Browsing by Author "Chabuka, Lucious Bestweek"

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    Molecular epidemiology of SARS-CoV-2 in Malawi: a comparative investigation of the COVID-19 pandemic mitigation and progression
    (Stellenbosch : Stellenbosch University, 2023-11) Chabuka, Lucious Bestweek; De Oliveira, Tulio; Wilkinson, Eduan; Baxter, Cheryl ; Van Wyk, Stephanie; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Biomedical Sciences. Molecular Biology and Human Genetics.
    ENGLISH ABSTRACT: Nations in Eastern and Southern Africa collectively reported >23 million cases of COVID-19 from 2020 until 2023. The case numbers are, however, likely to be widely underreported. Nevertheless, these African regions have endured high caseloads, placing severe strain on already burdened healthcare systems. Genome surveillance has proven invaluable for detecting harmful variants of the SARS-CoV-2 virus in the past, allowing for informed public health responses. As Variants of Interest (VOI) and Variants of Concern (VOC) commonly emerge from these regions, effective genome surveillance remains globally important. Nearly 20 million people live in Malawi, a landlocked country in South-Eastern Africa. It has been affected by five COVID-19 pandemic waves (2020-2022), comparable to other nations in the region. Despite the strain the epidemic has placed on Malawi's health services, the impact of the genomic surveillance system during the pandemic has not yet been thoroughly examined. To allow for data-driven and informed pandemic mitigation strategies to navigate the ongoing COVID-19 pandemic and to address concerns of future pandemics, a comparative investigation of the COVID-19 pandemic progression in Southern and Eastern African regions was conducted. This epidemiological information was complemented with genome surveillance data generated for Southern and Eastern African countries. This was done to gain an in-depth understanding of the data generated and circulating variants and to determine the way SARS CoV-2 variants fuelled national and international pandemic infectious waves. Therefore, this study aimed to place the South- and East-African pandemic progression and current genome surveillance initiatives into a global context. In this study, we hypothesised that investment in the laboratory and bioinformatic expertise improved the overall pathogen surveillance capacity within these regions, and most of the SARS-CoV-2 introductions into Malawi came from South Africa. However, the data generated with the surveillance networks established within Southern African regions outcompetes those in the East African regions with enhanced capacity for so-called "in country" sequencing, allowing for reduced turnaround times. Therefore, the Southern African regions, including countries such as South Africa and Botswana, served as a model for Eastern African countries such as Malawi, Tanzania, and Kenya. Moreover, import and export virus introduction events, determined using phylogenetic inferences, indicated that more introductions occurred from Southern African regions into Malawi than from East African regions. This may reflect higher sampling and subsequent genome sequencing from Southern African regions and the economic importance of these regions that largely constitute economic and travel hubs of the African continent. This comparative investigation on COVID-19 across nations highlighted areas requiring improvement in genomic surveillance to assist nations in being better prepared for future pandemics.