveillance and regulation at LPMs are critical. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Adeyinka J Adedeji
- National Veterinary Research Institute, Vom, Nigeria.,College of Natural Sciences, Makerere University, P.O. Box 7062, Kampala, Kampala, Uganda
| | | | - Helen E Gyang
- National Veterinary Research Institute, Vom, Nigeria
| | - Panzam Gambo
- Federal College of Animal Health and Production Technology, Vom, Nigeria
| | - Maimuna A Habib
- Animal Health and Clinical Services Division, Federal Ministry of Agriculture and Rural Development, Abuja, Nigeria
| | - Rebecca Weka
- National Veterinary Research Institute, Vom, Nigeria
| | - Vincent B Muwanika
- College of Agricultural & Environmental Sciences, Makerere University, Kampala, P.O. Box 7062, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, P.O. Box 7062, Kampala, Kampala, Uganda
| | - Pam D Luka
- National Veterinary Research Institute, Vom, Nigeria
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18
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Aliro T, Chenais E, Odongo W, Okello DM, Masembe C, Ståhl K. Prevention and Control of African Swine Fever in the Smallholder Pig Value Chain in Northern Uganda: Thematic Analysis of Stakeholders' Perceptions. Front Vet Sci 2022; 8:707819. [PMID: 35097036 PMCID: PMC8793068 DOI: 10.3389/fvets.2021.707819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022] Open
Abstract
African swine fever (ASF) is endemic in Uganda and considered a major constraint to pig production. In the absence of a vaccine, biosecurity is key for ASF prevention and control. To improve prevention and control on farm and community level there is need for more knowledge on current application of biosecurity practises, and better understanding of how pig value chain actors perceive prevention and control. To achieve this, a qualitative interview study involving focus group discussions (FGD) was conducted with actors from the smallholder pig value chain in northern Uganda. Six villages were purposively selected based on previous outbreaks of ASF, preliminary perceived willingness to control ASF, and the representation of several different value chain actors in the village. Results indicated that biosecurity practises such as basic hygiene routines including safe carcass handling, minimising direct and indirect contacts between pigs or between pigs and people, trade restrictions and sharing of disease information were implemented in some of the villages. Thematic analysis based on grounded theory revealed six categories of data relating to ASF prevention and control. Together these categories form a logical framework including both enablers and hindrances for ASF prevention and control. In summary participants mostly had positive perceptions of ASF biosecurity, describing measures as effective. Participants further possessed knowledge of ASF and its transmission, some of which was in line with known scientific knowledge and some not. Nevertheless, participants were hindered from preventing and controlling ASF due to biosecurity costs and a need to prioritise family livelihood over disease transmission risks, incompatibility of current biosecurity practises with local culture, traditions and social contexts and finally lack of access to veterinarians or, occasionally, low-quality veterinary services. The constraints could be addressed by applying participatory processes in designing biosecurity measures to ensure better adaptation to local cultural and social contexts.
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Affiliation(s)
- T. Aliro
- Faculty of Agriculture and Environment, Gulu University, Gulu, Uganda
| | - E. Chenais
- Department of Disease Control and Epidemiology, National Veterinary Institute, Uppsala, Sweden
- *Correspondence: E. Chenais
| | - W. Odongo
- Faculty of Agriculture and Environment, Gulu University, Gulu, Uganda
| | - D. M. Okello
- Faculty of Agriculture and Environment, Gulu University, Gulu, Uganda
| | - C. Masembe
- Department of Zoology, Entomology and Fisheries Science, College of Natural Sciences, Makerere University, Kampala, Uganda
| | - K. Ståhl
- Department of Disease Control and Epidemiology, National Veterinary Institute, Uppsala, Sweden
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Franzo G, Settypalli TBK, Agusi ER, Meseko C, Minoungou G, Ouoba BL, Habibata ZL, Wade A, de Barros JL, Tshilenge CG, Gelaye E, Yami M, Gizaw D, Chibssa TR, Anahory IV, Mapaco LP, Achá SJ, Ijomanta J, Jambol AR, Adedeji AJ, Luka PD, Shamaki D, Diop M, Bakhoum MT, Lo MM, Chang'a JS, Magidanga B, Mayenga C, Ziba MW, Dautu G, Masembe C, Achenbach J, Molini U, Cattoli G, Lamien CE, Dundon WG. Porcine circovirus-2 in Africa: Identification of continent-specific clusters and evidence of independent viral introductions from Europe, North America and Asia. Transbound Emerg Dis 2021; 69:e1142-e1152. [PMID: 34812571 DOI: 10.1111/tbed.14400] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/02/2021] [Accepted: 11/11/2021] [Indexed: 01/16/2023]
Abstract
Porcine circovirus-2 (PCV-2) is associated with several disease syndromes in domestic pigs that have a significant impact on global pig production and health. Currently, little is known about the status of PCV-2 in Africa. In this study, a total of 408 archived DNA samples collected from pigs in Burkina Faso, Cameroon, Cape Verde, Ethiopia, the Democratic Republic of the Congo, Mozambique, Nigeria, Senegal, Tanzania and Zambia between 2000 and 2018 were screened by PCR for the presence of PCV-2. Positive amplicons of the gene encoding the viral capsid protein (ORF2) were sequenced to determine the genotypes circulating in each country. Four of the nine currently known genotypes of PCV-2 were identified (i.e. PCV-2a, PCV-2b, PCV-2d and PCV-2 g) with more than one genotype being identified in Burkina Faso, Ethiopia, Nigeria, Mozambique, Senegal and Zambia. Additionally, a phylogeographic analysis which included 38 additional ORF2 gene sequences of PCV-2s previously identified in Mozambique, Namibia and South Africa from 2014 to 2016 and 2019 to 2020 and available in public databases, demonstrated the existence of several African-specific clusters and estimated the approximate time of introduction of PCV-2s into Africa from other continents. This is the first in-depth study of PCV-2 in Africa and it has important implications for pig production at both the small-holder and commercial farm level on the continent.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | - Tirumala B K Settypalli
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Centre, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | | | - Clement Meseko
- National Veterinary Research Institute, Vom, Plateau State, Nigeria
| | | | | | | | - Abel Wade
- National Veterinary Laboratory (LANAVET), Garoua, Cameroon
| | - José Luís de Barros
- Direction Génerale de l`Agriculture, Sylviculture et Élèvage, Direction des Services Vétérinaires, Cape Verde
| | | | - Esayas Gelaye
- National Veterinary Institute (NVI), Debre Zeit, Ethiopia
| | - Martha Yami
- National Veterinary Institute (NVI), Debre Zeit, Ethiopia
| | - Daniel Gizaw
- National Animal Health Diagnostic and Investigation Center (NAHDIC), Sebeta, Ethiopia
| | | | - Iolanda Vieira Anahory
- Directorate of Animal Science, Central Veterinary Laboratory, Agrarian Research Institute of Mozambique, Maputo, Mozambique
| | - Lourenço P Mapaco
- Directorate of Animal Science, Central Veterinary Laboratory, Agrarian Research Institute of Mozambique, Maputo, Mozambique
| | - Sara J Achá
- Directorate of Animal Science, Central Veterinary Laboratory, Agrarian Research Institute of Mozambique, Maputo, Mozambique
| | | | | | | | - Pam Dachung Luka
- National Veterinary Research Institute, Vom, Plateau State, Nigeria
| | - David Shamaki
- National Veterinary Research Institute, Vom, Plateau State, Nigeria
| | - Mariame Diop
- Laboratoire National de l'Elevage et de Recherches Vétérinaires, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Sénégal
| | - Mame Thierno Bakhoum
- Laboratoire National de l'Elevage et de Recherches Vétérinaires, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Sénégal
| | - Modou Moustapha Lo
- Laboratoire National de l'Elevage et de Recherches Vétérinaires, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Sénégal
| | - Jelly S Chang'a
- Centre for Infectious Diseases and Biotechnology, Tanzania Veterinary Laboratory Agency, Dares Salaam, Tanzania
| | - Bishop Magidanga
- Centre for Infectious Diseases and Biotechnology, Tanzania Veterinary Laboratory Agency, Dares Salaam, Tanzania
| | - Charles Mayenga
- Centre for Infectious Diseases and Biotechnology, Tanzania Veterinary Laboratory Agency, Dares Salaam, Tanzania
| | - Maureen Wakwamba Ziba
- Department of Veterinary Services Ministry of Fisheries and Livestock, Central Veterinary Research Institute, Lusaka, Zambia
| | - George Dautu
- Department of Veterinary Services Ministry of Fisheries and Livestock, Central Veterinary Research Institute, Lusaka, Zambia
| | - Charles Masembe
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | | | - Umberto Molini
- School of Veterinary Medicine, Faculty of Health Sciences and Veterinary Medicine, University of Namibia, Windhoek, Namibia.,Central Veterinary Laboratory (CVL), Windhoek, Namibia
| | - Giovanni Cattoli
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Centre, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - Charles E Lamien
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Centre, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - William G Dundon
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Centre, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
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20
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Ogweng P, Masembe C, Okwasiimire R, Keeya I, Vincent MB. The effectiveness of community-led initiatives in livestock disease control: a case of African swine fever in rural areas of Uganda. Trop Anim Health Prod 2021; 53:542. [PMID: 34762182 DOI: 10.1007/s11250-021-02991-x] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/05/2021] [Indexed: 11/28/2022]
Abstract
Proper implementation of biosecurity is currently the only control measure of African swine fever (ASF) in the absence of an effective vaccine or drug against the disease. Despite the efforts that Uganda's local and central governments have invested to reduce livestock diseases, ASF outbreaks still persist in the country. In this study, we assessed the effectiveness of community-led initiatives in the control of ASF in Mukono District, central Uganda. In Mukono district, a community-led pilot program was initiated where stakeholders in the pig value chain organized themselves into an ASF control task force to enforce on-farm and pig value chain activities intended to limit the spread of ASF. Semi-structured interviews with pig famers (n = 211) were conducted in two areas with contrasting practices: one with active community-initiated and monitored ASF control initiatives since 2016 (Kasawo and Namuganga) and the other without such initiative as the control (Mpunge and Ntenjeru). A significant decline (Wilcoxon ranked sign test: Z = - 5.412, p = 0.000) in the annual frequency of ASF outbreaks in both Kasawo and Namuganga sub-counties was observed after the implementation of community-led initiatives. The level of practice of most ASF control measures was significantly higher (p < 0.01) in sub-counties that instituted community-led ASF control initiatives than in the control sub-counties. The results of this study demonstrate the power of community-led initiatives in reducing ASF disease outbreaks in endemic areas.
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Affiliation(s)
- Peter Ogweng
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda.
