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

Petrography of pyrobitumens in middle – late Jurassic sandstones from thermally degraded hydrocarbon accumulations, East Greenland

A number of exhumed hydrocarbon traps have been described from the Traill Ø region of East Greenland. This study focuses on the Bjørnedal area where the distribution of bitumen has been mapped out. Bitumen staining clearly has a cross-cutting relationship to stratigraphic units and can be shown to form distinct palaeo-accumulations. Detailed petrographic studies show that bitumen occurs as late diagenetic phases in Middle to Late Jurassic sandstones, and is present both as both grain-coating and pore-filling phases. Geochemical analyses confirm that the bitumen is organic in composition and is composed largely of carbon and hydrogen. Both H/C ratios and bonds identified by FTIR behave as expected with increasing maturity measured using bitumen reflectance. Together, these results provide strong evidence that the material is pyrobitumen derived from the in situ thermal degradation of a liquid hydrocarbon precursor. On the basis of textures in transmitted and reflected light and quantitative bitumen reflectance distributions, two populations of pyrobitumen may be recognised in some samples.Two phases of Paleogene magmatism occurred in the Traill Ø region. The first late Paleocene – early Eocene phase was related to the opening of the northern North Atlantic in the earliest Eocene, and was experienced throughout East Greenland and the northwest European margin. The later magmatic phase was related to the gradual separation of the Jan Mayen microcontinent from East Greenland through the late Eocene – early Oligocene. A single pyrobitumen phase is recognised in accumulations only affected by the early magmatism, and a second phase is only observed in areas affected by both the early and later magmatism. This relationship is interpreted as evidence for a direct relationship between magmatic phases and bitumen generation. The presence of bitumen formed by the thermal degradation of liquid hydrocarbons during the later magmatic event suggests that a viable petroleum system remained active following the early magmatic event

Feasibility study of low force robotic friction stir process and its effect on cavitation erosion and electrochemical corrosion for Ni Al bronze alloys

Robotic friction stir processing (FSP) has not been widely researched to date. This is perhaps due to the limited force capabilities of industrial robots in comparison with dedicated commercial FSP equipment. When operating a FSP machine, the force used to plunge the tools may range from 5000 to 8000 N which is currently beyond the capability of most robots. However, the capacity of robotic manipulators is increasing, so low force friction stir processing is becoming feasible. The ability of the robot arm to apply a controlled force that is normal to a 3-dimensional surface without the need to reorient the workpiece makes it a very useful tool for FSP of complex components. In this analysis, a robot arm with a capacity of 2500 N is used to improve the surface properties of nickel aluminum bronze (NAB) using low force FSP. Multiple passes were applied to the surface of the test sample for a more consistent spread of the stir zone. The sample was then microhardness tested and demonstrated a 62 pct increase in surface hardness. Cavitation erosion testing of the original and processed surfaces was also performed as per ASTM G-32. The erosion rate of the processed NAB sample was 44 pct of the rate experienced by the original cast NAB sample. Finally, the corrosion potentials of FSP NAB were measured at 45 mV less anodic than the unprocessed material, indicating that the processed material is more noble relative to the cast NAB sample

High flow nasal cannula in the immediate post-operative period: a systematic review and meta-analysis

International audienceBackground: Studies have demonstrated that high-flow nasal cannula (HFNC) prevents intubation in acute hypoxic respiratory failure when compared with conventional oxygen therapy (COT). However, the data examining routine HFNC use in the immediate postoperative period are less clear.Research Question: Is routine HFNC use superior to COT or noninvasive ventilation (NIV) use in preventing intubation in patients postoperatively?Study Design and Methods: We comprehensively searched databases (PubMed, Embase, Web of Science) to identify randomized controlled trials (RCTs) that compared the effect of HFNC use with that of COT or NIV in the immediate postoperative period on reintubation, escalation of respiratory support, hospital mortality, ICU and hospital length of stay (LOS), postoperative hypoxemia, and treatment complications. We assessed individual study risk of bias (RoB) by using the revised Cochrane RoB 2 tool and rated certainty in outcomes by using the Grading of Recommendations Assessment, Development and Evaluation framework.Results: We included 11 RCTs enrolling 2,201 patients. Ten compared HFNC with COT and one with NIV. Compared with COT use, HFNC use in the postoperative period was associated with a lower reintubation rate (relative risk [RR], 0.32; 95% CI, 0.12-0.88; absolute risk reduction [ARR], 2.9%; moderate certainty) and decreased escalation of respiratory support (RR, 0.54; 95% CI, 0.31-0.94; ARR, 5.8%; very low certainty). Post hoc subgroup analysis suggested that this effect was driven by patients who were obese and/or at high risk (subgroup differences, P = .06). We did not find differences in any of the other stated outcomes between HFNC and COT. HFNC was also no different from NIV in reintubation rate, respiratory therapy failure, or ICU LOS.Interpretation: With evidence of moderate certainty, prophylactic HFNC reduces reintubation and escalation of respiratory support compared with COT in the immediate postoperative period after cardiothoracic surgery. This effect is likely driven by patients who are at high risk and/or obese. These findings support postoperative prophylactic HFNC use in the patients who are at high risk and/or obese undergoing cardiothoracic surger

