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

Weed control under integrated nutrient management systems in faba bean (Vicia faba) production in Egypt

Two field experiments were conducted in two successive seasons, 2005/2006 and 2006/2007, to determine whether management can improve faba bean competitiveness with weeds, thus helping to achieve its yield potential. The experiment included five treatments, composed of organic and mineral fertilizers, alone and mixed at different rates, along with a control and six weed control treatments, including oxadiargyl, prometryn, hand hoeing treatments alone or mixed with the herbicides, and a nonweeded treatment (control).The herbicide treatments were not superior to the two hand-hoeing treatments. Using compost favored growth and yield of faba bean more than of weeds. Adding fertilizer also improved most yield parameters. Application of compost alone or combined with 50 or 100% of the recommended NPK rate improved faba bean growth in terms of net assimilation rate, specific leaf area, and leaf weight ratio as components of relative growth rate. This improvement in growth resulted in increase of seed yield, yield components and protein of faba bean. Faba bean yield performance improved under interactive fertilizer effects and weed control treatments as growth improved, as a result of nutrient release from fertilizers and weed control

A fully integrated 2.4 dB NF capacitive cross coupling CG-LNA for LTE band

This paper presents a common gate low noise amplifier utilizing a passive feedback network that provides a competitive and highly integrated front-end solution for mobile handset devices. This design utilizes a resistive load instead of the inductive one used in other designs to reduce the on-chip silicon area. The design does not need an external matching network which decrease the area of the PCB while achieving a sufficient input impedance matching, S 11 . It achieves a measured gain higher than 20 dB, noise figure less than 3 dB and input referred third order intercept point (IIP3) value higher than − 2.5 dBm at 2.3 GHz. The design is implemented in 65 nm UMC CMOS technology, occupies a total area of 0.065 mm 2 and consumes 5 mW from a 1.4 V supply. © 2019, Springer Science+Business Media, LLC, part of Springer Nature

A highly integrated wideband LNA with multiple inputs for multi-band mobile devices

This paper presents a wideband common gate LNA (CG-LNA) that provides a competitive and highly integrated front-end solution for mobile handset devices. The proposed design supplies multiple inputs in a single LNA design to accommodate various on-board duplexers for multiple supported frequency bands without needing any external matching components. It achieves a gain higher than 21 dB, noise figure (NF) less than 2.65 dB and input referred third order intercept point (IIP3) value higher than 0 dBm in the frequency range of 0.7-2.7 GHz. This design is implemented in 65nm CMOS technology. It occupies a total area of 0.14 mm2 and consumes 4.5 mW from a 1.5 V supply

Relationship between phosphorus status and nitrogen fixation by common beans ( Phaseolus vulgaris L.) under drip irrigation

The current study aims to examine, the response of contrasted recombinant inbred lines of common bean to the application of phosphorus, to identify the bean recombinant inbred lines which were efficient in phosphorus utilization when dependent on nitrogen fixation as a source of nitrogen. The experiment was conducted at the experimental farm of Agricultural Research Station of the Nubaria district, Behera, Egypt, during the winter seasons of 2008-2009. Three levels of mineral phosphorus fertilizers were applied (0, 45 and 90 kg ha-1 phosphorus pentoxide). Nodulation, plant growth parameters, leaf area, soil Olsen phosphorus, pH, and phosphorus and nitrogen of shoots, nodules and seeds were measured. The results have shown that the recombinant inbred lines responded positively to P application levels. The best values were observed in recombinant inbred lines 75, 83 and 34. Vegetative growth parameters were significantly enhanced by increasing levels of phosphorus. The highest level of phosphorus, i.e., 90 kg ha-1 phosphorus pentoxide gave the optimal values of growth parameters for all common bean recombinant inbred lines while control plants obtained the lowest values. An increase of Olsen-P and a decrease of soil pH were also observed with increases in phosphorus. These results led to the conclusions that phosphorus applied to Nubaria soil: (1) improved the soil fertility; (2) enhanced the ability of root nodules of common bean recombinant inbred lines to fix atmospheric nitrogen; and (3) increased the release of hydrogen by roots, thus decreasing soil pH and reducing the immobilization of phosphorus in the soil solution and transforming it into available form for the plant