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

Proposed Developed Standards: Staff Nurses Compliance at Dialysis Unit Proposed Developed Standards: Staff Nurses Compliance at Dialysis Unit

ABSTRACT Background: Standards of practice provide a guide to the knowledge, skills, judgment and attitudes that are needed to practice safely moreover standard is a means of governing the practice of nurses at all levels of practice. This study aimed to: determine the compliance of nurses at dialysis unit with proposed developed performance standards. Design: Observational cross-sectional study was utilized to conduct this study. Subject: This study included all staff nurses working in dialysis unit. Setting: It was conducted at Dialysis Unit at Benha University Hospital. Tools: Two different tools were utilized, structured interviewing questionnaire and observational check list for nurses' performance according to the developed standards. Results: Showed that most of studied staff nurses agreed about all proposed (structure and process) standards (policy and objective standards, organizational chart, job description, human resources, documentation, safe handling of medications, infection control, nursing station, training, environmental factors, patient care and patient right standards), they have moderate level of performance according to the proposed standards. There was negative insignificant correlation between nurses' performance and their age, experience and experience in work place. Conclusion: The present study combines to conclude that the proposed developed standards are acceptable to be used in dialysis unit at Benha University Hospital. Recommendations: The developed standards should be applied and communicated to all staff nurses of the Dialysis Unit at Benha University Hospital through workshops, booklets and pursuers

Knowledge of the University students toward premarital screening program: A cross-sectional study

Premarital screening program is a method that can accurately identify asymptomatic carriers of hemoglobinopathies and provide genetic counselling to couples for a healthy reproductive life. To assess the university students’ knowledge of the premarital screening program. Method: a cross-sectional design using systematic random sample technique for selecting 265 students from the four constituent colleges of the university. Self-administered questionnaire consisted of 3 parts to collect data: students’ demographic data, students’ knowledge about hereditary diseases, and premarital screening program. The study findings revealed that more than half of the students had a positive family history of hereditary diseases. Most of them were aware that premarital screening program reduces the genetic and sexually-transmitted diseases. Around half of them had an average knowledge level about hereditary diseases and premarital screening program. The majority of the participants have an average knowledge level about the premarital screening program. Awareness and educational programs can be organized for university students and the community

Influence of the non-isothermal conditions on the activity of enzymes immobilized on nylon grafted membranes

β-Galactosidase was immobilized on a nylonmembrane chemically grafted with butylmethacrylate. Hexamethylenediamine was used as spacer and glutaraldehyde as coupling agent. The catalytic behaviour of the membrane was studied under isothermal and non-isothermalconditions. It was found that in the presence of temperature gradients, the catalytic membrane exhibited higher activity and greater affinity for the substrate. The increases of the enzyme reaction rate was found to be proportional to the intensity of the applied temperature gradient. Percentage increases of the activity were also found to decrease with the increase of the average temperature and concentration. All the results are phenomenologically discussed in terms of substrate traffic across the catalytic membrane induced by the processes of diffusion or thermodialysis under isothermal and non-isothermalconditions, respectively

Low incidence of SARS-CoV-2, risk factors of mortality and the course of illness in the French national cohort of dialysis patients

International audienceThe aim of this study was to estimate the incidence of COVID-19 disease in the French national population of dialysis patients, their course of illness and to identify the risk factors associated with mortality. Our study included all patients on dialysis recorded in the French REIN Registry in April 2020. Clinical characteristics at last follow-up and the evolution of COVID-19 illness severity over time were recorded for diagnosed cases (either suspicious clinical symptoms, characteristic signs on the chest scan or a positive reverse transcription polymerase chain reaction) for SARS-CoV-2. A total of 1,621 infected patients were reported on the REIN registry from March 16th, 2020 to May 4th, 2020. Of these, 344 died. The prevalence of COVID-19 patients varied from less than 1% to 10% between regions. The probability of being a case was higher in males, patients with diabetes, those in need of assistance for transfer or treated at a self-care unit. Dialysis at home was associated with a lower probability of being infected as was being a smoker, a former smoker, having an active malignancy, or peripheral vascular disease. Mortality in diagnosed cases (21%) was associated with the same causes as in the general population. Higher age, hypoalbuminemia and the presence of an ischemic heart disease were statistically independently associated with a higher risk of death. Being treated at a selfcare unit was associated with a lower risk. Thus, our study showed a relatively low frequency of COVID-19 among dialysis patients contrary to what might have been assumed