Geriatric assessment for older people with cancer: policy recommendations

Most cancers occur in older people and the burden in this age group is increasing. Over the past two decades the evidence on how best to treat this population has increased rapidly. However, implementation of new best practices has been slow and needs involvement of policymakers. This perspective paper explains why older people with cancer have different needs than the wider population. An overview is given of the recommended approach for older people with cancer and its benefits on clinical outcomes and cost-effectiveness. In older patients, the geriatric assessment (GA) is the gold standard to measure level of fitness and to determine treatment tolerability. The GA, with multiple domains of physical health, functional status, psychological health and socio-environmental factors, prevents initiation of inappropriate oncologic treatment and recommends geriatric interventions to optimize the patient’s general health and thus resilience for receiving treatments. Multiple studies have proven its benefits such as reduced toxicity, better quality of life, better patient-centred communication and lower healthcare use. Although GA might require investment of time and resources, this is relatively small compared to the improved outcomes, possible cost-savings and compared to the large cost of oncologic treatments as a whole

Perspective: Food Environment Research Priorities for Africa-Lessons from the Africa Food Environment Research Network.

Over the last 2 decades, many African countries have undergone dietary and nutrition transitions fueled by globalization, rapid urbanization, and development. These changes have altered African food environments and, subsequently, dietary behaviors, including food acquisition and consumption. Dietary patterns associated with the nutrition transition have contributed to Africa&#8217;s complex burden of malnutrition-obesity and other diet-related noncommunicable diseases (DR-NCDs)-along with persistent food insecurity and undernutrition. Available evidence links unhealthy or obesogenic food environments (including those that market and offer energy-dense, nutrient-poor foods and beverages) with suboptimal diets and associated adverse health outcomes. Elsewhere, governments have responded with policies to improve food environments. However, in Africa, the necessary research and policy action have received insufficient attention. Contextual evidence to motivate, enable, and create supportive food environments in Africa for better population health is urgently needed. In November 2020, the Measurement, Evaluation, Accountability, and Leadership Support for Noncommunicable Diseases Prevention Project (MEALS4NCDs) convened the first Africa Food Environment Research Network Meeting (FERN2020). This 3-d virtual meeting brought researchers from around the world to deliberate on future directions and research priorities related to improving food environments and nutrition across the African continent. The stakeholders shared experiences, best practices, challenges, and opportunities for improving the healthfulness of food environments and related policies in low- and middle-income countries. In this article, we summarize the proceedings and research priorities identified in the meeting to advance the food environment research agenda in Africa, and thus contribute to the promotion of healthier food environments to prevent DR-NCDs, and other forms of&nbsp;malnutrition.</p

Genetic correlation between amyotrophic lateral sclerosis and schizophrenia

We have previously shown higher-than-expected rates of schizophrenia in relatives of patients with amyotrophic lateral sclerosis (ALS), suggesting an aetiological relationship between the diseases. Here, we investigate the genetic relationship between ALS and schizophrenia using genome-wide association study data from over 100,000 unique individuals. Using linkage disequilibrium score regression, we estimate the genetic correlation between ALS and schizophrenia to be 14.3% (7.05-21.6; P=1 × 10) with schizophrenia polygenic risk scores explaining up to 0.12% of the variance in ALS (P=8.4 × 10). A modest increase in comorbidity of ALS and schizophrenia is expected given these findings (odds ratio 1.08-1.26) but this would require very large studies to observe epidemiologically. We identify five potential novel ALS-associated loci using conditional false discovery rate analysis. It is likely that shared neurobiological mechanisms between these two disorders will engender novel hypotheses in future preclinical and clinical studies