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

Wastewater treatment in horizontal subsurface flow constructed wetlands using different media (setup stage)

Wastewater treatment through horizontal subsurface flow (HSSF) constructed wetlands (CWs) using three different treatment media (gravel, pieces of plastic pipes, and shredded tire rubber chips) were investigated in Samaha village, Dakahliya, Egypt. The study focused on the wetland setup stage during the first months of its operation (setup stage). In this stage media porosity, bacterial biofilm, and plant roots growth were in progress and it was prior to the operational steady state stage. Objectives of this paper are to study the change in media porosity of HSSF wetland cells in order to estimate duration of wetland setup stage, and to evaluate the use of different bed media on biological oxygen demand (BOD), chemical oxygen demand (COD) and total suspended solids (TSS) treatment. The results showed that after 180 days of operation, the wetland cells had reached steady porosity and had started stable treatment. Also performance of plastic media bed in pollutants reduction was better than gravel and rubber beds and gravel media was in advanced than rubber media

Effect of Salt Stress and Foliar Application of Salicylic Acid on Morphological, Biochemical, Anatomical, and Productivity Characteristics of Cowpea (Vigna unguiculata L.) Plants

The present study aimed to investigate the impact of salinity on vegetative growth, chemical constituents, and yields of cowpeas (Vigna unguiculata) and the possible benefits of salicylic acid (SA) on these plants after damage from salinity. To achieve these objectives, two pot experiments were carried out at the Faculty of Agriculture, Al-Azhar University, Egypt, during the two growing seasons of 2019 and 2020. The results revealed that salinity significantly decreased, and SA treatment substantially increased the plant height, number of compound leaves, number of internodes per plant, fresh weights of leaves and stems, productivity, photosynthetic pigments content, and concentrations of nitrogen (N), phosphorus (P), and potassium (K) of the cowpea plants compared with the control. The anatomical structure of stems and leaves of the plants were also investigated, and it was found that positive variations in the anatomical structure of the median portion of the main stems and blades of mature foliage leaves were detected in the stressed and SA-treated plants. In conclusion, SA treatment increased the salt stress tolerance of cowpea plants by improving the morphological and physiological attributes of the plants

Novel slag/natural rubber composite as flexible material for protecting workers against radiation hazards

Abstract This work is an attempt to employ the electric arc furnace (EAF) slag as a by-product material to develop an alternative and environmentally friendly material for gamma-radiation protection applications such as in medical and industrial areas. For this purpose, different concentrations of micro-sized EAF slag (0, 20, 40, 60, 80, 100, 500, and 800 phr) were incorporated as fillers in the natural rubber (NR) matrix to produce the shielding composites. In addition, nano-sized EAF slag particles were prepared by using a high-energy ball milling technique to investigate the effect of particle size on the gamma-radiation shielding properties. The synthesized micro and nano EAF/NR composites were tested as protective materials against gamma-radiation by employing NaI(Tl) scintillation detector and standard radioactive point sources (152Eu, 137Cs, 133Ba, and 60Co). Different shielding parameters such as linear and mass attenuation coefficient, half value layer (HVL), tenth value layer, mean free path, effective atomic number (Zeff), and effective electron density (Neff) were determined to assess the radiation shielding capability of the EAF/NR composites. Furthermore, equivalent atomic number (Zeq) and the exposure buildup factor values for photon energy in the range from 0.015 to 15 MeV were also computed by Geometric Progression method. The experimental results of micro EAF/NR composites showed that at 121.78 keV, EAF0 composite (without EAF slag content) had the lowest μ value of 0.1695 cm−1, while the EAF800 composite (which was loaded with 800 phr of micro EAF slag) had the highest μ value of 0.2939 cm−1 at the same energy, which in turn decreases the HVL from 4.09 to 2.36 cm, respectively. Therefore, increasing the filler weight fractions of EAF slag in the NR matrix, increases the shielding properties of the composites. Moreover, the NR composite reinforced with 800 phr of nano EAF slag has better gamma-radiation shielding efficiency compared to that filled with 800 phr of micro EAF slag. The success of this work was to prepare a flexible, lightweight, low-cost, and lead-free material with better shielding capability

Effect of Dopamine on Growth, Some Biochemical Attributes, and the Yield of Crisphead Lettuce under Nitrogen Deficiency