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
| | | | - Ibrahim Keeya
- Production Department, Mukono District Local Government, Mukono, Uganda
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21
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Payne A, Ogweng P, Ståhl K, Masembe C, Jori F. Spatial-Temporal Movements of Free Ranging Pigs at the Wildlife-Livestock Interface of Murchison Falls National Park, Uganda: Potential of Disease Control at a Local Scale. Front Vet Sci 2021; 8:689377. [PMID: 34631845 PMCID: PMC8496937 DOI: 10.3389/fvets.2021.689377] [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: 03/31/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022] Open
Abstract
In many Ugandan rural communities, pigs are generally kept under traditional smallholder systems without basic biosecurity measures in place. In some instances, these systems are at the livestock-wildlife interface, as it is the case in Nwoya district, which is bordered by Murchison Falls National Park (MFNP). This pig system has potential for the maintenance and transmission of pathogens like African swine fever (ASF) between different herds, and also with wild pigs (warthogs and bushpigs). In this paper, we describe the spatial and temporal pattern of the movements of free ranging domestic pigs in a rural setting in Northern Uganda where ASF is endemic. We also determine their use of habitat to highlight the potential interaction hotspots between domestic pigs and between domestic and wild pig populations. We fitted 10 free-ranging domestic pigs owned by different homesteads with GPS harnesses during rainy and dry seasons. The pig home range, daily distance, activity pattern and habitat use were calculated. Our results show that the maximum area covered (MCP 100%) by the pigs varied between 35,965 and 475,077 m2. The core area varied from 1,317 to 50,769 m2. The pigs' home ranges were significantly bigger during the dry season than during the rainy season (Wilcoxon test, W = 22, p = 0.04). The mean full day (24 h) distance was longer in the dry season than in the rainy season (Student test, t = 2.7, p = 0.03). The pigs were mostly located within their own homestead, but they also used other homesteads, grass and crop fields. This study highlights that free-ranging domestic pigs may cover a wide area, especially during the dry season. Interestingly, the home range of pigs from different herds may overlap with areas used by wild pigs which share crops and other resources in this area. This study provides insights into a better understanding of the potential for spread of diseases such as ASF at small-scale and can be used to raise awareness of such risks and to better target implementation of preventive measures.
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Affiliation(s)
- Ariane Payne
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, Kampala, Uganda
| | - Peter Ogweng
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, Kampala, Uganda
| | - Karl Ståhl
- National Veterinary Institute, SVA, Uppsala, Sweden
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, Kampala, Uganda
| | - Ferran Jori
- CIRAD, UMR Animal, Santé, Territoires, Risque et Ecosystèmes (ASTRE), Montpellier, France.,UMR ASTRE, University of Montpellier, CIRAD, INRAE, Montpellier, France.,Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
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22
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Penrith ML, Kivaria FM, Masembe C. One hundred years of African swine fever: A tribute to R. Eustace Montgomery. Transbound Emerg Dis 2021; 68:2640-2642. [PMID: 34102005 DOI: 10.1111/tbed.14183] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/05/2021] [Indexed: 01/27/2023]
Affiliation(s)
- Mary-Louise Penrith
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Fredrick M Kivaria
- Emergency Centre for Transboundary Animal Diseases (ECTAD), Regional Office for Eastern Africa, Food and Agriculture Organization of the United Nations (FAO), Nairobi, Kenya
| | - Charles Masembe
- African Swine Fever Research Consortium, Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, Uganda
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23
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Dell B, Masembe C, Gerhold R, Willcox A, Okafor C, Souza M. Species misidentification in local markets: Discrepancies between reporting and molecular identification of bushmeat species in northern Uganda. One Health 2021; 13:100251. [PMID: 33997235 PMCID: PMC8102653 DOI: 10.1016/j.onehlt.2021.100251] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 11/19/2022] Open
Abstract
Bushmeat hunting and consumption, although widely utilized as necessary supplement to household income and nutrition in many regions, presents threats to public health and wildlife conservation efforts. In northern Uganda, consumption of bats and primates, two wildlife groups often implicated in zoonotic disease emergence, is not widely culturally accepted; however, these species are reported by hunters to often be hunted and sold as culturally desirable species, like antelope and warthog. To investigate the prevalence of market bushmeat misidentifiction, we collected 229 bushmeat samples from 23 communities adjacent to Murchison Falls National Park. Reported species was recorded on acquisition for each sample. PCR targeting mammalian cyt b and 12 s rRNA genes and sequencing were performed to identify samples to the lowest taxonomic unit using NCBI BLAST. Overall, 27.9% (61/219) of samples had disparate results between species reported and BLAST analysis. Thirty-four species were identified, with the most frequent wildlife being waterbuck (31.5%), warthog (13.7%), and black rat (5.9%). These data reveal a public health risk for bushmeat consumers in northern Uganda as they cannot assess species-related risk when purchasing bushmeat and take appropriate precautions against zoonotic pathogen exposure. These data also provide insight into regional hunter prey preference and market preference of local community members which may inform conservation strategy in the region. The most frequently identified wildlife species were antelopes. Nearly a 30% discrepancy between species reported at point of sale and PCR confirmation. Samples from hunters had statistically lower discrepancy than cooks and dealers.
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Affiliation(s)
- BreeAnna Dell
- The University of Tennessee at Knoxville, Department of Biomedical and Diagnostic Sciences, Knoxville, TN, USA
| | - Charles Masembe
- Makerere University College of Natural Sciences, Kampala, Uganda
| | - Richard Gerhold
- The University of Tennessee at Knoxville, Department of Biomedical and Diagnostic Sciences, Knoxville, TN, USA
| | - Adam Willcox
- The University of Tennessee at Knoxville, Department of Forestry, Wildlife and Fisheries, Knoxville, TN, USA
| | - Chika Okafor
- The University of Tennessee at Knoxville, Department of Biomedical and Diagnostic Sciences, Knoxville, TN, USA
| | - Marcy Souza
- The University of Tennessee at Knoxville, Department of Biomedical and Diagnostic Sciences, Knoxville, TN, USA
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24
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Badamasi I, Odong R, Masembe C. Gonadal development and intersex condition of marbled lungfish, Protopterus aethiopicus (Heckel, 1851), in contaminated sites in Lake Victoria, Uganda. African Zoology 2020. [DOI: 10.1080/15627020.2020.1811152] [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] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Inuwa Badamasi
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, Kampala, Uganda
| | - Robinson Odong
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, Kampala, Uganda
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, Kampala, Uganda
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25
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Masembe C, Phan MVT, Robertson DL, Cotten M. Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains. Virus Evol 2020; 6:veaa044. [PMID: 32913663 PMCID: PMC7474929 DOI: 10.1093/ve/veaa044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 11/14/2022] Open
Abstract
African swine fever virus (ASFV), belonging to the Asfarviridae family, was originally described in Africa almost 100 years ago and is now spreading uncontrolled across Europe and Asia and threatening to destroy the domestic pork industry. Neither effective antiviral drugs nor protective vaccines are currently available. Efforts to understand the basis for viral pathogenicity and the development of attenuated potential vaccine strains are complicated by the large and complex nature of the ASFV genome. We report here a novel alignment-free method of documenting viral diversity based on profile hidden Markov model domains on a genome scale. The method can be used to infer genomic relationships independent of genome alignments and also reveal ASFV genome sequence differences that determine the presence and characteristics of functional protein domains in the virus. We show that the method can quickly identify differences and shared patterns between virulent and attenuated ASFV strains and will be a useful tool for developing much-needed vaccines and antiviral agents to help control this virus. The tool is rapid to run and easy to implement, readily available as a simple Docker image.
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Affiliation(s)
- Charles Masembe
- College of Natural Sciences, Makerere University, Makerere Hill Road, P. O Box 7062 Kampala, Uganda
| | - My V T Phan
- Viral Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.,Department of Viroscience, Erasmus Medical Centre, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - David L Robertson
- MRC University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Glasgow G61 1QH, UK
| | - Matthew Cotten
- Viral Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.,MRC University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Glasgow G61 1QH, UK.,MRC/UVRI & LSHTM Uganda Research Unit, P.O. Box 49, Plot 51-59 Nakiwogo Road, Entebbe, Uganda
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26
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Tibihika PD, Curto M, Alemayehu E, Waidbacher H, Masembe C, Akoll P, Meimberg H. Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations. BMC Evol Biol 2020; 20:16. [PMID: 32000675 PMCID: PMC6990601 DOI: 10.1186/s12862-020-1583-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/16/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The need for enhancing the productivity of fisheries in Africa triggered the introduction of non-native fish, causing dramatic changes to local species. In East Africa, the extensive translocation of Nile tilapia (Oreochromis niloticus) is one of the major factors in this respect. Using 40 microsatellite loci with SSR-GBS techniques, we amplified a total of 664 individuals to investigate the genetic structure of O. niloticus from East Africa in comparison to Ethiopian and Burkina Faso populations. RESULTS All three African regions were characterized by independent gene-pools, however, the Ethiopian population from Lake Tana was genetically more divergent (Fst = 2.1) than expected suggesting that it might be a different sub-species. In East Africa, the genetic structure was congruent with both geographical location and anthropogenic activities (Isolation By Distance for East Africa, R2 = 0.67 and Uganda, R2 = 0.24). O. niloticus from Lake Turkana (Kenya) was isolated, while in Uganda, despite populations being rather similar to each other, two main natural catchments were able to be defined. We show that these two groups contributed to the gene-pool of different non-native populations. Moreover, admixture and possible hybridization with other tilapiine species may have contributed to the genetic divergence found in some populations such as Lake Victoria. We detected other factors that might be affecting Nile tilapia genetic variation. For example, most of the populations have gone through a reduction in genetic diversity, which can be a consequence of bottleneck (G-W, < 0.5) caused by overfishing, genetic erosion due to fragmentation or founder effect resulting from stocking activities. CONCLUSIONS The anthropogenic activities particularly in the East African O. niloticus translocations, promoted artificial admixture among Nile Tilapia populations. Translocations may also have triggered hybridization with the native congenerics, which needs to be further studied. These events may contribute to outbreeding depression and hence compromising the sustainability of the species in the region.
