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

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

Analysis of radioactivity levels and hazard assessment of black sand samples from Rashid area, Egypt

The aim of this study is to evaluate the radioactivity levels and radiological impacts of representative black sand samples collected from different locations in the Rashid area, Egypt. These samples were prepared and then analyzed using the high-resolution gamma ray spectroscopy technique with a high-purity germanium detector. The activity concentration (Ac), minimum detectable activity, absorbed gamma dose rate, external hazard index (Hex), annual effective dose rate equivalent, radium equivalent, as well as external and internal hazard index (Hex and Hin, respectively) were estimated based on the measured radionuclide concentration of the 238U(226Ra) and 232Th decay chains and 40K. The activity concentrations of the 238U, 232Th decay series and 40K of these samples varied from 45.11 ± 3.1 Bq/kg to 252.38 ± 34.3 Bq/kg, from 64.65 ± 6.1 Bq/kg to 579.84 ± 53.1 Bq/kg, and from 403.36 ± 20.8 Bq/kg to 527.47 ± 23.1 Bq/kg, respectively. The activity concentration of 232Th in Sample 1 has the highest value compared to the other samples; this value is also higher than the worldwide mean range as reported by UNSCEAR 2000. The total absorbed gamma dose rate and the annual effective dose for these samples were found to vary from 81.19 nGy/h to 497.81 nGy/h and from 99.86 μSv/y to 612.31 μSv/y, which are higher than the world average values of 59 nGy/h and 70 μSv/y, respectively. The Hex values were also calculated to be 3.02, 0.47, 0.63, 0.87, 0.87, 0.51 and 0.91. It was found that the calculated value of Hex for Sample 1 is significantly higher than the international acceptable limit of <1. The results are tabulated, depicted, and discussed within national and international frameworks, levels, and approaches

Alpha spectroscopy and X-ray induced photocurrent studies of a SC CVD diamond detector fabricated with PLD contacts

Using amorphous Carbon blended with Nickel (C/Ni) as electrodes for a polycrystalline diamond radiation detector (PC-C/Ni) was demonstrated previously as a novel technique to produce near-tissue equivalent X-ray dosimeters. In this project, we introduce the first characterisation of a (Chemical Vapour Deposited) single crystal diamond sandwich detector (with thickness of 0.4 mm) fabricated with this technique, labelled SC-C/Ni. To examine the performance of pulsed laser deposition (PLD) C/Ni as an electrode, alpha spectroscopy measurements and X-ray induced photocurrent measurements were studied as a function of the applied bias at room temperature and compared with those of the aforementioned PC-C/Ni. The alpha particle spectroscopy measurement data allows us to differentiate between electron and hole contributions to the charge transport signal, whilst the X-ray data was investigated in terms of dose rate-linearity, sensitivity, signal to noise ratio (SNR) and photoconductive gain. In the case of electron sensitive alpha induced signals, a Charge Collection Efficiency (CCE) higher than 90% has been observed at a bias of -40 V and 100% CCE at -300 V, with energy resolution of ∼3% for 5.48 MeV alpha particles. The sample showed very poor spectroscopy performance for hole sensitive signals up to 200 V. The X-ray induced photocurrents show a high SNR of ∼7.3 × 10³, an approximately linear relationship between the photocurrent versus dose rate and a sensitivity of 4.87 μC/Gy.mm³. The photoconductive gain of SC-C/Ni is calculated to be ∼20, this gain calculation might be explained by trapping effects as investigated in the alpha spectroscopy measurements.</p