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

ELECTRONIC DESIGN AUTOMATION FOR AN ENERGY-EFFICIENT COARSE-GRAIN RECONFIGURABLE FABRIC ARCHITECTURE

In the past those looking to accelerate computationally intensive applications through hardware implementations have had relatively few target platforms to choose from, each with wildly opposing benefits and drawbacks. The SuperCISC Energy-Efficient Coarse-Grain Reconfigurable Fabric provides an ultra-low power alternative to field-programmable gate array (FPGA) devices and application specific integrated circuits (ASICs). The proposed Fabric combines the reconfigurable nature and manageable Computer-Aided Design (CAD) flow of FPGAs with power and energy characteristic similar to those of an ASIC. This thesis establishes the design flow and explores issues central to the design space exploration of the SuperCISC Reconfigurable Fabric Project. The Fabric Interconnect Model specification facilitates rapid design space exploration for a range of Fabric Models. Significant effort was put into the development of the Greedy Heuristic Fabric Mapper which automates the problem of programming the Fabric to perform the desired hardware function. Coupled with additional automation the Mapper allows for conversion of C-code specified application kernels into Fabric Configurations. The FIMFabricPrinter automates the verification, simulation, statistics gathering, and visualization of these Fabric Configurations. Results show the Fabric achieving power improvements of 68X to 369X, and energy improvements of 38X to 127X over the same benchmarks performed on an FPGA device

Cooperation and individuality among man-eating lions

Cooperation is the cornerstone of lion social behavior. In a notorious case, a coalition of two adult male lions from Tsavo, southern Kenya, cooperatively killed dozens of railway workers in 1898. The “man-eaters of Tsavo” have since become the subject of numerous popular accounts, including three Hollywood films. Yet the full extent of the lions' man-eating behavior is unknown; estimates range widely from 28 to 135 victims. Here we use stable isotope ratios to quantify increasing dietary specialization on novel prey during a time of food limitation. For one lion, the δ13C and δ15N values of bone collagen and hair keratin (which reflect dietary inputs over years and months, respectively) reveal isotopic changes that are consistent with a progressive dietary specialization on humans. These findings not only support the hypothesis that prey scarcity drives individual dietary specialization, but also demonstrate that sustained dietary individuality can exist within a cooperative framework. The intensity of human predation (up to 30% reliance during the final months of 1898) is also associated with severe craniodental infirmities, which may have further promoted the inclusion of unconventional prey under perturbed environmental conditions