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Affiliation(s)
- Papius Dias Tibihika
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, 1180 Wien, Austria
- National Agricultural Research Organization, Kachwekano Zonal Agricultural Research and Development Institute, P.O. Box 421, Kabale, Uganda
| | - Manuel Curto
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, 1180 Wien, Austria
| | - Esayas Alemayehu
- National Agricultural Research Organization, Kachwekano Zonal Agricultural Research and Development Institute, P.O. Box 421, Kabale, Uganda
- Institute for Hydrobiology and Aquatic Ecosystems Management, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33/DG, 1180 Wien, Austria
| | - Herwig Waidbacher
- National Fishery and Aquatic Life Research Centre, P.O. Box 64, Addis Ababa, Sebeta Ethiopia
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences-Makerere University Kampala, P. O. Box, 7062 Kampala, Uganda
| | - Peter Akoll
- Department of Zoology, Entomology and Fisheries Sciences-Makerere University Kampala, P. O. Box, 7062 Kampala, Uganda
| | - Harald Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor Mendel Straße 33, 1180 Wien, Austria
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27
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Filipe ADS, Vattipally SB, Mair D, Ogweng P, Mayega J, Muwanika V, Palmarini M, Biek R, Masembe C. Host genome depletion to determine the evolution, genetic diversity and transmission patterns of full genome sequences of African swine fever genotype IX from Uganda. Access Microbiol 2019. [DOI: 10.1099/acmi.imav2019.po0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ana Da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | | | - Daniel Mair
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Peter Ogweng
- College of Natural Sciences, Makerere University, Kampala
| | - Johnson Mayega
- College of Natural Sciences, Makerere University, Kampala
| | | | | | | | - Charles Masembe
- College of Natural Sciences, Makerere University, Kampala
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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28
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Mulumba-Mfumu LK, Saegerman C, Dixon LK, Madimba KC, Kazadi E, Mukalakata NT, Oura CAL, Chenais E, Masembe C, Ståhl K, Thiry E, Penrith ML. African swine fever: Update on Eastern, Central and Southern Africa. Transbound Emerg Dis 2019; 66:1462-1480. [PMID: 30920725 DOI: 10.1111/tbed.13187] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [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: 10/09/2018] [Revised: 03/21/2019] [Accepted: 03/24/2019] [Indexed: 11/28/2022]
Abstract
Control of African swine fever (ASF) in countries in Eastern, Central and Southern Africa (ECSA) is particularly complex owing to the presence of all three known epidemiological cycles of maintenance of the virus, namely an ancient sylvatic cycle involving the natural hosts and vectors of the disease as well as domestic cycles with and without involvement of natural vectors. While the situation is well documented in some of the countries, for others very little information is available. In spite of the unfavourable ASF situation, the pig population in the sub-region has grown exponentially in recent decades and is likely to continue to grow in response to rapid urban growth resulting in increasing demand for animal protein by populations that are no longer engaged in livestock production. Better management of ASF will be essential to permit the pig sector to reach its full potential as a supplier of high quality protein and a source of income to improve livelihoods and create wealth. No vaccine is currently available and it is likely that, in the near future, the sub-region will continue to rely on the implementation of preventive measures, based on the epidemiology of the disease, to avoid both the devastating losses that outbreaks can cause and the risk the sub-region poses to other parts of Africa and the world. The current situation in the ECSA sub-region is reviewed and gaps in knowledge are identified in order to support ongoing strategy development for managing ASF in endemic areas.
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Affiliation(s)
- Léopold K Mulumba-Mfumu
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo.,Research Unit of Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR- ULiège), Fundamental and Applied Research for Animals & Health (FARAH) Center, Faculty of Veterinary Medicine, University of Liege, Liege, Belgium
| | - Claude Saegerman
- Research Unit of Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR- ULiège), Fundamental and Applied Research for Animals & Health (FARAH) Center, Faculty of Veterinary Medicine, University of Liege, Liege, Belgium
| | | | - Kapanga C Madimba
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Eric Kazadi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Ndeji T Mukalakata
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Chris A L Oura
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, Champ Fleurs, Trinidad and Tobago
| | - Erika Chenais
- Department of Disease Control and Epidemiology, SVA, Uppsala, Sweden
| | - Charles Masembe
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Karl Ståhl
- Department of Disease Control and Epidemiology, SVA, Uppsala, Sweden
| | - Etienne Thiry
- Veterinary Virology and Animal Viral Diseases, Fundamental and Applied Research for Animals & Health (FARAH) Center, Faculty of Veterinary Medicine, University of Liege, Liege, Belgium
| | - Mary Louise Penrith
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
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29
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Liu L, Atim S, LeBlanc N, Rauh R, Esau M, Chenais E, Mwebe R, Nelson WM, Masembe C, Nantima N, Ayebazibwe C, Ståhl K. Overcoming the challenges of pen-side molecular diagnosis of African swine fever to support outbreak investigations under field conditions. Transbound Emerg Dis 2018; 66:908-914. [PMID: 30554469 DOI: 10.1111/tbed.13103] [Citation(s) in RCA: 12] [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] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 12/03/2018] [Accepted: 12/06/2018] [Indexed: 11/30/2022]
Abstract
African swine fever (ASF) is a devastating disease of pigs. Without a vaccine, early detection and rapid diagnosis of ASF is a crucial step towards effective disease control. In many countries where ASF is endemic, laboratory infrastructure including sampling and sample shipment is inadequate, and a rapid laboratory confirmation would require that the diagnosis is performed at regional laboratories close to the pig farms of concern, or even at the farm-side. This study intended to evaluate measures including sample preparation methods, a dried-down assay, and a portable, battery-powered real-time PCR instrument, to improve molecular diagnosis under field conditions. A simple dilution of blood samples, either in Phosphate-buffered saline or a commercial buffer, worked similarly to beads-based nucleic acid extraction using a magnet as the core equipment; the latter method did work as well for those samples with low viral load or high Ct values. The real-time PCR assay using a Universal ProbeLibrary (UPL) probe tolerated suspected inhibitory substances present in the prepared samples better, whereas the dried-down assay had a higher diagnostic sensitivity. Additionally, an inhibition control assay proved to be helpful in avoiding false negative results when interpreting negative results of samples that might be of low quality or with inadequate reduction in inhibitory substances. When tested with synthetic DNA standards, the portable instrument performed at a level approaching stationary thermocyclers. In summary, the developments of suitable sample preparation methods, robust and thermal-stable real-time PCR assays with inhibition control, and battery-powered portable thermocyclers with middle-throughput offer one way forward to provide rapid, reliable molecular diagnosis under challenging field conditions.
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Affiliation(s)
- Lihong Liu
- National Veterinary Institute, Uppsala, Sweden
| | - Stella Atim
- National Animal Disease Diagnosis and Epidemiology Center, Entebbe, Uganda
| | - Neil LeBlanc
- Consultant molecular diagnostics, Uppsala, Sweden
| | | | - Martin Esau
- National Animal Disease Diagnosis and Epidemiology Center, Entebbe, Uganda
| | | | - Robert Mwebe
- National Animal Disease Diagnosis and Epidemiology Center, Entebbe, Uganda
| | | | | | - Noelina Nantima
- National Animal Disease Diagnosis and Epidemiology Center, Entebbe, Uganda
| | | | - Karl Ståhl
- National Veterinary Institute, Uppsala, Sweden
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30
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Payne A, Ogweng P, Ojok A, Etter E, Gilot-Fromont E, Masembe C, Ståhl K, Jori F. Comparison of Three Methods to Assess the Potential for Bushpig-Domestic Pig Interactions at the Wildlife-Livestock Interface in Uganda. Front Vet Sci 2018; 5:295. [PMID: 30619893 PMCID: PMC6305579 DOI: 10.3389/fvets.2018.00295] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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] [Received: 07/31/2018] [Accepted: 11/02/2018] [Indexed: 11/13/2022] Open
Abstract
Bushpigs (Potamochoerus larvatus) are considered a nuisance to farmers because of their crop raiding habits. Through their incursions into farmlands, they may interact with free-ranging domestic pigs and potentially cause transmission of infectious diseases such as African Swine Fever (ASF). The role of the bushpig in the epidemiology of ASF is poorly known and one of the gaps of knowledge is precisely the nature of interaction between bushpigs and domestic pigs. Thus, in this study, we investigated the frequency of bushpig visits to crop fields in rural communities where ASF is endemic, at the edge of a wildlife protected area in northwestern Uganda, to better understand the potential for interaction and disease transmission. We used three methods (questionnaires, camera traps, and observations for tracks) to assess bushpig visits to farmland. These methods were implemented concurrently in 28 farms during rainy and dry seasons. The results obtained by each of the three methods were analyzed by generalized linear mixed models. Potential risk factors including crop type, season, and landscape characteristics related to bushpig ecology were tested as explanatory variables. A generalized linear model and the Kendall test were used to compare the results and consistency of the frequency values obtained by the three methods. A high percentage (75%) of interviewed farmers reported visits from bushpigs in 29.6% of assessed crops (n = 145), and a frequency of 0.014 +/-0.05 visits per night was obtained through camera-trapping. Bushpig tracks were detected in 36% of sessions of observation. Cassava (Manihot esculenta) and groundnut (Arachis hypogaea L.) crop fields were the most visited, and these visits were more common during the rainy than the dry season. Distances from crop sites to the boundary of the protected area and to the river also influenced visit frequency. Camera-trapping was the least sensitive method while questionnaires and track observations presented consistent and complementary results to characterize spatial and temporal visits of bushpig into the crop fields. Evidence from our study shows that when used in combination, these methods can provide useful data to improve our understanding of the interactions between bushpigs and domestic pigs at the wildlife-domestic interface.
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Affiliation(s)
- Ariane Payne
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Peter Ogweng
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Alfred Ojok
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Eric Etter
- UMR ASTRE CIRAD-INRA, Department of Production Animals Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Emmanuelle Gilot-Fromont
- Lyon University, CNRS, Lyon 1 University, VetAgro Sup, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Marcy l'Etoile, France
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Karl Ståhl
- Department of Disease Control and Epidemiology, SVA, National Veterinary Institute, Uppsala, Sweden
| | - Ferran Jori
- UMR ASTRE CIRAD-INRA, Campus International de Baillarguet, Montpellier, France
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31
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Dione M, Masembe C, Akol J, Amia W, Kungu J, Lee HS, Wieland B. The importance of on-farm biosecurity: Sero-prevalence and risk factors of bacterial and viral pathogens in smallholder pig systems in Uganda. Acta Trop 2018; 187:214-221. [PMID: 29949731 DOI: 10.1016/j.actatropica.2018.06.025] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/21/2018] [Accepted: 06/23/2018] [Indexed: 01/06/2023]
Abstract
BACKGROUND The productivity of pigs in smallholder systems is affected by high disease burden, most of which might not be obvious, with their epidemiology and impact being poorly understood. This study estimated the seroprevalence and identified the risk factors of a range of bacterial and viral pathogens of potential economic and public health importance in domestic pigs in Uganda. A total of 522 clinically healthy pigs were randomly selected from 276 pig farms in Masaka (142) and Lira (134) districts of Uganda in 2015. RESULTS Overall the highest animal prevalence was found for Streptococcus suis 73.0% (CI95: 67.0-78.3) in Lira and 68.2% (CI95: 62.7-73.4) in Masaka; followed by Porcine circovirus type 2 with 50.8% (CI95: 44.5-57.2) in Lira and 40.7% (CI95: 35.2-46.5) in Masaka and Actinobacillus pleuro-pneumoniae, 25.6% (CI95: 20.4-31.6) in Lira and 20.5% (CI95: 16.2-25.6) in Masaka. Mycoplasma hyopneumonia prevalence was 20.9% (CI95: 16.2-26.6) in Lira and 10.1% (CI95: 7.1-14.1) in Masaka, while Porcine parvovirus was 6.2% (CI95: 4.0-9.7) in Masaka and 3.4% (CI95: 1.7-6.6) in Lira. Less common pathogens were Influenza A, 8.5% (CI95: 5.6-12.8) in Lira and 2.0% (CI95: 0.9-4.5) in Masaka and Porcine Reproductive and Respiratory Syndrome Virus, 1.7% (CI95: 0.7-4.3) in Lira and 1.3% (CI95: 0.5-3.5) in Masaka. Even less common was Rotavirus A with 0.8% (CI95: 0.2-3.0) in Lira and 0.7% (CI95: 0.2-2.5) in Masaka; the same was for Aujeszky virus with 0.4% (CI95: 0.7-2.4) in Lira and 0.0% (CI95: 0.0-0.1) in Masaka. Co-infection with two pathogens was common and there was a significant association of M. hyo and PCV2 co-occurrence (p = 0.016). Multivariate analysis showed that for S. suis the use of disinfectant reduced odds of sero-positivitey (OR = 0.15; p = 0.017) and pigs less than 6 months were more likely to be infected than older pigs (OR = 3.35; p = 0.047). For M. hyo, crossbred pigs had higher odd of infection compared to local breeds (OR = 1.59; p < 0.001). CONCLUSIONS The studied pathogens have high prevalences in smallholder pig production systems and might be silent killers, thus affecting productivity and there is a possibility that some pathogens could spread to humans. Given the limited knowledge of veterinary workers and the poor diagnostic capacities and capabilities in these systems, the diseases are potentially usually under-diagnosed. These findings constitute baseline data to measure the impact of future interventions aiming to reduce disease burden in the pig production systems in Uganda.
