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

Isolation and characterization of two malathiondegrading Pseudomonas sp. in Egypt

Pseudomonas aeruginosa and Pseudomonas mendocina degrading malathion were studied. Morphological, biochemical and 16S rRNA genes for bacterial identification were selected. Biodegradation of some organophosphorus compounds with the 2 bacterial isolates was determined by high performance liquid chromatography (HPLC). P. aeruginosa strain completely removed diazinon, malathion and fenitrothion, but not chlorpyrifos within 14 days. P. mendocina strain was not able to degrade malathion, diazinon and chlorpyrifos completely and no significant  degradation for chlorpyrifos. The bacterial growth curve showed a steady increase in the two bacterial isolates masses during malathion degradation. The highest growth rates were with yeast extract, glucose and citrate for the 2 isolates, but not with phenol. Shaked high inoculum density with incubation at 30°C of malathion bacterial cultures were found to be the optimum conditions for malathion degradation.  Bacterial culture extracts subjected to liquid chromatography/mass spectrometry (LC/MS) analysis revealed that the separated products were malathion  monocarboxylic acid and malathion dicarboxylic acid. Molecular characterization of carboxylesterase enzyme revealed that carboxylesterase amino acid sequences of the 2 isolates showed high identity to other carboxylesterase enzymes of P. aeruginosa and P. mendocina, respectively. Phylogenetic analysis showed that P. aeruginosa was localized in a separate branch from other carboxylesterase producing Pseudomonas sp. So, it is suggested that this enzyme is a novel esterase enzyme. Use of pesticide-degrading microbial systems for removal of organophosphorus compounds from the contaminated sites requires an understanding of ecological requirements of degrading strains. The results provided an important insight into determining the bioremediation potential of both strains. But the mentioned bacteria cannot be the aim of bioremediation due to risk of public health hazard, hence these bacteria cannot be used in bioremediation but their purified enzymes could.Key words: Biodegradation, carboxylestrase, organopgosphorus pesticides, Pseudomonas aeruginosa, Pseudomonas mendocina

Vitamin D as a Key Player in Modulating Rheumatoid Arthritis-derived Immune Response

Rheumatoid arthritis (RA) is a systemic inflammatory disease with chronic nature of joints related to autoimmunity. Vitamin D was found to modulate cell growth, function of immune cells and anti-inflammatory action. The aims of that study were to investigate serum level of vitamin D and some cytokines and to identify the correlation between vitamin D and these cytokines in RA. Totally 40 RA patients without vitamin D supplement were involved in this study. Serum level of vitamin D, interleukin-6 (IL-6), IL-10, IL-35, C-reactive protein (CRP) and tumor necrosis factor α (TNF-α), all of them were measure in all patients by enzyme-linked immunosorbent assay (ELISA). Patients were classified according to Vitamin D levels into two groups; RA patients with Vit. D deficiency (n=25) and RA patients with Vit. D sufficiency (n=15). IL-6 was lower significantly (P = 0.03) in RA patients with Vit. D sufficiency than RA patients with Vit. D deficiency. IL-10 and IL-35 were higher significantly (P = 0.0234, P = 0.0356 respectively) in RA patients with Vit. D sufficiency than RA patients with Vit. D deficiency. Vit. D was significantly positively correlated with both IL-10 (r = 0.4516, P = 0.0034) and IL-35 (r = 0.3424, P = 0.0329) and negatively correlated with IL-6 (r = -0.3188, P = 0.0479). Sufficient serum level of Vit. D is correlated with higher level of anti-inflammatory cytokines (IL-10 and IL-35) and lower level of IL-6. This support the immunomodulatory effect of Vit. D in RA

Parametric Study on Steel–Concrete Composite Beams Strengthened with Post-Tensioned CFRP Tendons

A sustainable environment can be achieved by strengthening the existing building to avoid new construction and by replacing the construction materials with long-lasting sustainable materials such as a fiber-reinforced polymer (FRP). Using post-tensioned (PT) FRP systems has proven to be an effective technique in strengthening the structure and decreasing cracks and deformability. In this study, a 3-D finite element model was built to investigate the flexural behavior of composite beams strengthened with external PT FRP tendons. Limited research studied the use of FRP tendons to enhance the structural behavior of composite beams. This paper represents a comprehensive study of the effect of several parameters that control the design of the FRP tendons. Parameters such as PT level, tendon material, tendon length, degree of shear connection (DOSC), and tendon profile shape were considered under loading. The 3-D model’s correctness is validated using published experimental data. It was observed that of all FRP materials, carbon FRP is the best type for upgrading the beam strength, and it was recommended to use a 30 to 40% PT level. In addition, applying external PT over the full length of the beam increases the ultimate load capacity significantly. However, due to the difficulty of construction, it was recommended to use 90% of the beam span length since the difference in beam capacity does not exceed 5%. Finally, adding PT tendons with a trapezoidal and parabola profile to composite beams significantly increases the yield load and the beam capacity

Exposure to a Low-Oxygen Environment Causes Implantation Failure and Transcriptomic Shifts in Mouse Uteruses and Ovaries

Hypoxia is a condition in which tissues of the body do not receive sufficient amounts of oxygen supply. Numerous studies have elucidated the intricate roles of hypoxia and its involvement in both physiological and pathological conditions. This study aimed to clarify the impact of a forced low-oxygen environment in early pregnancy by exposing mice to low-oxygen conditions for 24–72 h after fertilization. The treatment resulted in the complete failure of blastocyst implantation, accompanied by vascular hyperpermeability in the uterus. A transcriptome analysis of the uterus revealed remarkable alterations in gene expression between control normoxic- and hypoxic-treatment groups. These alterations were characterized by the differentially expressed genes categorized into the immune responses and iron coordination. Furthermore, exposure to a low-oxygen environment caused apoptosis in the corpus luteum within the ovary and a reduction in progesterone secretion. Consequently, diminished plasma progesterone levels were considered to contribute to implantation failure in combination with the activation of the hypoxic pathway in the uterus. Additionally, previous studies have demonstrated the impact of hypoxic reactions on blastocyst development and the pre-implantation process in the endometrium. Our findings suggest that the corpus luteum exhibits elevated susceptibility to hypoxia, thereby elucidating a critical aspect of its physiological response

Patient Doses in Ct Examinations in 18 Countries: Initial Results from International Atomic Energy Agency Projects

The purpose of this prospective study at 73 facilities in 18 countries in Africa, Asia and Eastern Europe was to investigate if the CT doses to adult patients in developing countries are higher than international standards. The dose assessment was performed in terms of weighted computed tomography dose index (CTDIw) and dose length product (DLP) for chest, chest (high resolution), lumbar spine, abdomen and pelvis CT examinations using standard methods. Except in one case, the mean CTDIw values were below diagnostic reference level (DRL) while for DLP, 17 % of situations were above DRLs. The resulting CT images were of adequate quality for diagnosis. The CTDIw and DLP data presented herein are largely similar to those from two recent national surveys. The study has shown a stronger need to create awareness and training of radiology personnel as well as monitoring of radiation doses in many developing countries so as to conform to the ALARA principle