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Ogola EO, Bastos ADS, Slothouwer I, Getugi C, Osalla J, Omoga DCA, Ondifu DO, Sang R, Torto B, Junglen S, Tchouassi DP. Viral diversity and blood-feeding patterns of Afrotropical Culicoides biting midges (Diptera: Ceratopogonidae). Front Microbiol 2024; 14:1325473. [PMID: 38249470 PMCID: PMC10797016 DOI: 10.3389/fmicb.2023.1325473] [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: 12/13/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction Culicoides biting midges (Diptera: Ceratopogonidae) are vectors of arboviral pathogens that primarily affect livestock represented by Schmallenberg virus (SBV), epizootic hemorrhagic disease virus (EHDV) and bluetongue virus (BTV). In Kenya, studies examining the bionomic features of Culicoides including species diversity, blood-feeding habits, and association with viruses are limited. Methods Adult Culicoides were surveyed using CDC light traps in two semi-arid ecologies, Baringo and Kajiado counties, in Kenya. Blood-fed specimens were analysed through polymerase chain reaction (PCR) and sequencing of cytochrome oxidase subunit 1 (cox1) barcoding region. Culicoides pools were screened for virus infection by generic RT-PCR and next-generation sequencing (NGS). Results Analysis of blood-fed specimens confirmed that midges had fed on cattle, goats, sheep, zebra, and birds. Cox1 barcoding of the sampled specimens revealed the presence of known vectors of BTV and epizootic hemorrhagic disease virus (EHDV) including species in the Imicola group (Culicoides imicola) and Schultzei group (C. enderleni, C. kingi, and C. chultzei). Culicoides leucostictus and a cryptic species distantly related to the Imicola group were also identified. Screening of generated pools (11,006 individuals assigned to 333 pools) by generic RT-PCR revealed presence of seven phylogenetically distinct viruses grouping in the genera Goukovirus, Pacuvirus and Orthobunyavirus. The viruses showed an overall minimum infection rate (MIR) of 7.0% (66/333, 95% confidence interval (CI) 5.5-8.9). In addition, full coding sequences of two new iflaviruses, tentatively named Oloisinyai_1 and Oloisinyai_2, were generated by next-generation sequencing (NGS) from individual homogenate of Culicoides pool. Conclusion The results indicate a high genetic diversity of viruses in Kenyan biting midges. Further insights into host-vector-virus interactions as well as investigations on the potential clinical significance of the detected viruses are warranted.
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Affiliation(s)
- Edwin O. Ogola
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Armanda D. S. Bastos
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Inga Slothouwer
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Caroline Getugi
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Josephine Osalla
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Dorcus C. A. Omoga
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Dickens O. Ondifu
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Sandra Junglen
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - David P. Tchouassi
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
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Omoga DCA, Tchouassi DP, Venter M, Ogola EO, Rotich G, Muthoni JN, Ondifu DO, Torto B, Junglen S, Sang R. Divergent Hantavirus in Somali Shrews ( Crocidura somalica) in the Semi-Arid North Rift, Kenya. Pathogens 2023; 12:pathogens12050685. [PMID: 37242355 DOI: 10.3390/pathogens12050685] [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: 02/10/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Hantaviruses are zoonotic rodent-borne viruses that are known to infect humans and cause various symptoms of disease, including hemorrhagic fever with renal and cardiopulmonary syndromes. They have a segmented single-stranded, enveloped, negative-sense RNA genome and are widely distributed. This study aimed to investigate the circulation of rodent-borne hantaviruses in peridomestic rodents and shrews in two semi-arid ecologies within the Kenyan Rift Valley. The small mammals were trapped using baited folding Sherman traps set within and around houses, then they were sedated and euthanatized through cervical dislocation before collecting blood and tissue samples (liver, kidney, spleen, and lungs). Tissue samples were screened with pan-hantavirus PCR primers, targeting the large genome segment (L) encoding the RNA-dependent RNA polymerase (RdRp). Eleven of the small mammals captured were shrews (11/489, 2.5%) and 478 (97.5%) were rodents. A cytochrome b gene-based genetic assay for shrew identification confirmed the eleven shrews sampled to be Crocidura somalica. Hantavirus RNA was detected in three (3/11, 27%) shrews from Baringo County. The sequences showed 93-97% nucleotide and 96-99% amino acid identities among each other, as well as 74-76% nucleotide and 79-83% amino acid identities to other shrew-borne hantaviruses, such as Tanganya virus (TNGV). The detected viruses formed a monophyletic clade with shrew-borne hantaviruses from other parts of Africa. To our knowledge, this constitutes the first report published on the circulation of hantaviruses in shrews in Kenya.