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Affiliation(s)
- Michel Dione
- International Livestock Research Institute, C/O Bioversity International, P. O. Box 24384 Kampala, Uganda.
| | - Charles Masembe
- College of Natural Sciences, Department of Zoology, Entomology and Fisheries Sciences Makerere University, P.O. Box 7062, Kampala, Uganda.
| | - Joyce Akol
- International Livestock Research Institute, C/O Bioversity International, P. O. Box 24384 Kampala, Uganda.
| | - Winfred Amia
- International Livestock Research Institute, C/O Bioversity International, P. O. Box 24384 Kampala, Uganda.
| | - Joseph Kungu
- College of Veterinary Medicine, Animal Resources and Biosecurity, Department of Biosecurity, Ecosystems and Veterinary Public Health, Makerere University, P. O. Box 7062, Kampala Uganda.
| | - Hu Suk Lee
- International Livestock Research Institute, 298 Kim Ma Street, Ba Dinh District, Hanoi, Vietnam.
| | - Barbara Wieland
- International Livestock Research Institute, P.O. Box 5689, Addis Ababa, Ethiopia.
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32
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Vajana E, Barbato M, Colli L, Milanesi M, Rochat E, Fabrizi E, Mukasa C, Del Corvo M, Masembe C, Muwanika VB, Kabi F, Sonstegard TS, Huson HJ, Negrini R, Joost S, Ajmone-Marsan P. Combining Landscape Genomics and Ecological Modelling to Investigate Local Adaptation of Indigenous Ugandan Cattle to East Coast Fever. Front Genet 2018; 9:385. [PMID: 30333851 PMCID: PMC6177531 DOI: 10.3389/fgene.2018.00385] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 05/18/2018] [Accepted: 08/27/2018] [Indexed: 11/30/2022] Open
Abstract
East Coast fever (ECF) is a fatal sickness affecting cattle populations of eastern, central, and southern Africa. The disease is transmitted by the tick Rhipicephalus appendiculatus, and caused by the protozoan Theileria parva parva, which invades host lymphocytes and promotes their clonal expansion. Importantly, indigenous cattle show tolerance to infection in ECF-endemically stable areas. Here, the putative genetic bases underlying ECF-tolerance were investigated using molecular data and epidemiological information from 823 indigenous cattle from Uganda. Vector distribution and host infection risk were estimated over the study area and subsequently tested as triggers of local adaptation by means of landscape genomics analysis. We identified 41 and seven candidate adaptive loci for tick resistance and infection tolerance, respectively. Among the genes associated with the candidate adaptive loci are PRKG1 and SLA2. PRKG1 was already described as associated with tick resistance in indigenous South African cattle, due to its role into inflammatory response. SLA2 is part of the regulatory pathways involved into lymphocytes' proliferation. Additionally, local ancestry analysis suggested the zebuine origin of the genomic region candidate for tick resistance.
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Affiliation(s)
- Elia Vajana
- Department of Animal Science, Food and Nutrition (DIANA), Biodiversity and Ancient DNA Research Centre (BioDNA), and Proteomics and Nutrigenomics Research Centre (PRONUTRIGEN), Università Cattolica del Sacro Cuore, Piacenza, Italy
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Mario Barbato
- Department of Animal Science, Food and Nutrition (DIANA), Biodiversity and Ancient DNA Research Centre (BioDNA), and Proteomics and Nutrigenomics Research Centre (PRONUTRIGEN), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Licia Colli
- Department of Animal Science, Food and Nutrition (DIANA), Biodiversity and Ancient DNA Research Centre (BioDNA), and Proteomics and Nutrigenomics Research Centre (PRONUTRIGEN), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Marco Milanesi
- Department of Animal Science, Food and Nutrition (DIANA), Biodiversity and Ancient DNA Research Centre (BioDNA), and Proteomics and Nutrigenomics Research Centre (PRONUTRIGEN), Università Cattolica del Sacro Cuore, Piacenza, Italy
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, Araçatuba, Brazil
- International Atomic Energy Agency (IAEA), Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Estelle Rochat
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Enrico Fabrizi
- Department of Economics and Social Sciences, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | | | - Marcello Del Corvo
- Department of Animal Science, Food and Nutrition (DIANA), Biodiversity and Ancient DNA Research Centre (BioDNA), and Proteomics and Nutrigenomics Research Centre (PRONUTRIGEN), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries, Makerere University, Kampala, Uganda
| | - Vincent B. Muwanika
- Department of Environmental Management, Makerere University, Kampala, Uganda
| | - Fredrick Kabi
- National Livestock Resources Research Institute (NaLIRRI), National Agricultural Research Organisation, Tororo, Uganda
| | | | - Heather Jay Huson
- Department of Animal Science, Cornell University, Ithaca, NY, United States
| | - Riccardo Negrini
- Department of Animal Science, Food and Nutrition (DIANA), Biodiversity and Ancient DNA Research Centre (BioDNA), and Proteomics and Nutrigenomics Research Centre (PRONUTRIGEN), Università Cattolica del Sacro Cuore, Piacenza, Italy
- Associazione Italiana Allevatori (AIA), Rome, Italy
| | | | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition (DIANA), Biodiversity and Ancient DNA Research Centre (BioDNA), and Proteomics and Nutrigenomics Research Centre (PRONUTRIGEN), Università Cattolica del Sacro Cuore, Piacenza, Italy
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Sternberg Lewerin S, Wolff C, Masembe C, Ståhl K, Boqvist S, Franko MA. Methodological aspects of serosurveillance in resource-poor settings. Vet Rec Open 2018; 5:e000273. [PMID: 29682293 PMCID: PMC5905835 DOI: 10.1136/vetreco-2017-000273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 12/28/2017] [Revised: 03/13/2018] [Accepted: 03/20/2018] [Indexed: 11/09/2022] Open
Abstract
Animal production is important for the agricultural economy in low-income countries, but is threatened by infectious diseases. Serosurveys are conducted for different reasons such as disease detection, risk factor studies, disease monitoring and establishing disease-free status. Most reports on such serosurveys include some discussion about methodological constraints but still, by necessity, rely on serological results for case definition. This study uses a cross-sectional serosurvey for foot-and-mouth disease (FMD), Rift Valley fever (RVF) and contagious bovine pleuropneumonia (CBPP) in cattle in three districts in Western Uganda to illustrate the limitations of this approach, addressing the questions of what flaws can be expected in sampling and diagnostics and how these influence the results. The target was to collect blood samples from 60 cattle herds per district. To reflect the recent infection history of the herd, young animals (two to five years) were prioritised. The farmers were interviewed about management, cattle trade, cattle health and vaccination. Commercial ELISAs were used for serological analyses: for CBPP the IDEXX CBPP Mycoplasma mycoides subspecies mycoides antibody test kit, for RVF the ID Screen Rift Valley Fever competitive ELISA, and for FMD the PrioCHECK FMDV NS. Apparent prevalence, true prevalence and associations with herd characteristics were assessed. The sampling plans could not be entirely fulfilled, nor the number of tests run in the laboratory. There were reactors to all three diseases with an apparent prevalence of approximately 30 per cent for CBPP, 6 per cent for RVF and 7 per cent for FMD. Calculation of true prevalence based on test sensitivity and specificity resulted in a slightly higher prevalence figure for CBPP and lower figures for RVF and FMD. The study illustrates the importance of considering diagnostic test performance when interpreting results from serosurveys, and the challenge of representative sampling and laboratory work in low-income countries.
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Affiliation(s)
- Susanna Sternberg Lewerin
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Cecilia Wolff
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Charles Masembe
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Karl Ståhl
- Department of Epidemiology and Disease Control, National Veterinary Institute SVA, Uppsala, Sweden
| | - Sofia Boqvist
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mikael Andersson Franko
- Department of Applied Statistics and Mathematics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Mujibi FD, Okoth E, Cheruiyot EK, Onzere C, Bishop RP, Fèvre EM, Thomas L, Masembe C, Plastow G, Rothschild M. Genetic diversity, breed composition and admixture of Kenyan domestic pigs. PLoS One 2018; 13:e0190080. [PMID: 29357367 PMCID: PMC5777648 DOI: 10.1371/journal.pone.0190080] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 06/03/2017] [Accepted: 12/07/2017] [Indexed: 01/23/2023] Open
Abstract
The genetic diversity of African pigs, whether domestic or wild has not been widely studied and there is very limited published information available. Available data suggests that African domestic pigs originate from different domestication centers as opposed to international commercial breeds. We evaluated two domestic pig populations in Western Kenya, in order to characterize the genetic diversity, breed composition and admixture of the pigs in an area known to be endemic for African swine fever (ASF). One of the reasons for characterizing these specific populations is the fact that a proportion of indigenous pigs have tested ASF virus (ASFv) positive but do not present with clinical symptoms of disease indicating some form of tolerance to infection. Pigs were genotyped using either the porcine SNP60 or SNP80 chip. Village pigs were sourced from Busia and Homabay counties in Kenya. Because bush pigs (Potamochoerus larvatus) and warthogs (Phacochoerus spp.) are known to be tolerant to ASFv infection (exhibiting no clinical symptoms despite infection), they were included in the study to assess whether domestic pigs have similar genomic signatures. Additionally, samples representing European wild boar and international commercial breeds were included as references, given their potential contribution to the genetic make-up of the target domestic populations. The data indicate that village pigs in Busia are a non-homogenous admixed population with significant introgression of genes from international commercial breeds. Pigs from Homabay by contrast, represent a homogenous population with a "local indigenous' composition that is distinct from the international breeds, and clusters more closely with the European wild boar than African wild pigs. Interestingly, village pigs from Busia that tested negative by PCR for ASFv genotype IX, had significantly higher local ancestry (>54%) compared to those testing positive, which contained more commercial breed gene introgression. This may have implication for breed selection and utilization in ASF endemic areas. A genome wide scan detected several regions under preferential selection with signatures for pigs from Busia and Homabay being very distinct. Additionally, there was no similarity in specific genes under selection between the wild pigs and domestic pigs despite having some broad areas under similar selection signatures. These results provide a basis to explore possible genetic determinants underlying tolerance to infection by ASFv genotypes and suggests multiple pathways for genetically mediated ASFv tolerance given the diversity of selection signatures observed among the populations studied.
