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

Response of Diverse Peanut Cultivars to Nano and Conventional Calcium Forms under Alkaline Sandy Soil

This article belongs to the Special Issue Plant Nutrition Volume II[Abstract] Calcium is one of the most limiting factors for the growth and reproduction of peanut, which ultimately affects pod and seed yields. A two-year field experiment was carried out to assess the impact of five calcium applications, including nano-calcium and conventional forms, on growth, leaf nutrient content, yield traits, and quality parameters of three diverse peanut cultivars (Ismailia-1, Giza-5, and Giza-6). The applied calcium applications were calcium sulfate, which is recommended for commercial peanut cultivation and commonly referred to as gypsum (coded as Ca-1), calcium nitrate (Ca-2), nano-calcium nitrate (Ca-3), 50% calcium nitrate + 50% nano-calcium (Ca-4), and 50% calcium sulfate + 50% nano-calcium (Ca-5). Calcium sulfate (gypsum, Ca-1) was soil-supplied during the seedbed preparation as recommended, while the other calcium applications (Ca-2, Ca-3, Ca-4, and Ca-5) were exogenously sprayed three times at 30, 45, and 60 days after sowing. The soil of the experimental site was alkaline, with a high pH of 8.6. The results revealed significant differences among cultivars, calcium applications, and their interactions. The soil-supplied gypsum Ca-1 displayed lower agronomic performance on all recorded growth, leaf nutrient content, yield traits, and quality parameters. On the other hand, the foliar-supplied calcium, particularly Ca-4 and Ca-5, displayed superior effects compared to the other simple calcium forms. Ca-4 and Ca-5 produced significantly higher seed yield (3.58 and 3.38 t/ha) than the simple recommended form (Ca-1, 2.34 t/ha). This could be due to the difficulty of calcium uptake from soil-supplied calcium under high soil pH compared to the exogenously sprayed nano-calcium form. Moreover, the superior performance of Ca-4 and Ca-5 could be caused by the mixture of fertilizers from the synergistic effect of calcium and nitrate or sulfate. Furthermore, the effect of nitrate was applied in nano form in the Ca4 and Ca-5 treatments, which contributed to improving nutrient uptake efficiency and plant growth compared to the other treatments. The peanut cultivar Giza-6 showed superiority for most measured traits over the other two cultivars. The interaction effect between the assessed cultivars and calcium applications was significant for various traits. The cultivar Giza-6 showed a significant advantage for most measured traits with the mixture of 50% calcium nitrate + 50% nano-calcium (Ca-4). Conclusively, the results pointed out the advantage of the exogenously sprayed nano-calcium form combined with calcium nitrate or calcium sulfate for promoting growth, leaf nutrient content, yield, and quality traits of peanut, particularly with high-yielding cultivars under sandy soil with high pH.This research was funded by the Deputyship for Research and Innovation, “Ministry of Education”, in Saudi Arabia, research number (IFKSUOR3-106-3)Arabia Saudí. Ministry of Education; IFKSUOR3-106-

Influence of Nano-Chitosan Loaded with Potassium on Potassium Fractionation in Sandy Soil and Strawberry Productivity and Quality

Under sandy soil conditions, increasing the efficiency of potassium (K) fertilizers is considered to be a major limiting factor for improving the productivity and quality of fruit crops. In this context, utilizing nanotechnology has emerged as a novel technique to increase the efficiency of K applications. In our study, two field trials were conducted, in two consecutive seasons (2019/2020 and 2020/2021), to compare the effects of nano-chitosan loaded with K as a foliar treatment with those of conventional soil applications of K on plant growth, yield, and quality of strawberry plants grown in sandy soil. Strawberry plants were treated with 12 different treatments, which were replicated three times in a randomized complete block design in each growing season. Potassium sulfate (K2SO4, 48% K2O) was applied to the soil at a rate of 150.0 kg acre−1 (recommended rate, 100%). Meanwhile, the spraying of nano-chitosan loaded with K was applied at 1000 mg L−1 as a control. In addition, K2SO4 was applied either individually or in combination at the rate of 112.5 or 75.0 kg acre−1 with four nano-chitosan-K dosages (250, 500, 750, and 1000 mg L−1). After harvesting, soil samples were collected and prepared to determine K fractions. As well, plant samples were collected to determine the vegetative growth parameters and the foliage content of NPK and chlorophyll. Eventually, the yield traits and quality parameters were evaluated. A principal component analysis was conducted to determine the interrelationships of the treatments’ averages and their effects on yield components and quality traits. A combined analysis was performed for the two studied seasons and the values were the mean of six replications. The results indicated that the application of common K fertilizer (150.0 kg K2SO4 acre−1) resulted in the maximum increase in soluble and exchangeable K in the soil, which was comparable to those observed with 112.5 kg K2SO4 acre−1 + 1000 mg L−1 nano-chitosan-K and 112.5 K2SO4 acre−1 + 750 mg L−1 nano-chitosan-K. The total yield, marketable yield, and fruit firmness were all significantly increased by the latter two treatments compared to the control group. Furthermore, plots treated with 112.5 kg K2SO4 acre−1 + 1000 mg L−1 nano-chitosan-K significantly increased the total soluble solids, vitamin C levels, acidity, total sugar, and anthocyanin levels in strawberry fruits. In conclusion, under sandy soil conditions, the utilization of nanoparticles could be an indispensable tool for manipulating fertilization management when cultivating strawberries. The K status of the soil was improved by applying 75% of the recommended dose of mineral K in combination with 1000 or 750 mg L−1 of nano-chitosan-K, without compromising strawberry yield or quality

