21 research outputs found

    The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

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    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

    Remarks on the Surface Area and Equality Conditions in Regular Forms. Part I: Triangular Prisms

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    Analysis and Interpretation of the Field and Laboratory Geophysical Measurements of Black-Sand Beach Deposits, East Rosetta, Egypt

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    The present study deals with the analysis and interpretation of the results of field geophysical survey and laboratory geophysical measurements. The study of the magnetic and electrical methods was selected because the beach sands contain many minerals that have magnetic and electric properties. Analysis and interpretation of the field and laboratory magnetic and geoelectric maps demonstrated that the investigated beach-alluvial deposits can be subdivided according to their magnetic and geoelectric properties into three main zones striking nearly parallel to the shoreline of the Mediterranean Sea at the study area. The northern zone is more enriched in black sands than the central or southern zones. Field and laboratory magnetic susceptibility measurements provided very useful maps for the concentration of heavy minerals. The deep-seated magnetic response was calculated at an average depth of 239.6 m, while the near-surface magnetic responses were computed at average depths of 9.1, 57.9, and 81.8 m, respectively. The correlation between the geophysical features, recorded on the total magnetic field intensity, the electric resistivity, the IP chargeability, and the calculated metal factor, was found to agree to a great extent. The heavymineral concentration was found to decrease with depth. However, the heavyminerals show parallel zones below the surface, suggesting similar sedimentation environments

    Pulmonary rehabilitation in chronic obstructive pulmonary disease

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    COPD has significant extrapulmonary effects as weight loss, nutritional abnormalities, and skeletal muscle dysfunction. Pulmonary rehabilitation (PR) programs are beneficial to COPD in order to improve exercise capacity, muscle force, symptoms, and health-related quality of life. The aim of this study is to evaluate the role of PR program to: Improve functional capacity as assessed by 6MWD test, improve dyspnea level as assessed by MRC dyspnoea scale, improve PFT and improve ABG. It was performed on forty-five COPD patients. They are divided into: 15 patients for aerobic training group, 15 patients for respiratory training group and 15 patients were control group. Regarding aerobic training group: There was a statistically significant improvement in 6MWD (P-value 0.001), BODE score (P-value 0.001) and both FEV1 (P-value 0.006) and FVC (P-value 0.002). Also there was a highly significant improvement of FVC% (P-value 0.006) than the respiratory training group. Regarding respiratory training group: There was a higher % of improvement (66.7%) of dyspnea score grade within the respiratory training group than aerobic training and control groups. Although there was no statistically significant difference of both physiological parameters and ABG variables between control and respiratory training groups, there was a significant improvement of both FVC (P-value 0.001) and FEV1 (P-value 0.047) and PO2 (P-value 0.001) and Sat O2 (P-value 0.001) within the respiratory training group. Short-term PR program (6–8 weeks) especially aerobic training program has the capacity to: Break the vicious circle of dyspnea, increasing inactivity and exercise intolerance. Improve physiological parameters (FVC and FEV1) and improve some components of BODE index

    Antiviral and Antioxidant Potential of Fungal Endophytes of Egyptian Medicinal Plants

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    This study aimed to explore the antioxidant potential and antiviral activity of endophytic fungi which were isolated from healthy living tissues of medicinal plants. Endophytic strains (29 different taxa) were isolated from 18 Egyptian medicinal plants collected from Saint Katherine Protectorate, Egypt. The fungal endophytes were identified based on morphological characters. All isolates were identified as ascomycetes, except two Zygomycetes strains (Absidia corymbifera and Mucor fuscus). Isolated endophytes were cultivated on potato dextrose media. The fungal metabolites were extracted by ethyl acetate and examined for their biological activities. Among 99 total extracts, only Chaetomium globosum, which was isolated from Adiantum capillus, showed a promising DPPH (1,1-diphenyl-2-picrylhydrazyl) scavenging activity (99% at 100 µg/mL). Fifteen extracts prohibited the reproduction of HSV-2 virus. On the other hand, the reproduction of VSV-virus was inhibited by sixteen endophytic extracts. The promising anti-(HSV-2 and VSV) extract of endophytic Pleospora tarda strain; that was originally isolated from the medicinal plant Ephedra aphylla, showed viral inhibitory activity of 40.7% and 15.2%, respectively. Two compounds, for which antiviral activates could be attributed, were isolated and identified as alternariol and alternariol-(9)-methyl ether using different NMR techniques from P. tarda extract. For the first time, we report here the ability of the endophytic fungus P. tarda to produce alternariol and alternariol-(9)-methyl ether. The results indicate that the endophytic fungi from medicinal plants are promising sources of bioactive compounds

    PCR-detected fungal infection is associated with fatal outcomes in cirrhotic patients with spontaneous peritonitis