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Affiliation(s)
- Fidalis Denis Mujibi
- Nelson Mandela Africa Institution of Science and Technology, Arusha, Tanzania
- USOMI Limited, Hardy Post, Karen, Nairobi, Kenya
- * E-mail:
| | - Edward Okoth
- International Livestock Research Institute, Nairobi, Kenya
| | | | - Cynthia Onzere
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Richard P. Bishop
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Eric M. Fèvre
- International Livestock Research Institute, Nairobi, Kenya
- Institute of Infection and Global Health, Department of Epidemiology and Population Health, University of Liverpool, Cheshire, United Kingdom
| | - Lian Thomas
- Centre for Infection Immunity, and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Charles Masembe
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Graham Plastow
- Department of Agriculture, Food and Nutrition Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Max Rothschild
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
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35
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Wolff C, Boqvist S, Ståhl K, Masembe C, Sternberg-Lewerin S. Biosecurity aspects of cattle production in Western Uganda, and associations with seroprevalence of brucellosis, salmonellosis and bovine viral diarrhoea. BMC Vet Res 2017; 13:382. [PMID: 29212482 PMCID: PMC5719755 DOI: 10.1186/s12917-017-1306-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 01/20/2017] [Accepted: 11/27/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Many low-income countries have a human population with a high number of cattle owners depending on their livestock for food and income. Infectious diseases threaten the health and production of cattle, affecting both the farmers and their families as well as other actors in often informal value chains. Many infectious diseases can be prevented by good biosecurity. The objectives of this study were to describe herd management and biosecurity routines with potential impact on the prevalence of infectious diseases, and to estimate the burden of infectious diseases in Ugandan cattle herds, using the seroprevalence of three model infections. RESULTS Farmer interviews (n = 144) showed that biosecurity measures are rarely practised. Visitors' hand-wash was used by 14%, cleaning of boots or feet by 4 and 79% put new cattle directly into the herd. During the 12 months preceding the interviews, 51% of farmers had cattle that died and 31% had noticed abortions among their cows. Interestingly, 72% were satisfied with the health status of their cattle during the same time period. The prevalence (95% CI) of farms with at least one seropositive animal was 16.7% (11.0;23.8), 23.6% (16.9;31.4), and 53.4% (45.0;61.8) for brucella, salmonella and BVD, respectively. A poisson regression model suggested that having employees looking after the cattle, sharing pasture with other herds, and a higher number of dead cattle were associated with a herd being positive to an increasing number of the diseases. An additive bayesian network model with biosecurity variables and a variable for the number of diseases the herd was positive to resulted in three separate directed acyclic graphs which illustrate how herd characteristics can be grouped together. This model associated the smallest herd size with herds positive to a decreasing number of diseases and having fewer employees. CONCLUSION There is potential for improvement of biosecurity practices in Ugandan cattle production. Salmonella, brucella and BVD were prevalent in cattle herds in the study area and these infections are, to some extent, associated with farm management practices.
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Affiliation(s)
- C Wolff
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - S Boqvist
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - K Ståhl
- Department of Disease Control and Epidemiology, National Veterinary Institute, Uppsala, Sweden
| | - C Masembe
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - S Sternberg-Lewerin
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
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36
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Stucki S, Orozco-terWengel P, Forester BR, Duruz S, Colli L, Masembe C, Negrini R, Landguth E, Jones MR, Bruford MW, Taberlet P, Joost S. High performance computation of landscape genomic models including local indicators of spatial association. Mol Ecol Resour 2017. [PMID: 27801969 DOI: 10.1111/1755-0998.1262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics - that is the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental data sets. samβada identifies candidate loci using genotype-environment associations while also incorporating multivariate analyses to assess the effect of many environmental predictor variables. This enables the inclusion of explanatory variables representing population structure into the models to lower the occurrences of spurious genotype-environment associations. In addition, samβada calculates local indicators of spatial association for candidate loci to provide information on whether similar genotypes tend to cluster in space, which constitutes a useful indication of the possible kinship between individuals. To test the usefulness of this approach, we carried out a simulation study and analysed a data set from Ugandan cattle to detect signatures of local adaptation with samβada, bayenv, lfmm and an FST outlier method (FDIST approach in arlequin) and compare their results. samβada - an open source software for Windows, Linux and Mac OS X available at http://lasig.epfl.ch/sambada - outperforms other approaches and better suits whole-genome sequence data processing.
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Affiliation(s)
- S Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - P Orozco-terWengel
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, CF10 3AX, UK
| | - B R Forester
- Nicholas School of the Environment, University Program in Ecology, Duke University, Durham, NC, 27708, USA
| | - S Duruz
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - L Colli
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Istituto di Zootecnica, Università Cattolica del S. Cuore, via E. Parmense 84, 29100, Piacenza, Italy
| | - C Masembe
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, Box 7062, Kampala, Uganda
| | - R Negrini
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Istituto di Zootecnica, Università Cattolica del S. Cuore, via E. Parmense 84, 29100, Piacenza, Italy
- Associazione Italiana Allevatori, 00161, Roma, Italy
| | - E Landguth
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - M R Jones
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - M W Bruford
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, CF10 3AX, UK
| | - P Taberlet
- Laboratoire d'Ecologie Alpine (LECA), CNRS, Grenoble, 38000, France
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble, 38000, France
| | - S Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
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37
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Chenais E, Sternberg-Lewerin S, Boqvist S, Liu L, LeBlanc N, Aliro T, Masembe C, Ståhl K. African swine fever outbreak on a medium-sized farm in Uganda: biosecurity breaches and within-farm virus contamination. Trop Anim Health Prod 2016; 49:337-346. [PMID: 27966070 PMCID: PMC5253150 DOI: 10.1007/s11250-016-1197-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 06/22/2016] [Accepted: 11/24/2016] [Indexed: 11/30/2022]
Abstract
In Uganda, a low-income country in east Africa, African swine fever (ASF) is endemic with yearly outbreaks. In the prevailing smallholder subsistence farming systems, farm biosecurity is largely non-existent. Outbreaks of ASF, particularly in smallholder farms, often go unreported, creating significant epidemiological knowledge gaps. The continuous circulation of ASF in smallholder settings also creates biosecurity challenges for larger farms. In this study, an on-going outbreak of ASF in an endemic area was investigated on farm level, including analyses of on-farm environmental virus contamination. The study was carried out on a medium-sized pig farm with 35 adult pigs and 103 piglets or growers at the onset of the outbreak. Within 3 months, all pigs had died or were slaughtered. The study included interviews with farm representatives as well as biological and environmental sampling. ASF was confirmed by the presence of ASF virus (ASFV) genomic material in biological (blood, serum) and environmental (soil, water, feed, manure) samples by real-time PCR. The ASFV-positive biological samples confirmed the clinical assessment and were consistent with known virus characteristics. Most environmental samples were found to be positive. Assessment of farm biosecurity, interviews, and the results from the biological and environmental samples revealed that breaches and non-compliance with biosecurity protocols most likely led to the introduction and within-farm spread of the virus. The information derived from this study provides valuable insight regarding the implementation of biosecurity measures, particularly in endemic areas.
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Affiliation(s)
- Erika Chenais
- National Veterinary Institute, Uppsala, Sweden. .,Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | | | - Sofia Boqvist
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lihong Liu
- National Veterinary Institute, Uppsala, Sweden
| | | | - Tonny Aliro
- Directorate of Production and Marketing, Gulu District Local Government, Gulu, Uganda
| | | | - Karl Ståhl
- National Veterinary Institute, Uppsala, Sweden.,Swedish University of Agricultural Sciences, Uppsala, Sweden
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Stucki S, Orozco-terWengel P, Forester BR, Duruz S, Colli L, Masembe C, Negrini R, Landguth E, Jones MR, Bruford MW, Taberlet P, Joost S. High performance computation of landscape genomic models including local indicators of spatial association. Mol Ecol Resour 2016; 17:1072-1089. [PMID: 27801969 DOI: 10.1111/1755-0998.12629] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [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: 04/07/2015] [Revised: 08/05/2016] [Accepted: 09/19/2016] [Indexed: 12/11/2022]
Abstract
With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics - that is the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental data sets. samβada identifies candidate loci using genotype-environment associations while also incorporating multivariate analyses to assess the effect of many environmental predictor variables. This enables the inclusion of explanatory variables representing population structure into the models to lower the occurrences of spurious genotype-environment associations. In addition, samβada calculates local indicators of spatial association for candidate loci to provide information on whether similar genotypes tend to cluster in space, which constitutes a useful indication of the possible kinship between individuals. To test the usefulness of this approach, we carried out a simulation study and analysed a data set from Ugandan cattle to detect signatures of local adaptation with samβada, bayenv, lfmm and an FST outlier method (FDIST approach in arlequin) and compare their results. samβada - an open source software for Windows, Linux and Mac OS X available at http://lasig.epfl.ch/sambada - outperforms other approaches and better suits whole-genome sequence data processing.
