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

Data from: Hypothesis-driven and field-validated method to prioritize fragmentation mitigation efforts in road projects

The active field of connectivity conservation has provided numerous methods to identify wildlife corridors with the aim of reducing the ecological effect of fragmentation. Nevertheless, these methods often rely on untested hypotheses of animal movements, usually fail to generate fine-scale predictions of road crossing sites, and do not allow managers to prioritize crossing sites for implementing road fragmentation mitigation measures. We propose a new method that addresses these limitations. We illustrate this method with data from southwestern Gabon (central Africa). We used stratified random transect surveys conducted in two seasons to model the distribution of African forest elephant (Loxodonta cyclotis), forest buffalo (Syncerus caffer nanus), and sitatunga (Tragelaphus spekii) in a mosaic landscape along a 38.5 km unpaved road scheduled for paving. Using a validation data set of recorded crossing locations, we evaluated the performance of three types of models (local suitability, local least-cost movement, and regional least-cost movement) in predicting actual road crossings for each species, and developed a unique and flexible scoring method for prioritizing road sections for the implementation of road fragmentation mitigation measures. With a data set collected in <10 weeks of fieldwork, the method was able to identify seasonal changes in animal movements for buffalo and sitatunga that shift from a local exploitation of the site in the wet season to movements through the study site in the dry season, whereas elephants use the entire study area in both seasons. These three species highlighted the need to use species- and season-specific modeling of movement. From these movement models, the method ranked road sections for their suitability for implementing fragmentation mitigation efforts, allowing managers to adjust priority thresholds based on budgets and management goals. The method relies on data that can be obtained in a period compatible with environmental impact assessment constraints, and is flexible enough to incorporate other potential movement models and scoring criteria. This approach improves upon available methods and can help inform prioritization of road and other linear infrastructure segments that require impact mitigation methods to ensure long-term landscape connectivity

RoadFragmentationDataset

This dataset accompanies Vanthomme H., Kolowski J., Nzamba, B.S., Alonso A. 2015. Hypothesis-driven and field-validated method to prioritize fragmentation mitigation efforts in road projects. Ecological Applications (in press). It contains a copy of the main data file exactly as used for this paper

Appendix B. Spatial aggregation of actual crossings points.

Spatial aggregation of actual crossings points

Appendix A. Habitat suitability modeling.

Habitat suitability modeling

Increase in malaria prevalence and age of at risk population in different areas of Gabon

Abstract Background Following the deployment of new recommendations for malaria control according to the World Health Organization, an estimation of the real burden of the disease is needed to better identify populations at risk and to adapt control strategies. The aim of the present study was to estimate the clinical burden of malaria among febrile children aged less than 11 years, before and after six-year of deployment of malaria control strategies in different areas of Gabon. Methods Cross-sectional surveys were carried out in health care facilities at four locations: two urban areas (Libreville and Port-Gentil), one semi-urban area (Melen) and one rural area (Oyem), between 2005 and 2011. Febrile paediatric patients, aged less than 11 years old were screened for malaria using microscopy. Body temperature, history of fever, age, sex, and location were collected. Results A total of 16,831 febrile children were enrolled; 78.5% (n=13,212) were less than five years old. The rate of Plasmodium falciparum-infection was the lowest in Port-gentil (below 10%) and the highest at Oyem (above 35%). Between 2005 and 2008, malaria prevalence dropped significantly from 31.2% to 18.3%, followed by an increase in 2011 in Libreville (24.1%), Port-Gentil (6.5%) and Oyem (44.2%) (ppp0.01). The risk of being P. falciparum-infected in children aged less than five years old significantly decreased from 2008 to 2011 (p Conclusions This study shows an increased risk of malaria infection in different areas of Gabon with over-five year-old children tending to become the most at-risk population, suggesting a changing epidemiology. Moreover, the heterogeneity of the malaria burden in the country highlights the importance of maintaining various malaria control strategies and redefining their implementation.</p