Nitrogen (N) represents the most important nutrient for plant growth and productivity, but extreme and ineffective usage of N fertilizer results in boosted plant production expenditures and environmental contamination. For the world’s sustainable food production and environmental profits, there has been increased research interest in reducing the use of N fertilization along with improving plant N deficiency (ND) tolerance. Dopamine (DA), a potential antioxidant, mediates several physio-biochemical processes in plants under normal or stressful conditions. However, their roles in increasing ND tolerance in crisphead lettuce are not well-documented. We investigate the role of DA concentration (0.50 and 100 µM) on the growth and yield of crisphead lettuce plants under ND. Under normal conditions (100% recommended N fertilizer dose), DA (50 and 100 μM) application significantly enhanced growth, chlorophyll concentration, N%, antioxidant enzymes activity, as well as yield and its components, decreased nitrate accumulation and oxidative biomarkers compared to untreated plants (0 μM DA). ND significantly decreased plant growth and yield attributes as well as evoked oxidative impairment and nitrate accumulation as compared to 100% recommended N fertilizer dose in the absence of DA. However, within ND conditions, the application of DA concentrations significantly mitigated ND-induced oxidative burst and improved plant growth, chlorophyll concentration, N%, nitrate concentration, peroxidase, catalase, superoxide dismutase, total soluble solid, vitamin C, dry matter %, and total sugars, over 0 μM DA treated plants. Current findings highlighted that exogenous application of 100 μM DA could reinforce the crisphead lettuce plant’s resilience to ND by minimizing reactive oxygen species accumulation and promoting enzymatic antioxidants alongside growth, yield, and quality improvement. The beneficial effects of DA in lessening ND’s drastic impacts on crisphead lettuce resulted from upregulating antioxidant enzyme activity, impairment of oxidative biomarkers, and maintaining chlorophyll levels. The current findings open pioneering prospects to reduce nitrogen fertilization by DA application without any drastic effect on plant productivity. But further research is needed to fully understand DA effects and their mechanisms in inducing ND tolerance in different plant species, including crisphead lettuce

Effect of Titanium and Vanadium on Antioxidants Content and Productivity of Red Cabbage

The present work studied the effect of foliar spray of different concentrations of titanium (Ti, applied as titanium dioxide) and vanadium (V, applied as vanadium pentoxide) on growth, chemical composition, antioxidant contents, antioxidant enzymes, antioxidant capacity, yield and quality criteria of red cabbage plants. For this purpose, 2.0, 4.0 and 6.0 mg L−1 of Ti and V were used to treat red cabbage plants. The control plants were treated with tap water. Our results showed that plants treated with 4.0 mg L−1 of Ti recorded the highest values of plant growth and bioactive compounds, while antioxidant capacity was decreased compared to the other treatments. In addition, plants treated with Ti and V at 2.0 and 4.0 mg L−1, respectively, showed higher values of all of the growth, yield, non-enzymatic antioxidants and antioxidants enzymes’ parameters compared to the untreated plants. Based on the obtained results, it could be concluded that the low concentrations of both Ti and V (2.0 and 4.0 mg L−1) were able to enhance red cabbage growth and yield, as well as the antioxidant contents, enzymes and capacity

Effect of Titanium and Vanadium on Antioxidants Content and Productivity of Red Cabbage

The present work studied the effect of foliar spray of different concentrations of titanium (Ti, applied as titanium dioxide) and vanadium (V, applied as vanadium pentoxide) on growth, chemical composition, antioxidant contents, antioxidant enzymes, antioxidant capacity, yield and quality criteria of red cabbage plants. For this purpose, 2.0, 4.0 and 6.0 mg L−1 of Ti and V were used to treat red cabbage plants. The control plants were treated with tap water. Our results showed that plants treated with 4.0 mg L−1 of Ti recorded the highest values of plant growth and bioactive compounds, while antioxidant capacity was decreased compared to the other treatments. In addition, plants treated with Ti and V at 2.0 and 4.0 mg L−1, respectively, showed higher values of all of the growth, yield, non-enzymatic antioxidants and antioxidants enzymes’ parameters compared to the untreated plants. Based on the obtained results, it could be concluded that the low concentrations of both Ti and V (2.0 and 4.0 mg L−1) were able to enhance red cabbage growth and yield, as well as the antioxidant contents, enzymes and capacity