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Affiliation(s)
- S Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - P Orozco-terWengel
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, CF10 3AX, UK
| | - B R Forester
- Nicholas School of the Environment, University Program in Ecology, Duke University, Durham, NC, 27708, USA
| | - S Duruz
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - L Colli
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Istituto di Zootecnica, Università Cattolica del S. Cuore, via E. Parmense 84, 29100, Piacenza, Italy
| | - C Masembe
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, Box 7062, Kampala, Uganda
| | - R Negrini
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Istituto di Zootecnica, Università Cattolica del S. Cuore, via E. Parmense 84, 29100, Piacenza, Italy.,Associazione Italiana Allevatori, 00161, Roma, Italy
| | - E Landguth
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - M R Jones
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | | | - M W Bruford
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, CF10 3AX, UK
| | - P Taberlet
- Laboratoire d'Ecologie Alpine (LECA), CNRS, Grenoble, 38000, France.,Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble, 38000, France
| | - S Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
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39
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Kukielka EA, Jori F, Martínez-López B, Chenais E, Masembe C, Chavernac D, Ståhl K. Wild and Domestic Pig Interactions at the Wildlife-Livestock Interface of Murchison Falls National Park, Uganda, and the Potential Association with African Swine Fever Outbreaks. Front Vet Sci 2016; 3:31. [PMID: 27148545 PMCID: PMC4831202 DOI: 10.3389/fvets.2016.00031] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [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: 11/27/2015] [Accepted: 03/31/2016] [Indexed: 12/27/2022] Open
Abstract
Bushpigs (BPs) (Potamochoerus larvatus) and warthogs (WHs) (Phacochoerus africanus), which are widely distributed in Eastern Africa, are likely to cohabitate in the same environment with domestic pigs (DPs), facilitating the transmission of shared pathogens. However, potential interactions between BP, WH, and DP, and the resulting potential circulation of infectious diseases have rarely been investigated in Africa to date. In order to understand the dynamics of such interactions and the potential influence of human behavior and husbandry practices on them, individual interviews (n = 233) and participatory rural appraisals (n = 11) were carried out among Ugandan pig farmers at the edge of Murchison Falls National Park, northern Uganda. In addition, as an example of possible implications of wild and DP interactions, non-linear multivariate analysis (multiple correspondence analyses) was used to investigate the potential association between the aforementioned factors (interactions and human behavior and practices) and farmer reported African swine fever (ASF) outbreaks. No direct interactions between wild pigs (WPs) and DP were reported in our study area. However, indirect interactions were described by 83 (35.6%) of the participants and were identified to be more common at water sources during the dry season. Equally, eight (3.4%) farmers declared exposing their DP to raw hunting leftovers of WPs. The exploratory analysis performed suggested possible associations between the farmer reported ASF outbreaks and indirect interactions, free-range housing systems, dry season, and having a WH burrow less than 3 km from the household. Our study was useful to gather local knowledge and to identify knowledge gaps about potential interactions between wild and DP in this area. This information could be useful to facilitate the design of future observational studies to better understand the potential transmission of pathogens between wild and DPs.
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Affiliation(s)
- Esther A Kukielka
- Center for Animal Disease Modeling and Surveillance (CADMS), VM: Medicine & Epidemiology, University of California Davis , Davis, CA , USA
| | - Ferran Jori
- Integrated Animal Risk Management (AGIRs), CIRAD Campus International de Baillarguet, Montpellier, France; Department of Animal Science and Production, Botswana University of Agriculture and Natural Resources, Gaborone, Botswana
| | - Beatriz Martínez-López
- Center for Animal Disease Modeling and Surveillance (CADMS), VM: Medicine & Epidemiology, University of California Davis , Davis, CA , USA
| | - Erika Chenais
- Department of Disease Control and Epidemiology, National Veterinary Institute (SVA), Uppsala, Sweden; Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Science (SLU), Uppsala, Sweden
| | - Charles Masembe
- Department of Biological Sciences, Makerere University , Kampala , Uganda
| | - David Chavernac
- Control of Exotic and Emerging Animal Diseases (CMAEE), CIRAD Campus International de Baillarguet , Montpellier , France
| | - Karl Ståhl
- Department of Disease Control and Epidemiology, National Veterinary Institute (SVA), Uppsala, Sweden; Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Science (SLU), Uppsala, Sweden
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Chemurot M, Akol AM, Masembe C, de Smet L, Descamps T, de Graaf DC. Factors influencing the prevalence and infestation levels of Varroa destructor in honeybee colonies in two highland agro-ecological zones of Uganda. Exp Appl Acarol 2016; 68:497-508. [PMID: 26801158 DOI: 10.1007/s10493-016-0013-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 11/03/2015] [Accepted: 01/13/2016] [Indexed: 06/05/2023]
Abstract
Varroa mites are ecto-parasites of honeybees and are a threat to the beekeeping industry. We identified the haplotype of Varroa mites and evaluated potential factors that influence their prevalence and infestation levels in the eastern and western highland agro-ecological zones of Uganda. This was done by collecting samples of adult worker bees between December 2014 and September 2015 in two sampling moments. Samples of bees were screened for Varroa using the ethanol wash method and the mites were identified by molecular techniques. All DNA sequences obtained from sampled mite populations in the two zones were 100 % identical to the Korean Haplotype (AF106899). Mean mite prevalence in the apiaries was 40 and 53 % for the western and eastern zones, respectively, during the first sampling. Over the second sampling, mean mite prevalence increased considerably in the western (59 %) but not in the eastern (51 %) zone. Factors that were associated with Varroa mite infestation levels include altitude, nature of apiary slope and apiary management practices during the first sampling. Our results further showed that Varroa mites were spreading from lower to higher elevations. Feral colonies were also infested with Varroa mites at infestation levels not significantly different from those in managed colonies. Colony productivity and strength were not correlated to mite infestation levels. We recommend a long-term Varroa mite monitoring strategy in areas of varying landscape and land use factors for a clear understanding of possible changes in mite infestation levels among African honeybees for informed decision making.
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Affiliation(s)
- Moses Chemurot
- Laboratory of Molecular Entomology and Bee Pathology, Ghent University, Krijgslaan 281 S2, 9000, Ghent, Belgium.
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda.
| | - Anne M Akol
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Lina de Smet
- Laboratory of Molecular Entomology and Bee Pathology, Ghent University, Krijgslaan 281 S2, 9000, Ghent, Belgium
| | - Tine Descamps
- Laboratory of Molecular Entomology and Bee Pathology, Ghent University, Krijgslaan 281 S2, 9000, Ghent, Belgium
| | - Dirk C de Graaf
- Laboratory of Molecular Entomology and Bee Pathology, Ghent University, Krijgslaan 281 S2, 9000, Ghent, Belgium
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Chenais E, Sternberg-Lewerin S, Boqvist S, Emanuelson U, Aliro T, Tejler E, Cocca G, Masembe C, Ståhl K. African Swine Fever in Uganda: Qualitative Evaluation of Three Surveillance Methods with Implications for Other Resource-Poor Settings. Front Vet Sci 2015; 2:51. [PMID: 26664978 PMCID: PMC4673915 DOI: 10.3389/fvets.2015.00051] [Citation(s) in RCA: 24] [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] [Received: 08/21/2015] [Accepted: 10/14/2015] [Indexed: 01/06/2023] Open
Abstract
Animal diseases impact negatively on households and on national economies. In low-income countries, this pertains especially to socio-economic effects on household level. To control animal diseases and mitigate their impact, it is necessary to understand the epidemiology of the disease in its local context. Such understanding, gained through disease surveillance, is often lacking in resource-poor settings. Alternative surveillance methods have been developed to overcome some of the hurdles obstructing surveillance. The objective of this study was to evaluate and qualitatively compare three methods for surveillance of acute infectious diseases using African swine fever in northern Uganda as an example. Report-driven outbreak investigations, participatory rural appraisals (PRAs), and a household survey using a smartphone application were evaluated. All three methods had good disease-detecting capacity, and each of them detected many more outbreaks compared to those reported to the World Organization for Animal Health during the same time period. Apparent mortality rates were similar for the three methods although highest for the report-driven outbreak investigations, followed by the PRAs, and then the household survey. The three methods have different characteristics and the method of choice will depend on the surveillance objective. The optimal situation might be achieved by a combination of the methods: outbreak detection via smartphone-based real-time surveillance, outbreak investigation for collection of biological samples, and a PRA for a better understanding of the epidemiology of the specific outbreak. All three methods require initial investments and continuous efforts. The sustainability of the surveillance system should, therefore, be carefully evaluated before making such investments.
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Affiliation(s)
- Erika Chenais
- National Veterinary Institute , Uppsala , Sweden ; Swedish University of Agricultural Sciences , Uppsala , Sweden
| | | | - Sofia Boqvist
- Swedish University of Agricultural Sciences , Uppsala , Sweden
| | - Ulf Emanuelson
- Swedish University of Agricultural Sciences , Uppsala , Sweden
| | - Tonny Aliro
- Gulu District Local Government , Gulu , Uganda
| | | | | | | | - Karl Ståhl
- National Veterinary Institute , Uppsala , Sweden ; Swedish University of Agricultural Sciences , Uppsala , Sweden
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Bruford MW, Ginja C, Hoffmann I, Joost S, Orozco-terWengel P, Alberto FJ, Amaral AJ, Barbato M, Biscarini F, Colli L, Costa M, Curik I, Duruz S, Ferenčaković M, Fischer D, Fitak R, Groeneveld LF, Hall SJG, Hanotte O, Hassan FU, Helsen P, Iacolina L, Kantanen J, Leempoel K, Lenstra JA, Ajmone-Marsan P, Masembe C, Megens HJ, Miele M, Neuditschko M, Nicolazzi EL, Pompanon F, Roosen J, Sevane N, Smetko A, Štambuk A, Streeter I, Stucki S, Supakorn C, Telo Da Gama L, Tixier-Boichard M, Wegmann D, Zhan X. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025. Front Genet 2015; 6:314. [PMID: 26539210 PMCID: PMC4612686 DOI: 10.3389/fgene.2015.00314] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/05/2015] [Indexed: 12/20/2022] Open
Abstract
Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that “…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.” However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.
