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

Rights-based services for adolescents living with HIV:adolescent self-efficacy and implications for health systems in Zambia

A rights-based approach in HIV service delivery for adults is increasingly taking root in sub-Saharan Africa in the context of greater availability of antiretroviral therapy. Yet there has been comparatively little progress in strengthening a rights-based approach to adolescent HIV services, which we learned during a qualitative study in 2010 among 111 adolescents living with HIV, 21 parents and 38 health providers in three districts in Zambia. Adolescents in the study expressed a range of information and support needs and wanted locally relevant interventions to meet those needs. They wanted greater access to HIV, sexual and reproductive health information, information on how to protect themselves, privacy and confidentiality in service sites, skills training so as to be able to earn money, and better control over disclosure of their HIV status to others. Both health workers and parents acknowledged that information and services needed to be improved to meet those needs far better. This paper provides examples of successful programmes in Zimbabwe, Uganda, Tanzania, Botswana and South Africa and calls for adolescent services to be linked to both paediatric and adult services, peer networks to be established to increase adolescents' ability to collectively voice their concerns and support each other, interventions supporting adolescents' control over self-disclosure, and lastly that adolescent health should become a training specialty in sub-Saharan Africa