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

Field Measured Pre-Stress Concrete Losses Versus Design Code Estimates

In Florida, pre-stressed concrete bridges with a hybrid structural configuration, consisting of simply supported girders and continuous deck units providing composite action, are prevalent. In this study, an actual bridge with this configuration is instrumented with embedded vibrating wire strain gages during construction. The axial strain data are utilized to determine the time-dependent pre-stress loss variation and distribution in the pre-tensioned concrete girders used for the bridge. In this paper, however, we discuss the bridge instrumentation and monitoring technique used, and the deduced pre-stress losses obtained from field-measured strains up to 150 days, before placement of the composite slab. A comparison of the measured loss with the estimates of the Precast/Prestressed Concrete Institute (PCI) and the American Association of State Highway and Transportation Officials (AASHTO) indicates that the field-measured pre-stress loss is non-uniform across the girder depth, opposed to a uniform distribution implicitly assumed in most codes. The measured pre-stress variation is used in computing the concrete stress distribution in the girder at different depths within the given cross-section. When compared to the concrete stress from using the PCI and AASHTO suggested losses, the stress distribution resulting from using the field-measured loss is found to be non-linear, and in most cases higher

An overview of cancer chemopreventive potential and safety of proanthocyanidins

Cancer is a major public health problem worldwide. Over two-thirds of cancer-related deaths could most probably be prevented through lifestyle modification, particularly through dietary means. Proanthocyanidins (PAs), the most abundant polyphenolic substances after lignin in the plant kingdom, have been widely investigated for their chemopreventive potential. The PAs literature has, however, been mostly concerned with positive cardiovascular activities, and recent reviews about cancer chemoprevention are scarce. The present review highlights a series of in vitro and in vivo studies indicating (1) that PAs can act as anticarcinogenic agents through their antioxidant, apoptosis-inducing, immuno-modulating, and/or enzyme modulating properties, effects on epigenetics; and (2) that PAs could be particularly safe dietary compounds. These convergent data encourage further research to better understand the many aspects of cancer chemoprevention by PAs. © 2011 Copyright Taylor and Francis Group, LLC.http://dx.doi.org/10.1080/01635581.2011.607549SCOPUS: re.jinfo:eu-repo/semantics/publishe

AMMA-CATCH, a critical zone observatory in West Africa monitoring a megion in transition

International audienceWest Africa is a region in fast transition from climate, demography, and land use perspectives. In this context, the African Monsoon Multidisciplinary Analysis (AMMA)-Couplage de l'Atmosphere Tropicale et du Cycle eco-Hydrologique (CATCH) long-term regional observatory was developed to monitor the impacts of global change on the critical zone of West Africa and to better understand its current and future dynamics. The observatory is organized into three thematic axes, which drive the observation and instrumentation strategy: (i) analyze the long-term evolution of eco-hydrosystems from a regional perspective; (ii) better understand critical zone processes and their variability; and (iii) meet socioeconomic and development needs. To achieve these goals, the observatory has gathered data since 1990 from four densely instrumented mesoscale sites (similar to 10(4) km(2) each), located at different latitudes (Benin, Niger, Mali, and Senegal) so as to sample the sharp eco-climatic gradient that is characteristic of the region. Simultaneous monitoring of the vegetation cover and of various components of the water balance at these four sites has provided new insights into the seemingly paradoxical eco-hydrological changes observed in the Sahel during the last decades: groundwater recharge and/ or runoff intensification despite rainfall deficit and subsequent re-greening with still increasing runoff. Hydrological processes and the role of certain key landscape features are highlighted, as well as the importance of an appropriate description of soil and subsoil characteristics. Applications of these scientific results for sustainable development issues are proposed. Finally, detecting and attributing eco-hydrological changes and identifying possible regime shifts in the hydrologic cycle are the next challenges that need to be faced

AMMA-CATCH, a critical zone observatory in West Africa monitoring a region in transition

West Africa is a region in fast transition from climate, demography, and land use perspectives. In this context, the African Monsoon Multidisciplinary Analysis (AMMA)-Couplage de l'Atmosphere Tropicale et du Cycle eco-Hydrologique (CATCH) long-term regional observatory was developed to monitor the impacts of global change on the critical zone of West Africa and to better understand its current and future dynamics. The observatory is organized into three thematic axes, which drive the observation and instrumentation strategy: (i) analyze the long-term evolution of eco-hydrosystems from a regional perspective; (ii) better understand critical zone processes and their variability; and (iii) meet socioeconomic and development needs. To achieve these goals, the observatory has gathered data since 1990 from four densely instrumented mesoscale sites (similar to 10(4) km(2) each), located at different latitudes (Benin, Niger, Mali, and Senegal) so as to sample the sharp eco-climatic gradient that is characteristic of the region. Simultaneous monitoring of the vegetation cover and of various components of the water balance at these four sites has provided new insights into the seemingly paradoxical eco-hydrological changes observed in the Sahel during the last decades: groundwater recharge and/ or runoff intensification despite rainfall deficit and subsequent re-greening with still increasing runoff. Hydrological processes and the role of certain key landscape features are highlighted, as well as the importance of an appropriate description of soil and subsoil characteristics. Applications of these scientific results for sustainable development issues are proposed. Finally, detecting and attributing eco-hydrological changes and identifying possible regime shifts in the hydrologic cycle are the next challenges that need to be faced