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Affiliation(s)
- Dorcus C A Omoga
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
- Zoonotic arbo and Respiratory Virus Research Program, Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health, University of Pretoria, Gezina 0031, South Africa
| | - David P Tchouassi
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Marietjie Venter
- Zoonotic arbo and Respiratory Virus Research Program, Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health, University of Pretoria, Gezina 0031, South Africa
| | - Edwin O Ogola
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Gilbert Rotich
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Joseph N Muthoni
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Dickens O Ondifu
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Sandra Junglen
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
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Chiuya T, Villinger J, Masiga DK, Ondifu DO, Murungi MK, Wambua L, Bastos ADS, Fèvre EM, Falzon LC. Molecular prevalence and risk factors associated with tick-borne pathogens in cattle in western Kenya. BMC Vet Res 2021; 17:363. [PMID: 34838023 PMCID: PMC8627057 DOI: 10.1186/s12917-021-03074-7] [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: 05/25/2021] [Accepted: 11/05/2021] [Indexed: 11/29/2022] Open
Abstract
Background Tick-borne pathogens (TBPs) are of global importance, especially in sub-Saharan Africa where they represent a major constraint to livestock production. Their association with human disease is also increasingly recognized, signalling their zoonotic importance. It is therefore crucial to investigate TBPs prevalence in livestock populations and the factors associated with their presence. We set out to identify TBPs present in cattle and to determine associated risk factors in western Kenya, where smallholder livestock production is important for subsistence and market-driven income. Results Tick-borne pathogen infections in blood samples collected from cattle at livestock markets and slaughterhouses between May 2017 and January 2019 were identified by high-resolution melting analysis and sequencing of PCR products of genus-specific primers. Of the 422 cattle sampled, 30.1% (127/422) were infected with at least one TBP, while 8.8% (37/422) had dual infections. Anaplasma spp. (19.7%) were the most prevalent, followed by Theileria (12.3%), Ehrlichia (6.6%), and Babesia (0.2%) spp. Sequence analysis of the TBPs revealed them to be Anaplasma platys-like organisms (13.5%), Theileria velifera (7.4%), Anaplasma marginale (4.9%), Theileria mutans (3.1%), Theileria parva (1.6%), and Babesia bigemina (0.2%). Ehrlichia ruminantium, Rickettsia spp., and arboviruses were not detected. Exotic breeds of cattle were more likely to be infected with A. marginale compared to local breeds (OR: 7.99, 95% CI: 3.04–22.02, p < 0.001). Presence of ticks was a significant predictor for Anaplasma spp. (OR: 2.18, 95% CI: 1.32–3.69, p = 0.003) and Ehrlichia spp. (OR: 2.79, 95% CI: 1.22–7.23, p = 0.022) infection. Cattle sampled at slaughterhouses were more likely to be positive for Anaplasma spp. (OR: 1.64, 95% CI: 1.01–2.70, p = 0.048) and A. marginale (OR: 3.84, 95% CI: 1.43–12.21, p = 0.012), compared to those sampled at livestock markets. Conclusion This study reports TBP prevalence and associated risk factors in western Kenya, factors which are key to informing surveillance and control measures.
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Affiliation(s)
- Tatenda Chiuya
- International Centre of Insect Physiology and Ecology (icipe), P.O Box 30772-00100, Nairobi, Kenya. .,Department of Zoology and Entomology, University of Pretoria, Private Bag 20, Pretoria, 0028, South Africa.
| | - Jandouwe Villinger
- International Centre of Insect Physiology and Ecology (icipe), P.O Box 30772-00100, Nairobi, Kenya
| | - Daniel K Masiga
- International Centre of Insect Physiology and Ecology (icipe), P.O Box 30772-00100, Nairobi, Kenya
| | - Dickens O Ondifu
- International Centre of Insect Physiology and Ecology (icipe), P.O Box 30772-00100, Nairobi, Kenya
| | - Maurice K Murungi
- International Livestock Research Institute, Old Naivasha Road, P.O Box 30709, Nairobi, 00100, Kenya
| | - Lillian Wambua
- International Livestock Research Institute, Old Naivasha Road, P.O Box 30709, Nairobi, 00100, Kenya
| | - Armanda D S Bastos
- Department of Zoology and Entomology, University of Pretoria, Private Bag 20, Pretoria, 0028, South Africa
| | - Eric M Fèvre
- International Livestock Research Institute, Old Naivasha Road, P.O Box 30709, Nairobi, 00100, Kenya.,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, UK
| | - Laura C Falzon
- International Livestock Research Institute, Old Naivasha Road, P.O Box 30709, Nairobi, 00100, Kenya. .,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, UK.
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