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    AbstractBackground & aimsThe rate of mortality from Spontaneous Peritonitis (SP) in cirrhotic patients is still high despite the development of new antibiotic treatments and intensive hospital care. The coexistence of spontaneous fungal peritonitis (SFP) is almost entirely ignored health problem, because it is difficult to be diagnosed at an early stage by conventional culture-based methods. Therefore, this study was designed to employ PCR-based method in evaluating the prevalence of fungal infection in cirrhotic patients with peritonitis who failed to respond to the recommended therapy and to determine its association with in-hospital mortality.Subjects and MethodsA total of 80 cirrhotic patients admitted to the hospital with ascitis (June-2013 to April-2015) were followed in this study.ResultsDuring hospitalization, 23 (42%) of patients had died although they received guideline-driven treatment. The demographics, clinical, hematological, and biochemical data were similar in both mortality and survival groups. However, the incidence of fungus infection was the only significantly elevated parameter in the mortality group than in the survival group (7/23;30% vs.0/32;0%, P=0.0012). This fungal infection was significantly associated with SP drug resistance development (P=0.007). Intriguingly, all the cases of fungal infection were detected by PCR-based method while culture-based diagnosis was able to detect the fungal infection in only 4 of these cases indicating a diagnostic sensitivity of 57%.ConclusionOur results reflect a strong association between SFP and in-hospital mortality in cirrhotic patients with SP that may offer a coherent explanation for the antibiotic treatment failure in such patients. Prompt PCR-detection and antifungal coverage is warranted in these cases

    Virulence Characteristics of Biofilm-Forming <i>Acinetobacter baumannii</i> in Clinical Isolates Using a <i>Galleria mellonella</i> Model

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    Acinetobacter baumannii is a Gram-negative coccobacillus responsible for severe hospital-acquired infections, particularly in intensive care units (ICUs). The current study was designed to characterize the virulence traits of biofilm-forming carbapenem-resistant A. baumannii causing pneumonia in ICU patients using a Galleria mellonella model. Two hundred and thirty patients with hospital-acquired or ventilator-associated pneumonia were included in our study. Among the total isolates, A. baumannii was the most frequently isolated etiological agent in ICU patients with pneumonia (54/165, 32.7%). All A. baumannii isolates were subjected to antimicrobial susceptibility testing by the Kirby–Bauer disk diffusion method, while the minimum inhibitory concentrations of imipenem and colistin were estimated using the broth microdilution technique. The biofilm formation activity of the isolates was tested using the microtiter plate technique. Biofilm quantification showed that 61.1% (33/54) of the isolates were strong biofilm producers, while 27.7% (15/54) and 11.1% (6/54) showed moderate or weak biofilm production. By studying the prevalence of carbapenemases-encoding genes among isolates, blaOXA-23-like was positive in 88.9% of the isolates (48/54). The BlaNDM gene was found in 27.7% of the isolates (15/54 isolates). BlaOXA-23-like and blaNDM genes coexisted in 25.9% (14/54 isolates). Bap and blaPER-1 genes, the biofilm-associated genes, coexisted in 5.6% (3/54) of the isolates. For in vivo assessment of A. baumannii pathogenicity, a Galleria mellonella survival assay was used. G. mellonella survival was statistically different between moderate and poor biofilm producers (p p A. baumannii that causes pneumonia in the ICU

    Virulence Characteristics of Biofilm-Forming Acinetobacter baumannii in Clinical Isolates Using a Galleria mellonella Model

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    Acinetobacter baumannii is a Gram-negative coccobacillus responsible for severe hospital-acquired infections, particularly in intensive care units (ICUs). The current study was designed to characterize the virulence traits of biofilm-forming carbapenem-resistant A. baumannii causing pneumonia in ICU patients using a Galleria mellonella model. Two hundred and thirty patients with hospital-acquired or ventilator-associated pneumonia were included in our study. Among the total isolates, A. baumannii was the most frequently isolated etiological agent in ICU patients with pneumonia (54/165, 32.7%). All A. baumannii isolates were subjected to antimicrobial susceptibility testing by the Kirby–Bauer disk diffusion method, while the minimum inhibitory concentrations of imipenem and colistin were estimated using the broth microdilution technique. The biofilm formation activity of the isolates was tested using the microtiter plate technique. Biofilm quantification showed that 61.1% (33/54) of the isolates were strong biofilm producers, while 27.7% (15/54) and 11.1% (6/54) showed moderate or weak biofilm production. By studying the prevalence of carbapenemases-encoding genes among isolates, blaOXA-23-like was positive in 88.9% of the isolates (48/54). The BlaNDM gene was found in 27.7% of the isolates (15/54 isolates). BlaOXA-23-like and blaNDM genes coexisted in 25.9% (14/54 isolates). Bap and blaPER-1 genes, the biofilm-associated genes, coexisted in 5.6% (3/54) of the isolates. For in vivo assessment of A. baumannii pathogenicity, a Galleria mellonella survival assay was used. G. mellonella survival was statistically different between moderate and poor biofilm producers (p &lt; 0.0001). The killing effect of the strong biofilm-producing group was significantly higher than that of the moderate and poor biofilm producers (p &lt; 0.0001 for each comparison). These findings highlight the role of biofilm formation as a powerful virulence factor for carbapenem-resistant A. baumannii that causes pneumonia in the ICU
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