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

Comparative study of using Water-Based mud containing Multiwall Carbon Nanotubes versus Oil-Based mud in HPHT fields

Water-Based mud (WBM) and Oil-Based mud (OBM) are the most common drilling fluids currently used and both have several characteristics that qualify them for High Pressure High Temperature (HPHT) purposes. This paper compares the different characteristics of WBM containing Multiwall Carbon Nanotubes (MWCNTs) and OBM to help decide the most suitable mud type for HPHT drilling by considering mud properties through several laboratory tests to generate some engineering guidelines. The tests were formulated at temperatures from 120 °F up to 500 °F and pressures from 14.7 psi to 25,000 psi. The comparison will mainly consider the rheological properties of the two mud types and will also take into account the environmental feasibility of using them. The results showing that the Water-Based offers a more environmental friendly choice yet some of additives that are used to enhance its performance at (HPHT) conditions, such as (MWCNTs), thus it is necessary to develop new formulas for (HPHT) Water-Based muds that could act like Oil-Based mud but cause less harm to the environment

Evaluation of the Assessment Plan for Undergraduate Clerkship in Obstetrics and Gynecology, King Abdulaziz University

Background The standards set by accreditation bodies for student assessment during higher education, such as those of the National Commission for Academic Accreditation & Assessment (NCAAA), are necessary in formulating educational programs. These serve as a benchmark for how colleges or universities are assessed and reflect students' learning. Following the implementation of these guidelines, the Department of Obstetrics and Gynaecology, within the Faculty of Medicine in King Abdulaziz University (KAU), established assessment strategies appropriate to their curriculum, which were valid and reliable, thus enabling students to be fairly assessed throughout their undergraduate course. Since KAU is currently preparing for accreditation by the NCAAA, this study was a necessary undertaking to ensure that the assessment strategies designed by the Department of Obstetrics and Gynaecology are aligned and conform to the NCAAA student assessment guidelines, thereby outlining the standard of expected performance and learning outcomes for students. Objectives This study aimed to evaluate the assessment plan of the obstetrics and gynecology clerkship for undergraduate medical students within the Faculty of Medicine, KAU, in comparison to the standard criteria for student assessment as implemented by the NCAAA. Materials and Methods A cross-sectional study was conducted, which employed two questionnaires containing questions based on the NCAAA guidelines. The surveys were distributed among the teaching staff and students rotating for 12 weeks within the Department of Obstetrics and Gynaecology, KAU, from September to November 2013. In total, 100/116 (86.2%) students and 26/36 (81.25%) teaching staff participated in the study. Results Two sets of results were obtained regarding the student assessment practices in the Department of Obstetrics and Gynaecology, KAU, one from fifth-year medical students and the second from the teaching staff. The results showed that the majority of student respondents agreed that the department conformed to the guidelines and standards as set out by the NCAAA. However, the statistics gathered from the teaching staff participants implied that although the department is adhering to the standards, further improvements are still required in terms of the implementation and design of assessment strategies. Conclusions Adherence to the NCAAA student assessment guidelines and its strict implementation are vital to achieving effective learning outcomes among obstetrics and gynecology students. Faculty staff need be appropriately trained in the field of exam preparation and assessment. Further improvements to the existing student assessment strategies used by the Department of Obstetrics and Gynaecology, KAU, are recommended

Mechanic-elastic properties and radiation attenuation efficiency of TeO2/WO3/K2O composite glass systems for nuclear and medical application

