The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Nieuwe aanpak voor natuurbescherming en armoedebestrijding : de Koija case in Kenia

In de afgelopen twintig jaar zijn in Oostelijk en Zuidelijk Afrika, vaak financieel ondersteund door (internationale) donoren, steeds meer samenwerkingsverbanden ontstaan tussen lokale bevolking, natuurbeschermingsorganisaties en particuliere toeristische ondernemingen. Deze partnerschappen streven naar natuurbescherming en armoedebestrijding buiten nationale parken en reservaten en zien toerisme als een effectief mechanisme om dit te realiseren. Dit artikel analyseert één van deze samenwerkingsverbanden. Het voorbeeld van de tien jaar oude Koija Starbeds lodge, gelegen in Laikipia, Kenia, laat zien dat er zowel baten als bedreigingen verbonden zijn aan de marktgerichte benadering van natuurbescherming

Tourism-conservation enterprises as a land-use strategy in Kenya

Since the early 1990s, nature conservation organizations in Eastern and Southern Africa have increasingly attempted to integrate their objectives with those of international development organizations, the land-use objectives of local communities and the commercial objectives of tourism businesses, in order to find new solutions for the protection of nature and wildlife outside state-protected areas. The increased inclusion of the market in conservation initiatives has led to diverse institutional arrangements involving various societal actors, such as private game reserves, conservancies and conservation enterprises. The Koija Starbeds ecolodge in Kenya – a partnership between communities, private investors and a non-governmental organization – serves as a case study for emerging institutional arrangements aimed at enabling value creation for communities from nature conservation. Based on a content analysis of data from individual semi-structured interviews and focus group interviews, as well as a document and literature review, this article reveals a range of benefits for community livelihood and conservation. It also identifies a range of longer term governance challenges, such as the need to address local political struggles, the relations between partners and transparency and accountability in the arrangement

Nieuwe aanpak voor natuurbescherming en armoedebestrijding : de Koija case in Kenia

In de afgelopen twintig jaar zijn in Oostelijk en Zuidelijk Afrika, vaak financieel ondersteund door (internationale) donoren, steeds meer samenwerkingsverbanden ontstaan tussen lokale bevolking, natuurbeschermingsorganisaties en particuliere toeristische ondernemingen. Deze partnerschappen streven naar natuurbescherming en armoedebestrijding buiten nationale parken en reservaten en zien toerisme als een effectief mechanisme om dit te realiseren. Dit artikel analyseert één van deze samenwerkingsverbanden. Het voorbeeld van de tien jaar oude Koija Starbeds lodge, gelegen in Laikipia, Kenia, laat zien dat er zowel baten als bedreigingen verbonden zijn aan de marktgerichte benadering van natuurbescherming

Tourism-conservation enterprises as a land-use strategy in Kenya

Since the early 1990s, nature conservation organizations in Eastern and Southern Africa have increasingly attempted to integrate their objectives with those of international development organizations, the land-use objectives of local communities and the commercial objectives of tourism businesses, in order to find new solutions for the protection of nature and wildlife outside state-protected areas. The increased inclusion of the market in conservation initiatives has led to diverse institutional arrangements involving various societal actors, such as private game reserves, conservancies and conservation enterprises. The Koija Starbeds ecolodge in Kenya – a partnership between communities, private investors and a non-governmental organization – serves as a case study for emerging institutional arrangements aimed at enabling value creation for communities from nature conservation. Based on a content analysis of data from individual semi-structured interviews and focus group interviews, as well as a document and literature review, this article reveals a range of benefits for community livelihood and conservation. It also identifies a range of longer term governance challenges, such as the need to address local political struggles, the relations between partners and transparency and accountability in the arrangement