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Affiliation(s)
- Michael W Bruford
- School of Biosciences, Cardiff University Cardiff, UK ; Sustainable Places Research Institute, Cardiff University Cardiff, UK
| | - Catarina Ginja
- Faculdade de Ciências, Centro de Ecologia, Evolução e Alterações Ambientais (CE3C), Universidade de Lisboa Lisboa, Portugal ; Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Campus Agrário de Vairão Portugal
| | - Irene Hoffmann
- Food and Agriculture Organization of the United Nations, Animal Genetic Resources Branch, Animal Production and Health Division Rome, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Florian J Alberto
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes Grenoble, France
| | - Andreia J Amaral
- Faculty of Sciences, BioISI- Biosystems and Integrative Sciences Institute, University of Lisbon Campo Grande, Portugal
| | - Mario Barbato
- School of Biosciences, Cardiff University Cardiff, UK
| | | | - Licia Colli
- BioDNA Centro di Ricerca sulla Biodiversità a sul DNA Antico, Istituto di Zootecnica, Università Cattolica del Sacro Cuore di Piacenza Italy
| | - Mafalda Costa
- School of Biosciences, Cardiff University Cardiff, UK
| | - Ino Curik
- Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - Solange Duruz
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Daniel Fischer
- Natural Resources Institute Finland (Luke), Green Technology Jokioinen, Finland
| | - Robert Fitak
- Institut für Populationsgenetik Vetmeduni, Vienna, Austria
| | | | | | - Olivier Hanotte
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Faiz-Ul Hassan
- School of Life Sciences, University of Nottingham Nottingham, UK ; Department of Animal Breeding and Genetics, University of Agriculture Faisalabad, Pakistan
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp Antwerp, Belgium
| | - Laura Iacolina
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Denmark
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Green Technology Jokioinen, Finland ; Department of Biology, University of Eastern Finland Kuopio, Finland
| | - Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Paolo Ajmone-Marsan
- BioDNA Centro di Ricerca sulla Biodiversità a sul DNA Antico, Istituto di Zootecnica, Università Cattolica del Sacro Cuore di Piacenza Italy
| | - Charles Masembe
- Institute of the Environment and Natural Resources, Makerere University Kampala, Uganda
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen University Wageningen, Netherlands
| | - Mara Miele
- School of Planning and Geography, Cardiff University Cardiff, UK
| | | | | | - François Pompanon
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes Grenoble, France
| | - Jutta Roosen
- TUM School of Management, Technische Universität München Munich, Germany
| | - Natalia Sevane
- Department of Animal Production, Veterinary Faculty, Universidad Complutense de Madrid Madrid, Spain
| | | | - Anamaria Štambuk
- Department of Biology, Faculty of Science, University of Zagreb Zagreb, Croatia
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, UK
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - China Supakorn
- School of Life Sciences, University of Nottingham Nottingham, UK ; School of Agricultural Technology, Walailak University Tha Sala, Thailand
| | - Luis Telo Da Gama
- Centre of Research in Animal Health (CIISA) - Faculty of Veterinary Medicine, University of Lisbon Lisbon, Portugal
| | | | - Daniel Wegmann
- Department of Biology, University of Fribourg Fribourg, Switzerland
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Beijing, China ; Cardiff University - Institute of Zoology, Joint Laboratory for Biocomplexity Research Beijing, China
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Kato AB, Hyseni C, Okedi LM, Ouma JO, Aksoy S, Caccone A, Masembe C. Mitochondrial DNA sequence divergence and diversity of Glossina fuscipes fuscipes in the Lake Victoria basin of Uganda: implications for control. Parasit Vectors 2015; 8:385. [PMID: 26197892 PMCID: PMC4511262 DOI: 10.1186/s13071-015-0984-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 07/02/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glossina fuscipes fuscipes is the main vector of African Trypanosomiasis affecting both humans and livestock in Uganda. The human disease (sleeping sickness) manifests itself in two forms: acute and chronic. The Lake Victoria basin in Uganda has the acute form and a history of tsetse re-emergence despite concerted efforts to control tsetse. The government of Uganda has targeted the basin for tsetse eradication. To provide empirical data for this initiative, we screened tsetse flies from the basin for genetic variation at the mitochondrial DNA cytochrome oxidase II (mtDNA COII) gene with the goal of investigating genetic diversity and gene flow among tsetse, tsetse demographic history; and compare these results with results from a previous study based on microsatellite loci data in the same area. METHODS We collected 429 Gff tsetse fly samples from 14 localities in the entire Ugandan portion of the Lake Victoria coast, covering 40,000 km(2). We performed genetic analyses on them and added data collected for 56 Gff individuals from 4 additional sampling sites in the basin. The 529 pb partial mitochondrial DNA cytochrome oxidase II (mtDNA COII) sequences totaling 485 were analysed for genetic differentiation, structuring and demographic history. The results were compared with findings from a previous study based on microsatellite loci data from the basin. RESULTS The differences within sampling sites explained a significant proportion of the genetic variation. We found three very closely related mtDNA population clusters, which co-occurred in multiple sites. Although Φ ST (0 - 0.592; P < 0.05) and Bayesian analyses suggest some level of weak genetic differentiation, there is no correlation between genetic divergence and geographic distance (r = 0.109, P = 0.185), and demographic tests provide evidence of locality-based demographic history. CONCLUSION The mtDNA data analysed here complement inferences made in a previous study based on microsatellite data. Given the differences in mutation rates, mtDNA afforded a look further back in time than microsatellites and revealed that Gff populations were more connected in the past. Microsatellite data revealed more genetic structuring than mtDNA. The differences in connectedness and structuring over time could be related to vector control efforts. Tsetse re-emergence after control interventions may be due to re-invasions from outside the treated areas, which emphasizes the need for an integrated area-wide tsetse eradication strategy for sustainable removal of the tsetse and trypanosomiasis problem from this area.
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Affiliation(s)
- Agapitus B Kato
- Department of Biological Sciences, College of Natural Sciences, Makerere University, Box 7062, Kampala, Uganda.
| | - Chaz Hyseni
- Department of Biology, University of Mississippi, Oxford, MS, 38677, USA.
| | - Loyce M Okedi
- National Livestock Resources Research Institute, Tororo, Uganda.
| | - Johnson O Ouma
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya.
| | - Serap Aksoy
- Division of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, 06520, USA.
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
| | - Charles Masembe
- Department of Biological Sciences, College of Natural Sciences, Makerere University, Box 7062, Kampala, Uganda.
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Kabi F, Muwanika V, Masembe C. Spatial distribution of Brucella antibodies with reference to indigenous cattle populations among contrasting agro-ecological zones of Uganda. Prev Vet Med 2015; 121:56-63. [PMID: 26100405 DOI: 10.1016/j.prevetmed.2015.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 12/11/2014] [Revised: 06/02/2015] [Accepted: 06/08/2015] [Indexed: 12/26/2022]
Abstract
Indigenous cattle populations exhibit various degrees of agro-ecological fitness and provide desirable opportunities for investments to improve sustainable production for better rural small-scale farmers' incomes globally. However, they could be a source of infection to their attendants and other susceptible livestock if their brucellosis status remains unknown. This study investigated the spatial distribution of Brucella antibodies among indigenous cattle populations in Uganda. Sera from a total of 925 indigenous cattle (410 Ankole Bos taurus indicus, 50 Nganda and 465 East African Shorthorn Zebu (EASZ) - B. indicus) obtained randomly from 209 herds spread throughout Uganda were sequentially analysed for Brucella antibodies using the indirect (I) and competitive (C) enzyme linked Immuno-sorbent assays (ELISA). Recent incidences of abortion within the previous 12 months and routine hygienic practices during parturition were explored for public health risks. Brucella antibodies occurred in approximately 8.64% (80/925) and 28.70% (95% CI: 22.52, 34.89) of the sampled individual cattle and herds, respectively. Findings have shown that Ankole and EASZ cattle had similar seroprevalences. Indigenous cattle from the different study agro-ecological zones (AEZs) exhibited varying seroprevalences ranging from approximately 1.78% (95% CI: 0, 5.29) to 19.67% (95% CI: 8.99, 30.35) in the Lake Victoria Crescent (LVC) and North Eastern Drylands (NED) respectively. Significantly higher odds for Brucella antibodies occurred in the NED (OR: 3.40, 95% CI: 1.34, 8.57, p=0.01) inhabited by EASZ cattle compared to the KP (reference category) AEZ. Recent incidences of abortions within the previous 12 months were significantly (p<0.001) associated with seropositive herds. These findings add critical evidence to existing information on the widespread occurrence of brucellosis among indigenous cattle populations in Uganda and could guide allocation of meagre resources for awareness creation. And deployment of control strategies including culling of older cattle and those which have aborted during advanced gestation, enforcement of hygiene practices and mass vaccination.
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Affiliation(s)
- Fredrick Kabi
- Department of Environmental Management, Molecular Genetics Laboratory, College of Agricultural and Environmental Sciences, Makerere University, P. O. Box 7062/7298, Kampala, Uganda; National Livestock Resources Research Institute (NaLIRRI), P.O. Box 96, Tororo, Uganda.
| | - Vincent Muwanika
- Department of Environmental Management, Molecular Genetics Laboratory, College of Agricultural and Environmental Sciences, Makerere University, P. O. Box 7062/7298, Kampala, Uganda
| | - Charles Masembe
- Department of Bio-Sciences, College of Natural Sciences, Makerere University, Box 7062, Kampala, Uganda
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Noce A, Amills M, Manunza A, Muwanika V, Muhangi D, Aliro T, Mayega J, Ademun R, Sànchez A, Egbhalsaied S, Mercadé A, Masembe C. East African pigs have a complex Indian, Far Eastern and Western ancestry. Anim Genet 2015; 46:433-6. [PMID: 26011180 DOI: 10.1111/age.12305] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2015] [Indexed: 11/28/2022]
Abstract
In this study, we have characterized the mitochondrial diversity of 81 swine from Uganda. Median-joining network analysis of D-loop sequences from these individuals and others characterized in previous studies allowed us to determine that Ugandan pigs cluster with populations from the West (Europe/North Africa), Far East and India. In addition, partial sequencing of the Y-chromosome UTY locus in 18 Ugandan domestic pigs revealed the segregation of a single HY1 lineage that has a cosmopolitan distribution. A Western and Far Eastern ancestry for East African pigs had been already reported, but this is the first study demonstrating an additional contribution from the Indian porcine gene pool. This result is consistent with the high frequency of zebuine alleles in cattle from East Africa. The geographic coordinates of East Africa, at the crossroads of many trading routes that, through the ages, linked Europe, Africa and Asia, might explain the rich and complex genetic heritage of livestock native to this area.
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Affiliation(s)
- A Noce
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - M Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - A Manunza
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - V Muwanika
- Molecular Genetics Laboratory, Department of Environmental Management, College of Agricultural and Environmental Sciences, Makerere University, P.O.Box 7026, Kampala, Uganda
| | - D Muhangi
- Department of Wildlife and Aquatic Resources, School of Veterinary Medicine and Animal Resources, College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P. O. Box 7062, Kampala, Uganda
| | - T Aliro
- Directorate of Production and Marketing, Gulu District Local Government, P. O. Box 2, Gulu, Uganda
| | - J Mayega
- Molecular Genetics Laboratory, Department of Environmental Management, College of Agricultural and Environmental Sciences, Makerere University, P.O.Box 7026, Kampala, Uganda
| | - R Ademun
- Ministry of Agriculture Animal Industry and Fisheries, National Animal Disease Diagnostics and Epidemiology Centre, P. O. Box 513, Entebbe, Uganda
| | - A Sànchez
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - S Egbhalsaied
- Young Researchers and Elite Club, Isfahan (Khorasgan) branch, Islamic Azad University, Isfahan, Iran
| | - A Mercadé
- Departament de Ciencia Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - C Masembe
- Department of Biological Sciences, School of BioSciences, Makerere University, Box 7062, Kampala, Uganda
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Muhangi D, Masembe C, Emanuelson U, Boqvist S, Mayega L, Ademun RO, Bishop RP, Ocaido M, Berg M, Ståhl K. A longitudinal survey of African swine fever in Uganda reveals high apparent disease incidence rates in domestic pigs, but absence of detectable persistent virus infections in blood and serum. BMC Vet Res 2015; 11:106. [PMID: 25967670 PMCID: PMC4432512 DOI: 10.1186/s12917-015-0426-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 09/02/2014] [Accepted: 05/05/2015] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND African swine fever (ASF) is a fatal, haemorrhagic disease of domestic pigs, that poses a serious threat to pig farmers and is currently endemic in domestic pigs in most of sub-Saharan Africa. To obtain insight into the factors related to ASF outbreaks at the farm-level, a longitudinal study was performed in one of the major pig producing areas in central Uganda. Potential risk factors associated with outbreaks of ASF were investigated including the possible presence of apparently healthy ASF-virus (ASFV) infected pigs, which could act as long-term carriers of the virus. Blood and serum were sampled from 715 pigs (241 farms) and 649 pigs (233 farms) to investigate presence of ASFV and antibodies, during the periods of June-October 2010 and March-June 2011, respectively. To determine the potential contribution of different risks to ASF spread, a questionnaire-based survey was administered to farmers to assess the association between ASF outbreaks during the study period and the risk factors. RESULTS Fifty-one (21 %) and 13 (5.6 %) farms reported an ASF outbreak on their farms in the previous one to two years and during the study period, respectively. The incidence rate for ASF prior to the study period was estimated at 14.1 per 100 pig farm-years and 5.6 per 100 pig farm-years during the study. Three pigs tested positive for ASFV using real-time PCR, but none tested positive for ASFV specific antibodies using two different commercial ELISA tests. CONCLUSIONS There was no evidence for existence of pigs that were long-term carriers for the virus based on the analysis of blood and serum as there were no seropositive pigs and the only three ASFV DNA positive pigs were acutely infected and were linked to outbreaks reported by farmers during the study. Potential ASF risk factors were present on both small and medium-scale pig farms, although small scale farms exhibited a higher proportion with multiple potential risk factors (like borrowing boars for sows mating, buying replacement from neighboring farms without ascertaining health status, etc) and did not implement any biosecurity measures. However, no risk factors were significantly associated with ASF reports during the study.