Effect of Titanium and Vanadium on Antioxidants Content and Productivity of Red Cabbage

The present work studied the effect of foliar spray of different concentrations of titanium (Ti, applied as titanium dioxide) and vanadium (V, applied as vanadium pentoxide) on growth, chemical composition, antioxidant contents, antioxidant enzymes, antioxidant capacity, yield and quality criteria of red cabbage plants. For this purpose, 2.0, 4.0 and 6.0 mg L−1 of Ti and V were used to treat red cabbage plants. The control plants were treated with tap water. Our results showed that plants treated with 4.0 mg L−1 of Ti recorded the highest values of plant growth and bioactive compounds, while antioxidant capacity was decreased compared to the other treatments. In addition, plants treated with Ti and V at 2.0 and 4.0 mg L−1, respectively, showed higher values of all of the growth, yield, non-enzymatic antioxidants and antioxidants enzymes’ parameters compared to the untreated plants. Based on the obtained results, it could be concluded that the low concentrations of both Ti and V (2.0 and 4.0 mg L−1) were able to enhance red cabbage growth and yield, as well as the antioxidant contents, enzymes and capacity

Effect of Titanium and Vanadium on Antioxidants Content and Productivity of Red Cabbage

The present work studied the effect of foliar spray of different concentrations of titanium (Ti, applied as titanium dioxide) and vanadium (V, applied as vanadium pentoxide) on growth, chemical composition, antioxidant contents, antioxidant enzymes, antioxidant capacity, yield and quality criteria of red cabbage plants. For this purpose, 2.0, 4.0 and 6.0 mg L−1 of Ti and V were used to treat red cabbage plants. The control plants were treated with tap water. Our results showed that plants treated with 4.0 mg L−1 of Ti recorded the highest values of plant growth and bioactive compounds, while antioxidant capacity was decreased compared to the other treatments. In addition, plants treated with Ti and V at 2.0 and 4.0 mg L−1, respectively, showed higher values of all of the growth, yield, non-enzymatic antioxidants and antioxidants enzymes’ parameters compared to the untreated plants. Based on the obtained results, it could be concluded that the low concentrations of both Ti and V (2.0 and 4.0 mg L−1) were able to enhance red cabbage growth and yield, as well as the antioxidant contents, enzymes and capacity

The strategic plan for combating antimicrobial resistance in Gulf Cooperation Council States

Summary: The Gulf Cooperation Council Center for Infection Control (GCC-IC) has placed the emergence of antimicrobial resistance (AMR) on the top of its agenda for the past four years. The board members have developed the initial draft for the GCC strategic plan for combating AMR in 2014. The strategic plan stems from the WHO mandate to combat AMR at all levels. The need for engaging a large number of stakeholders has prompted the GCC-IC to engage a wider core of professionals in finalizing the plan. A multi-disciplinary group of more than 40 experts were then identified. And a workshop was conducted in Riyadh January 2015 and included, for the first time, representation of relevant ministries and agencies as well as international experts in the field. Participants worked over a period of two and a half days in different groups. International experts shared the global experiences and challenges in addressing human, food, animal, and environmental aspects of controlling AMR. Participants were then divided into 4 groups each to address the human, animal, microbiological and diagnostic, or the environmental aspect of AMR. At the end of the workshop, the strategic plan was revised and endorsed by all participants. The GCC-IC board members then approved it as the strategic plan for AMR. The document produced here is the first GCC strategic plan addressing AMR, which shall be adopted by GCC countries to develop country-based plans and related key performance indicators (KPIs). It is now the role of each country to identify the body that will be accountable for implementing the plan at the country level. Keywords: Strategic plan, Antimicrobial resistance, AMR, GCC, Saudi Arabia, United Arab Emirates, Qatar, Bahrain, Oman, Kuwai

