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Integrating genomic, epidemiological and environmental modelling to uncover the dynamics of chikungunya transmission in Africa
Thesis (MSc)--Stellenbosch University, 2024.
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Stellenbosch : Stellenbosch University
2025
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| _version_ | 1867613804515295232 |
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| access_status_str | Open Access |
| author | Ramphal, Yajna |
| author2 | De Oliveira, Tulio |
| author_browse | De Oliveira, Tulio Ramphal, Yajna |
| author_facet | De Oliveira, Tulio Ramphal, Yajna |
| author_sort | Ramphal, Yajna |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MSc)--Stellenbosch University, 2024. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/131895 |
| institution | Stellenbosch University (South Africa) |
| last_indexed | 2026-06-10T12:41:58.332Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/131895 Integrating genomic, epidemiological and environmental modelling to uncover the dynamics of chikungunya transmission in Africa Ramphal, Yajna De Oliveira, Tulio Tegally, Houriiyah Moir, Monika Stellenbosch University. Faculty of Science. Centre for Bioinformatics & Computational Biology. Chikungunya -- Epidemiology Mosquitoes as carriers of disease Chikungunya -- Transmission -- Africa Communicable diseases -- Genetics aspects Climatic changes Virus diseases -- Effect of environment on Computational biology Public health -- Africa UCTD Thesis (MSc)--Stellenbosch University, 2024. ENGLISH ABSTRACT: The Chikungunya virus (CHIKV) poses a significant global public health concern, with Africa remaining an endemic region. Since its discovery in Tanzania in 1953, CHIKV has caused multiple epidemics across the continent, affecting millions and straining healthcare resources in low-income communities. In Africa, the virus is primarily transmitted by the Aedes mosquito, with humans serving as the primary amplifying host. This research employs literature review methods, phylodynamic analysis and environmental suitability modelling to explore the disease transmission, endemicity and susceptibility risk of CHIKV across the African continent. A comprehensive literature review was conducted to elucidate the historical and current burden of CHIKV in Africa. We conducted a secondary phylodynamic analysis to describe the transmission dynamics of CHIKV across the continent. We found that geographically distinct lineages are circulating in Africa. Enzootic spillover events were likely identified in West Africa, while in East Africa, the virus was introduced into the continent from Asian outbreaks, including the recent reintroduction of the Indian Ocean lineage from the Indian subcontinent. Climate- driven environmental modelling was used to uncover the regional transmission risk of CHIKV in Kenya. The results indicate that the transmission potential was greater in regions with an increase in temperature. Increased transmission risk was identified during the two wet rainy seasons in Kenya, particularly in regions that experience warmer temperatures.This research enhances the understanding of CHIKV transmission history and viral movement patterns in Africa, providing pivotal insights for public health planning and intervention strategies. Surveillance challenges and knowledge gaps were identified, revealing potential blind spots in CHIKV control and aiding in the identification of high-risk areas. This thesis contributes to the ongoing efforts within the CLIMADE Africa Consortium, which aims to mitigate and control climate-driven emerging and reemerging infectious diseases in Africa. AFRIKAANSE OPSOMMING: Die Chikungunya-virus (CHIKV) vorm 'n beduidende wereldwye openbare gesondheidsorg, met Afrika wat 'n endemiese streek bly. Sedert sy ontdekking in Tanzanie in 1953, het CHIKV verskeie epidemies regoor die vasteland veroorsaak, wat miljoene geraak het en gesondheidsorghulpbronne in lae- inkomste gemeenskappe onder druk geplaas het. In Afrika word die virus hoofsaaklik deur die Aedes- muskiet oorgedra met mense wat as die primere versterkende gasheer dien. Hierdie navorsing gebruik literatuuroorsigmetodes, filodinamiese analise en omgewingsgeskiktheidsmodellering om die siekteoordrag, endemiese en vatbaarheidsrisiko van CHIKV oor die Afrika-kontinent te ondersoek. 'n Omvattende literatuuroorsig is gedoen om die historiese en huidige las van CHIKV in Afrika toe te lig. Ons het 'n sekondere filodinamiese analise uitgevoer om die transmissiedinamika van CHIKV oor die kontinent te beskryf. Ons het gevind dat daar geografiese afsonderlike afstammelinge in Afrika sirkuleer. Waarskynlike gebeure van ensootiese oorspoeling is in Wes-Afrika geidentifiseer, wat in kontras staan met die verskil van afgeleide transmissiedinamika in Oos-Afrika, waar die virus dikwels deur Asiatiese uitbrekings bekendgestel word, insluitend die onlangse herinvoering van die Indiese Oseaan-lyn vanaf die Indiese subkontinent na Oos-Afrika . Klimaatgedrewe omgewingsmodellering was om die streeksoordragrisiko van CHIKV in Kenia te ontbloot. Die resultate dui daarop dat die oordragpotensiaal groter was in streke met 'n toename in temperatuur. groter oordragrisiko is tydens die twee nat reenseisoene in Kenia geidentifiseer, veral in streke wat warmer temperature ervaar. Hierdie navorsing verbeter die begrip van CHIKV-oordraggeskiedenis en virale bewegingspatrone in Afrika. Bied deurslaggewende insigte vir openbare gesondheidsbeplanning en intervensiestrategiee. Toesiguitdagings en kennisgapings is geidentifiseer, wat potensiele blindekolle in CHIKV-beheer aan die lig gebring het, terwyl dit gehelp het om areas met hoe risiko te identifiseer. Hierdie tesis dra by tot die voortdurende pogings binne die CLIMADE Africa Consortium, wat daarop gemik is om klimaatgedrewe opkomende en heropkomende aansteeklike siektes in Afrika te versag en te beheer. Masters 2025-04-07T13:19:02Z 2025-04-07T13:19:02Z 2024-12 Thesis https://scholar.sun.ac.za/handle/10019.1/131895 Stellenbosch University xv,121 pages : illustrations, maps application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Chikungunya -- Epidemiology Mosquitoes as carriers of disease Chikungunya -- Transmission -- Africa Communicable diseases -- Genetics aspects Climatic changes Virus diseases -- Effect of environment on Computational biology Public health -- Africa UCTD Ramphal, Yajna Integrating genomic, epidemiological and environmental modelling to uncover the dynamics of chikungunya transmission in Africa |
| title | Integrating genomic, epidemiological and environmental modelling to uncover the dynamics of chikungunya transmission in Africa |
| title_full | Integrating genomic, epidemiological and environmental modelling to uncover the dynamics of chikungunya transmission in Africa |
| title_fullStr | Integrating genomic, epidemiological and environmental modelling to uncover the dynamics of chikungunya transmission in Africa |
| title_full_unstemmed | Integrating genomic, epidemiological and environmental modelling to uncover the dynamics of chikungunya transmission in Africa |
| title_short | Integrating genomic, epidemiological and environmental modelling to uncover the dynamics of chikungunya transmission in Africa |
| title_sort | integrating genomic epidemiological and environmental modelling to uncover the dynamics of chikungunya transmission in africa |
| topic | Chikungunya -- Epidemiology Mosquitoes as carriers of disease Chikungunya -- Transmission -- Africa Communicable diseases -- Genetics aspects Climatic changes Virus diseases -- Effect of environment on Computational biology Public health -- Africa UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/131895 |
| work_keys_str_mv | AT ramphalyajna integratinggenomicepidemiologicalandenvironmentalmodellingtouncoverthedynamicsofchikungunyatransmissioninafrica |