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Affiliation(s)
- Denis Muhangi
- Department of Wildlife and Aquatic Resources, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda.
| | - Charles Masembe
- Department of Biological Sciences, College of Natural Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda.
| | - Ulf Emanuelson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, P. O. Box 7054, SE-750 07, Uppsala, Sweden.
| | - Sofia Boqvist
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, P. O. Box 7028, SE-750 07, Uppsala, Sweden.
| | - Lawrence Mayega
- District Veterinary Office, under the Ministry of Agriculture, Animal Industry and Fisheries, Masaka, Uganda.
| | - Rose Okurut Ademun
- Ministry of Agriculture, Animal Industry and Fisheries, P. O. Box 102, Entebbe, Uganda.
| | - Richard P Bishop
- International Livestock Research Institute (ILRI), P.O. Box 30709, GPO 00100, Nairobi, Kenya.
| | - Michael Ocaido
- Department of Wildlife and Aquatic Resources, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda.
| | - Mikael Berg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, P. O. Box 7028, SE-750 07, Uppsala, Sweden.
| | - Karl Ståhl
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, P. O. Box 7028, SE-750 07, Uppsala, Sweden.
- Department of Disease Control and Epidemiology, National Veterinary Institute (SVA), SE-751 89, Uppsala, Sweden.
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47
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Barongo MB, Ståhl K, Bett B, Bishop RP, Fèvre EM, Aliro T, Okoth E, Masembe C, Knobel D, Ssematimba A. Estimating the Basic Reproductive Number (R0) for African Swine Fever Virus (ASFV) Transmission between Pig Herds in Uganda. PLoS One 2015; 10:e0125842. [PMID: 25938429 PMCID: PMC4418717 DOI: 10.1371/journal.pone.0125842] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [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: 11/24/2014] [Accepted: 03/26/2015] [Indexed: 11/29/2022] Open
Abstract
African swine fever (ASF) is a highly contagious, lethal and economically devastating haemorrhagic disease of domestic pigs. Insights into the dynamics and scale of virus transmission can be obtained from estimates of the basic reproduction number (R0). We estimate R0 for ASF virus in small holder, free-range pig production system in Gulu, Uganda. The estimation was based on data collected from outbreaks that affected 43 villages (out of the 289 villages with an overall pig population of 26,570) between April 2010 and November 2011. A total of 211 outbreaks met the criteria for inclusion in the study. Three methods were used, specifically; (i) GIS- based identification of the nearest infectious neighbour based on the Euclidean distance between outbreaks, (ii) epidemic doubling time, and (iii) a compartmental susceptible-infectious (SI) model. For implementation of the SI model, three approaches were used namely; curve fitting (CF), a linear regression model (LRM) and the SI/N proportion. The R0 estimates from the nearest infectious neighbour and epidemic doubling time methods were 3.24 and 1.63 respectively. Estimates from the SI-based method were 1.58 for the CF approach, 1.90 for the LRM, and 1.77 for the SI/N proportion. Since all these values were above one, they predict the observed persistence of the virus in the population. We hypothesize that the observed variation in the estimates is a consequence of the data used. Higher resolution and temporally better defined data would likely reduce this variation. This is the first estimate of R0 for ASFV in a free range smallholder pig keeping system in sub-Saharan Africa and highlights the requirement for more efficient application of available disease control measures.
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Affiliation(s)
- Mike B. Barongo
- Department of Academic Registrar (ICT Division), Makerere University, Kampala, Uganda
- International Livestock Research Institute, Nairobi, Kenya
- * E-mail:
| | - Karl Ståhl
- Department of Disease Control and Epidemiology, National Veterinary Institute, Uppsala, Sweden
| | - Bernard Bett
- International Livestock Research Institute, Nairobi, Kenya
| | | | - Eric M. Fèvre
- International Livestock Research Institute, Nairobi, Kenya
| | - Tony Aliro
- Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda
| | - Edward Okoth
- International Livestock Research Institute, Nairobi, Kenya
| | - Charles Masembe
- Department of Biological Sciences, College of Natural and applied Sciences, Makerere University, Kampala, Uganda
| | - Darryn Knobel
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Amos Ssematimba
- International Livestock Research Institute, Nairobi, Kenya
- Department of Mathematics, Faculty of Science, Gulu University, Gulu, Uganda
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Mwanja MT, Muwanika VB, Masembe C, Mwanja WW, Nyakaana S. Microsatellite DNA analyses reveal population subdivisions among the recently introduced Nile perch (Latesspp.) in Lake Victoria. African Zoology 2015. [DOI: 10.1080/15627020.2014.11407634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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49
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Chenais E, Boqvist S, Sternberg-Lewerin S, Emanuelson U, Ouma E, Dione M, Aliro T, Crafoord F, Masembe C, Ståhl K. Knowledge, Attitudes and Practices Related to African Swine Fever Within Smallholder Pig Production in Northern Uganda. Transbound Emerg Dis 2015; 64:101-115. [PMID: 25876769 DOI: 10.1111/tbed.12347] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [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: 11/14/2014] [Indexed: 11/30/2022]
Abstract
Uganda is a low-income country with the largest pig population in East Africa. Pig keeping has a large potential, commercially and as a tool for poverty reduction, but African swine fever (ASF) is a major hurdle for development of the sector. The objective of this study was to evaluate knowledge, attitudes and practices related to ASF in the smallholder pig production value chain in northern Uganda. The study included three separate series of participatory rural appraisals (PRA), comprising purposively selected farmers and other actors in the pig production value chain. In the PRAs, various participatory epidemiology tools were used. A total of 49 PRAs and 574 participants, representing 64 different villages, were included. The results indicate that participants were well aware of the clinical signs of ASF, routes for disease spread and measures for disease control. However, awareness of the control measures did not guarantee their implementation. A majority of middlemen and butchers acknowledged having sold live pigs, carcasses or pork they believed infected with ASF. Outbreaks of ASF had a strong negative impact on participants' socio-economic status with loss of revenue and reversal into more severe poverty. In conclusion, lack of knowledge is not what is driving the continuous circulation of ASF virus in this setting. To control ASF and reduce its impact, initiatives that stimulate changes in management are needed. Because the behaviour of all actors in the value chain is largely influenced by the deep rural poverty in the region, this needs to be combined with efforts to reduce rural poverty.
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Affiliation(s)
- E Chenais
- National Veterinary Institute, Uppsala, Sweden.,Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - S Boqvist
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - U Emanuelson
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - E Ouma
- International Livestock Research Institute, Kampala, Uganda
| | - M Dione
- International Livestock Research Institute, Kampala, Uganda
| | - T Aliro
- Directorate of Production and Marketing, Gulu District Local Government, Gulu, Uganda
| | | | - C Masembe
- Makerere University, Kampala, Uganda
| | - K Ståhl
- National Veterinary Institute, Uppsala, Sweden.,Swedish University of Agricultural Sciences, Uppsala, Sweden
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50
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Kabi F, Masembe C, Muwanika V, Kirunda H, Negrini R. Geographic distribution of non-clinical Theileria parva infection among indigenous cattle populations in contrasting agro-ecological zones of Uganda: implications for control strategies. Parasit Vectors 2014; 7:414. [PMID: 25175844 PMCID: PMC4261563 DOI: 10.1186/1756-3305-7-414] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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] [Received: 05/12/2014] [Accepted: 08/26/2014] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Non-clinical Theileria parva infection among indigenous cattle occurs upon recovery from primary disease during the first year of life. Continuous exposure to infection through contaminated tick infestations with absence of clinical disease gives rise to endemic stability. Endemic stable populations may become sources of infection if contaminated tick vectors are shared with susceptible exotic cattle. This study aimed at establishing a nationwide distribution of non-clinical T. parva infection among indigenous cattle populations to inform novel control strategies. METHODS The occurrence of non-clinical T. parva infection among apparently healthy 925 indigenous cattle from 209 herds spread out in 10 agro-ecological zones (AEZs) was determined using a nested PCR assay. The influence of AEZ, breed, sex, age and farmers' ranking of ECF importance were interrogated for influence of non-clinical parasite occurrence. RESULTS The overall prevalence of non-clinical T. parva infection was 30% (278/925). A gradual increase of non-clinical T. parva infection was observed ranging from 17% (95% CI: 0.03-0.23) to 43% (95% CI: 0.3-0.55) in the North Eastern Savannah Grasslands (NESG) to the Western Highland Ranges (WHR) respectively. A similarly associated 18% (95% CI: 0.07-0.28) and 35% (95% CI: 0.3-0.39) non-clinical parasite prevalence was observed among the East African shorthorn Zebu (EASZ) and Ankole cattle respectively. Average herd level non-clinical T. parva prevalence was 28%, ranging from zero to 100%. The likelihood of non-clinical T. parva infection was 35.5% greater in the western highlands compared to the northeastern semi-arid AEZs. CONCLUSIONS Non-clinical T. parva occurs countrywide, structured along patterns of AEZ and breed gradients. These findings may guide policy formulation, deployment of integrated control strategies and local cattle improvement programs.
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Affiliation(s)
- Fredrick Kabi
- Department of Environmental Management, Molecular Genetics Laboratory, College of Agricultural and Environmental Sciences, Makerere University, P,O, Box 7062/7298 Kampala, Uganda.
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