Global economic burden of unmet surgical need for appendicitis

Background There is a substantial gap in provision of adequate surgical care in many low- and middle-income countries. This study aimed to identify the economic burden of unmet surgical need for the common condition of appendicitis. Methods Data on the incidence of appendicitis from 170 countries and two different approaches were used to estimate numbers of patients who do not receive surgery: as a fixed proportion of the total unmet surgical need per country (approach 1); and based on country income status (approach 2). Indirect costs with current levels of access and local quality, and those if quality were at the standards of high-income countries, were estimated. A human capital approach was applied, focusing on the economic burden resulting from premature death and absenteeism. Results Excess mortality was 4185 per 100 000 cases of appendicitis using approach 1 and 3448 per 100 000 using approach 2. The economic burden of continuing current levels of access and local quality was US $92 492 million using approach 1 and$73 141 million using approach 2. The economic burden of not providing surgical care to the standards of high-income countries was $95 004 million using approach 1 and$75 666 million using approach 2. The largest share of these costs resulted from premature death (97.7 per cent) and lack of access (97.0 per cent) in contrast to lack of quality. Conclusion For a comparatively non-complex emergency condition such as appendicitis, increasing access to care should be prioritized. Although improving quality of care should not be neglected, increasing provision of care at current standards could reduce societal costs substantially

Global economic burden of unmet surgical need for appendicitis

Background There is a substantial gap in provision of adequate surgical care in many low- and middle-income countries. This study aimed to identify the economic burden of unmet surgical need for the common condition of appendicitis. Methods Data on the incidence of appendicitis from 170 countries and two different approaches were used to estimate numbers of patients who do not receive surgery: as a fixed proportion of the total unmet surgical need per country (approach 1); and based on country income status (approach 2). Indirect costs with current levels of access and local quality, and those if quality were at the standards of high-income countries, were estimated. A human capital approach was applied, focusing on the economic burden resulting from premature death and absenteeism. Results Excess mortality was 4185 per 100 000 cases of appendicitis using approach 1 and 3448 per 100 000 using approach 2. The economic burden of continuing current levels of access and local quality was US $92 492 million using approach 1 and$73 141 million using approach 2. The economic burden of not providing surgical care to the standards of high-income countries was $95 004 million using approach 1 and$75 666 million using approach 2. The largest share of these costs resulted from premature death (97.7 per cent) and lack of access (97.0 per cent) in contrast to lack of quality. Conclusion For a comparatively non-complex emergency condition such as appendicitis, increasing access to care should be prioritized. Although improving quality of care should not be neglected, increasing provision of care at current standards could reduce societal costs substantially

SARS-CoV-2 vaccination modelling for safe surgery to save lives: data from an international prospective cohort study

Background Preoperative SARS-CoV-2 vaccination could support safer elective surgery. Vaccine numbers are limited so this study aimed to inform their prioritization by modelling. Methods The primary outcome was the number needed to vaccinate (NNV) to prevent one COVID-19-related death in 1 year. NNVs were based on postoperative SARS-CoV-2 rates and mortality in an international cohort study (surgical patients), and community SARS-CoV-2 incidence and case fatality data (general population). NNV estimates were stratified by age (18-49, 50-69, 70 or more years) and type of surgery. Best- and worst-case scenarios were used to describe uncertainty. Results NNVs were more favourable in surgical patients than the general population. The most favourable NNVs were in patients aged 70 years or more needing cancer surgery (351; best case 196, worst case 816) or non-cancer surgery (733; best case 407, worst case 1664). Both exceeded the NNV in the general population (1840; best case 1196, worst case 3066). NNVs for surgical patients remained favourable at a range of SARS-CoV-2 incidence rates in sensitivity analysis modelling. Globally, prioritizing preoperative vaccination of patients needing elective surgery ahead of the general population could prevent an additional 58 687 (best case 115 007, worst case 20 177) COVID-19-related deaths in 1 year. Conclusion As global roll out of SARS-CoV-2 vaccination proceeds, patients needing elective surgery should be prioritized ahead of the general population.The aim of this study was to inform vaccination prioritization by modelling the impact of vaccination on elective inpatient surgery. The study found that patients aged at least 70 years needing elective surgery should be prioritized alongside other high-risk groups during early vaccination programmes. Once vaccines are rolled out to younger populations, prioritizing surgical patients is advantageous