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

Changes in Fertility Decline in Rwanda: A decomposition Analysis

After having stalled in the 1990s, fertility in Rwanda resumed its downward trajectory between 2005 and 2010. The total fertility rate declined from 6.1 to 4.6 and modern contraceptive use increased. However, it is unclear which determinants lay behind the previous stall and the recent strong drop in fertility. This paper contributes to an ongoing debate on the impact of social upheavals on fertility decline. We use a decomposition analysis, focusing on the change in characteristics and reproductive behaviour of women and their contributions to levels of fertility during 1992–2000 and 2000–2010. Results show that due to widowhood and separation the proportion of women who were married decreased between 1992 and 2000, but their fertility increased in the same period due to replacement fertility and an unmet need for family planning. After 2000, postponement of marriage and lower infant mortality contributed to lower fertility, but the most important effect is the overall lower fertility due not only to improved family planning provision but perhaps also to the sensitizing campaigns of the Rwandan government

Role of Conflict in shaping fertility preferences in Rwanda

Conflicts affect the social and economic conditions that could account for the stall in fertility decline in Sub-Saharan Africa. For Rwanda, the total fertility rate decreased very rapidly to 6.1 in the eighties but stalled at that level in the nineties. Part of the stall can be attributed to a lack of fertility control, but the question is whether social upheaval also affects fertility preferences. We identify three mechanisms through which the Rwanda conflict have led to a preference for larger families: mortality experience, modernization and the attitudes of third parties. Using data from DHS, we tested the contribution of these mechanisms to the preference for small, medium or large families. With the exception of sibling mortality, there is a strong impact of these mechanisms on the preference for large families, yet they do not fully account for the shifts in preferences over the years