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

Improvement of Bacillus thuringiensis bioinsecticide production by sporeless and sporulating strains using response surface methodology

Statistical experimental designs, involving a Plackett-Burman design followed by a rotatable central composite design were used to optimize the culture medium constituents for Bacillus thuringiensis bioinsecticide production. This was carried out by using firstly an asporogenic strain and extrapolated to some sporeless and sporulating strains. Initial screening of production parameters was performed and the variables with statistically significant effects on delta-endotoxin production were identified: glucose, glycerol, yeast extract and MnSO(4). These variables were selected for further optimization by response surface methodology. The obtained results revealed that the optimum culture medium for delta-endotoxin production consists of 22.5 g/l of glucose, 4.8g/l of glycerol, 5.8 g/l of yeast extract and 0.008 g/l of MnSO(4). Under these conditions, delta-endotoxin production was 2,130 and 2,260 mg/l into 250 and 1,000 ml flask respectively, which represent more than 38% improvement in toxin production over the basal medium (1,636 mg/l). Such medium composition was shown to be suitable for overproducing delta-endotoxins by sporeless and sporulating strains.Tunisian Ministry of Higher Education, Scientific Research and Technolog

DVF-fog: Distributed virtual firewall in fog computing based on risk analysis

To eliminate network saturation during data exchanges, fog computing is deployed as the technology that benefits from both cloud computing and internet of things (IoT) paradigms. Therefore, we focus on network access control issues that are considered as grave challenges in a distributed environment such as fog/cloud computing. Therefore, we present an architecture for distributed fog with a divided topology into zones and implement distributed firewall/controller. This way, we can combine user-based access control and distributed network-based access control based on risk analysis and estimation. The simulation results show that our proposed technique improves the network performance in terms of throughput and blocking rate and it is able to prevent DDoS. Furthermore, the comparison with existing approaches based on the openstack framework illustrates that the fog-based distributed virtual firewall (DVF) approach decreases significantly the false positive rate (FPR) to be 0.0942% and increases the true positive rate (TPR) to be 99.9%. 2019 Inderscience Enterprises Ltd.Scopus2-s2.0-8508648485

Nanostructured Fe,Co-Codoped MoO₃ Thin Films

Molybdenum oxide (MoO3) and Fe,Co-codoped MoO3 thin films obtained by spray pyrolysis have been in-depth investigated to understand the effect of Co and Fe codoping on MoO3 thin films. The effect of Fe and Co on the structural, morphological and optical properties of MoO3 thin films have been studied using X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and energy-dispersive X-ray analysis (EDAX), optical and photoluminescence (PL) spectroscopy, and electropyroelectric methods. The XRD patterns demonstrated the formation of orthorhombic α-MoO3 by spray pyrolysis. SEM characterization has shown an increase in roughness of MoO3 thin films by Fe and Co doping. Optical reflectance and transmittance measurements have shown an increase in optical band gap with the increase in Fe and Co contents. Thermal conductivity and thermal diffusivity of Fe,Co-doped MoO3 were 24.10⁻25.86 Wm−1K−1 and 3.80 × 10−6⁻5.15 × 10−6 m2s−1, respectively. MoO3 thin films have shown PL emission. Doping MoO3 with Fe and Co increases emission in the visible range due to an increase number of chemisorbed oxygen atoms. The photodegradation of an aqueous solution of methylene blue (MB) depended on the content of the codoping elements (Fe,Co). The results showed that a degradation efficiency of 90% was observed after 60 min for MoO3: Fe 2%-Co 1%, while the degradation efficiency was about 35% for the undoped MoO3 thin film

Application of Asymetrical and Hoke Designs for Optimization of Laccase Production by the White-Rot Fungus Fomes fomentarius in Solid-State Fermentation

Statistical approaches were employed for the optimization of different cultural parameters for the production of laccase by the white rot fungus Fomes fomentarius MUCL 35117 in wheat bran-based solid medium. first, screening of production parameters was performed using an asymmetrical design 2533//16, and the variables with statistically significant effects on laccase production were identified. Second, inoculum size, CaCl2 concentration, CuSO4 concentration, and incubation time were selected for further optimization studies using a Hoke design. The application of the response surface methodology allows us to determine a set of optimal conditions (CaCl2, 5.5 mg/gs, CuSO4, 2.5 mg/gs, inoculum size, 3 fungal discs (6 mm Ø), and 13 days of static cultivation). Experiments carried out under these conditions led to a laccase production yield of 150 U/g dry substrate

Combinatorial effect of mutagenesis and medium component optimization on Bacillus amyloliquefaciens antifungal activity and efficacy in eradicating Botrytis cinerea

This work is directed towards Bacillus amyloliquefaciens strain BLB371 metabolite production for biocontrol of fungal phytopathogens. In order to maximise antifungal metabolite production by this strain, two approaches were combined: random mutagenesis and medium component optimization. After three rounds of mutagenesis, a hyper active mutant, named M3-7, was obtained. It produces 7 fold more antifungal metabolites (1800 AU/mL) than the wild strain in MC medium. A hybrid design was applied to optimise a new medium to enhance antifungal metabolite production by M3-7. The new optimized medium (35 g/L of peptone, 32.5 g/L of sucrose, 10.5 g/L of yeast extract, 2.4 g/L of KH2PO4, 1.3 g/L of MgSO4 and 23 mg/L of MnSO4) achieved 1.62 fold enhancement in antifungal compound production (3000 AU/mL) by this mutant, compared to that achieved in MC medium. Therefore, combinatory effect of these two approaches (mutagenesis and medium component optimization) allowed 12 fold improvement in antifungal activity (from 250 UA/mL to 3000 UA/mL). This improvement was confirmed against several phytopathogenic fungi with an increase of MIC and MFC over than 50%. More interestingly, a total eradication of gray mold was obtained on tomato fruits infected by Botrytis cinerea and treated by M3-7, compared to those treated by BLB371. From the practical point of view, combining random mutagenesis and medium optimization could be considered as an excellent tool for obtaining promising biological products useful against phytopathogenic fungi.Scopu