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

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

3D seismic and formation micro-imager (FMI) integrated study to delineate depositional pattern of Abu Madi (Upper Miocene) clastic reservoir rocks in El-Wastani gas field, onshore Nile Delta, Egypt

Ten wells (EW-4, EW-5, EW-6, EW-7, EW-8, EW-9, EW-10, EW-12, EW-13 and EW-15) were interpreted using the composite well logs, data of core analysis, gamma-ray logs, formation micro-imager logs (FMI), and 3D seismic data in SEGY format to understand the stratigraphy of the onshore, Nile Delta, Egypt.The amplitude analysis of 3-D seismic horizon slice of Lower Abu Madi rock unit together with the lithostratigraphic correlation through the study area depending on the gamma-ray log “HSGR” (left to right increasing), and the identification of type of bed geometry, nature of bed contacts, type of the sedimentary structures and the dominant formative paleocurrents by using some available borehole micro-resistivity images (FMI) and core photos. All of these techniques are used together to define the different depositional facies and depositional environment of the Messinian clastics (Lower Abu Madi rock unit), which is considered to be the main reservoir in the El-Wastani gas field, onshore Nile Delta, Egypt.The present study of depositional pattern of the Upper Miocene clastics reservoir (Lower Abu Madi rock unit) revealed that it is represented by high sinuous meandering channels or paleo-valley and three types of fluvial facies were defined; channel fill, channel margin, and floodplain basin. Keywords: Depositional pattern, 3D seismic, Formation micro-imager (FMI), Nile Delta, Egyp

Assessment of petrophysical parameters of clastics using well logs: The Upper Miocene in El-Wastani gas field, onshore Nile Delta, Egypt

Based on logs of ten wells in the El-Wastani gas field, onshore Nile Delta, Egypt, petrophysical evaluation for the Upper-Miocene Qawasim Formation and Abu Madi Formation in the El-Wastani gas field was accomplished. The lithology of these formations was analyzed using cross plots of logging parameters, and petrophysical parameters including shale volume, porosity, water saturation and hydrocarbon pore volume were assessed. The Neutron/Density, Neutron/Gamma-ray and Litho-saturation cross plots of the wells show that the main lithology of the Lower Abu Madi unit is sandstone with shale intercalations, while the lithology of the Qawasim Formation is mainly composed of shale with sandstone intercalations. The cut-offs of shale volume, porosity and water saturation for productive hydrocarbon pay zones are 50%, 10% and 70%, respectively, which were got based on cross-plots and Gamma-ray log data. Contour maps for parameters such as net pay thickness, average porosity, shale volume and water saturation were prepared and it is found out that the Abu Madi Formation and Qawasim Formation in the study area have promising reservoir characteristics; A prospective region for gas accumulation trends northwest-southeast in the study area, especially favorable in the central part. Key words: well log, petrophysical parameter, Upper Miocene, El-Wastani gas field, Nile Delta, Egyp

The impact of rainfall distribution patterns on hydrological and hydraulic response in arid regions:case study Medina, Saudi Arabia

Abstract Rainfall distribution patterns (RDPs) are crucial for hydrologic design. Hydrologic modeling is based on Soil Conservation Services (SCS) type RDPs (SCS type I, IA, II, and III). SCS type II method is widely used by hydrologists in arid regions. These RDPs were designed for the USA and similar temperate regions. There is no scientific justification for using SCS type II method in arid regions. The consequences of using SCS type II have impacts on the hydrologic and hydraulic modeling studies. The current paper investigates the validity of the SCS type II and in arid regions. New temporal RDPs were applied and compared with SCS type II RDPs. The produced peak discharges, volumes, maximum inundation depths, top widths, and velocities from both approaches were analyzed. An application is made on the protection channel in Taibah and Islamic Universities campuses in Medina, Saudi Arabia. A methodology was followed which included frequency analysis, catchment modeling, hydrological modeling, and hydraulic modeling. Results indicated that there are considerable consequences on infrastructural design, and hydrologic and hydraulic parameters if inappropriate RDPs are used. The investigation confirmed that the SCS type RDPs do not reflect the actual flood features in arid regions

Rational Design and Synthesis of New Selective COX-2 Inhibitors with In Vivo PGE2-Lowering Activity by Tethering Benzenesulfonamide and 1,2,3-Triazole Pharmacophores to Some NSAIDs

New selective COX-2 inhibitors were designed and synthesized by tethering 1,2,3-triazole and benzenesulfonamide pharmacophores to some NSAIDs. Compounds 6b and 6j showed higher in vitro COX-2 selectivity and inhibitory activity (IC50 = 0.04 µM and S.I. = 329 and 312, respectively) than celecoxib (IC50 = 0.05 µM and S.I. = 294). Compound 6e revealed equipotent in vitro COX-2 inhibitory activity to celecoxib. Furthermore, 6b and 6j expressed more potent relief of carrageenan-induced paw edema thickness in mice than celecoxib, with ED50 values of 11.74 µmol/kg and 13.38 µmol/kg vs. 16.24 µmol/kg, respectively. Compounds 6b and 6j inhibited the production of PGE2 with a % inhibition of PGE2 production of 90.70% and 86.34%, respectively, exceeding celecoxib’s percentage (78.62%). Moreover, 6b and 6j demonstrated a gastric safety profile comparable to celecoxib. In conclusion, compounds 6b and 6j better achieved the target goal as more potent and selective COX-2 inhibitors than celecoxib in vitro and in vivo