WO3 effects on neutron and ionizing radiation defending factors of ternary tellurite-based glass blocks with molecular formula 80TeO2 –(20-x)WO3 – xK2O; x = 0–20 mol% (denoted as TKW-glass) has been reported via Phy-X theoretical calculations and Geant4 simulation code. Correlations between shielding factors and kinetics properties of the investigated glasses at different photon energy have been examined. The highest values of mass (MAC) attenuation coefficient were noted at 15 keV of the examined TKW-glass materials with the values of 38.408, 44.388, 49.855, 54.872, 59.492 cm2/g for TKW-0, TKW-5, TKW-10, TKW-15, and TKW-20, respectively. Generally, these values of the TKW-glasses obey the sequence: (TKW-0)MAC (TKW-5)HVL,MFP > (TKW-10)HVL,MFP > (TKW-15)HVL,MFP > (TKW-20)HVL,MFP. The maximum values of effective atomic number (EAN) took place at gamma energy of 15 keV corresponding to 44.35, 48.86, 52.63, 55.83, and 58.58 for TKW-0, TKW-5, TKW-10, TKW-15, and TKW-20, respectively. The trend of the buildup factors was similar for all of the glass specimens. The fast neutron removal cross-section (ΣR) enhanced as WO3 content increased in the specimens. Thus, the peaked value of ΣR is 0.1059 cm−1 was noted in the TKW-20 sample. Mechanical properties, neutron and γ-rays protection parameters were observed to improve with enhanced WO3 mol% in the TKW-glasses. The current results bear their utilization for neutron and gamma protection purposes

Low cost chemical oxygen demand sensor based on electrodeposited nano-copper film

A commercially available copper electrical cable and pure Cu disk were used as substrates for the electrodeposition of copper nanoparticles (nano-Cu). The surface morphology of the prepared nano-Cu/Cu electrodes was investigated by scanning electron microscope (SEM) and energy dispersive X-ray spectrometer (EDX). The bare copper substrates and the nano-copper modified electrodes were utilized and optimized for electrochemical assay of chemical oxygen demand (COD) using glycine as a standard. A comparison was made among the four electrodes (i.e., bare and nano-Cu coated copper cable and pure copper disk) as potential COD sensors. The oxidation behavior of glycine was investigated on the surface of the prepared sensors using linear sweep voltammetry (LSV). The results indicate significant enhancement of the electrochemical oxidation of glycine by the deposited nano-Cu. The effects of different deposition parameters, such as Cu2+ concentration, deposition potential, deposition time, pH, and scan rate on the response of the prepared sensors were investigated. Under optimized conditions, the optimal nano-Cu based COD sensor exhibited a linear range of 2–595 mg/L, lower limit of detection (LOD) as low as 1.07 mg/L (S/N = 3). The developed method exhibited high tolerance level to Cl− ion where 1.0 M Cl− exhibited minimal influence. The sensor was utilized for the detection of COD in different real water samples. The results obtained were validated using the standard dichromate method

The combined impact of shallow groundwater and soil salinity on evapotranspiration using remote sensing in an agricultural alluvial setting

Study region: The Nile Delta, Egypt Study focus: Shallow groundwater (GW) and soil salinity are major issues for irrigated agriculture, particularly in arid and semi-arid regions, but more research is needed to link both issues with evapotranspiration. Satellite-based evapotranspiration from Landsat images (ETLS) has the potential to be an efficient method of estimating evapotranspiration (ET), which can integrate ETLS with groundwater and soil salinity, particularly in data-scarce areas. This study examines shallow GW and soil salinity effects on crop water use in the North Nile Delta during the summer season of 2017 and winter season of 2017/2018. New hydrological insights for the region: The ETLS was moderately affected by groundwater depth (GWD), decreasing from 4.3 to 4.0 mm day−1 when GWD was reduced from 75 to 120 cm, then increasing to 4.4 mm day−1 when GWD was increased to 140 cm. The study also highlighted a significant negative correlation between ETgw and GWD; which increased with shallower GW (>75 cm) and then decreased with deeper GW. The shallower the GW, the greater the contribution to crop water requirements, with GW contributing 1.6 and 1.7 mm day−1 for seed melon and cotton, respectively, while GW contributed 0.9 mm day−1 for sugar beet and 1.3 mm day−1 for wheat and clover. The study's findings highlight the importance of remote sensing and GIS techniques for quickly and cheaply assessing the impact of shallow GW and soil salinity on evapotranspiration over large geographic areas