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

Improved oil formation volume factor (Bo) correlation for volatile oil reservoirs: An integrated non-linear regression and genetic programming approach

AbstractIn this paper, two correlations for oil formation volume factor (Bo) for volatile oil reservoirs are developed using non-linear regression technique and genetic programming using commercial software. More than 1200 measured values obtained from PVT laboratory analyses of five representative volatile oil samples are selected under a wide range of reservoir conditions (temperature and pressure) and compositions. Matching of PVT experimental data with an equation of state (EOS) model using a commercial simulator (Eclipse Simulator), was achieved to generate the oil formation volume factor (Bo). The obtained results of the Bo as compared with the most common published correlations indicate that the new generated model has improved significantly the average absolute error for volatile oil fluids. The hit-rate (R2) of the new non-linear regression correlation is 98.99% and the average absolute error (AAE) is 1.534% with standard deviation (SD) of 0.000372. Meanwhile, correlation generated by genetic programming gave R2 of 99.96% and an AAE of 0.3252% with a SD of 0.00001584.The importance of the new correlation stems from the fact that it depends mainly on experimental field production data, besides having a wide range of applications especially when actual PVT laboratory data are scarce or incomplete

Improved oil formation volume factor (Bo) correlation for volatile oil reservoirs: An integrated non-linear regression and genetic programming approach

In this paper, two correlations for oil formation volume factor (Bo) for volatile oil reservoirs are developed using non-linear regression technique and genetic programming using commercial software. More than 1200 measured values obtained from PVT laboratory analyses of five representative volatile oil samples are selected under a wide range of reservoir conditions (temperature and pressure) and compositions. Matching of PVT experimental data with an equation of state (EOS) model using a commercial simulator (Eclipse Simulator), was achieved to generate the oil formation volume factor (Bo). The obtained results of the Bo as compared with the most common published correlations indicate that the new generated model has improved significantly the average absolute error for volatile oil fluids. The hit-rate (R2) of the new non-linear regression correlation is 98.99% and the average absolute error (AAE) is 1.534% with standard deviation (SD) of 0.000372. Meanwhile, correlation generated by genetic programming gave R2 of 99.96% and an AAE of 0.3252% with a SD of 0.00001584.The importance of the new correlation stems from the fact that it depends mainly on experimental field production data, besides having a wide range of applications especially when actual PVT laboratory data are scarce or incomplete. Keywords: Oil formation factor correlation, Volatile oil, PVT, Non-linear regression, Genetic programming, Black oil simulatio

Superior fracture-seal material using crushed date palm seeds for oil and gas well drilling operations

Expenses for drilling represent 25% of the total oilfield exploitation cost. Drilling fluids represent 15–18% of the total cost of well petroleum drilling operations. The main drilling fluids problem is the loss into fractured and vugs. Prevention or mitigation of severe lost circulation is a main challenge while drilling in fractured formations where conventional lost circulation materials (LCM) will not cure these losses. Therefore, specialized treatment is required when drilling fractured formations.In this study, a superior LCM made from crushed date palm seeds was tested at laboratory for its ability to seal artificially fractured cores under High Temperature High Pressure (HT-HP) conditions. For this purpose, the conventional 500 ml HT-HP filter press was modified to accommodate a fractured core plug of length and diameter equal to 38.1 mm (1.5 inch) instead of the ceramic disc.Using the modified HT-HP filter press, crushed date palm seeds proved its ability to completely seal the artificially made fracture in the test core samples at overbalance pressures up to 1000 psi and temperatures up to 90 °C. The optimum mud composition was fresh water, 7% by weight bentonite, 3.5% fine crushed date palm seeds, and 3.5% coarse crushed date palm seeds in weight bases. In addition to its superior ability to seal fractured formation, the crushed date palm seeds material is cheap, locally available in commercially quantities, and environmentally friendly material

Atividade antimicrobiana de óleos essenciais em bactérias patogênicas de origem alimentar Antimicrobial activity of essential oils against sessile and planktonic pathogens of food source

Objetivou-se identificar e quantificar os constituintes e avaliar a atividade antimicrobiana dos óleos essenciais de Mentha piperita, Cymbopogon citratus, Ocimum basilicum e Origanum majorana contra cepas de Escherichia coli enteropatogênica, Salmonella enterica Enteritidis, Listeria monocytogenes e Enterobacter sakazaki. A obtenção dos óleos essenciais foi realizada a partir de folhas secas, empregando-se a técnica de hidrodestilação e utilizando-se a aparelho de Clevenger modificado. A atividade antibacteriana dos óleos essenciais foi determinada pelo método de difusão em ágar. Observou-se que os óleos essenciais inibiram o crescimento bacteriano, mas a efetividade foi variada. Entre os óleos essenciais testados, M. piperita apresentou maior atividade antibacteriana para E. coli, (8.106 UA mL-1) quando comparada as demais bactérias, atividade moderada para Salmonella enterica Enteritidis e Enterobacter sakazakii (1.706 e 3.200 UA mL-1 respectivamente) e baixa atividade para Listeria monocytogenes (106,67 UA mL-1). Já óleo essencial de Cymbopogon citratus apresentou maior atividade antimicrobiana frente a E. coli (9.386 UA mL-1) e atividade moderada frente a Enterobacter sakazakii, Salmonella enterica Enteritidis e Listeria monocytogenes (2.773 UA mL-1 para ambas). Ocimum basilicum apresentou maior atividade antibacteriana frente E. coli e Enterobacter sakazakii (6.826 e 8.106 UA mL-1 respectivamente), moderada atividade frente a Salmonella enterica Enteritidis (1.600 UA mL-1) e não apresentou atividade frente a Listeria monocytogenes.Origanum majorana também foi testado neste estudo e apresentou maior atividade antimicrobiana frente E. coli (5.973 UA mL-1), atividade moderada para Salmonella enterica Enteritidis e Enterobacter sakazakii (1.706 e 2.346 UA mL-1 , respectivamente) e não apresentou atividade para Listeria monocytogenes.<br>ABSTRACT The objective of this work was to identify and quantify the constituents, and to evaluate the antimicrobial activity of the essential oils from Mentha piperita, Cymbopogon citratus, Ocimum basilicum and Origanum majorana, against enteropathogenic Escherichia coli, Salmonella enterica Enteritidis, Listeria monocytogenes and Enterobacter sakazakii. The essential oils were obtained from dried leaves by using the hydrodistillation technique and the modified Clevenger apparatus, and their bacterial activity was determined by using the agar diffusion technique. The essential oils inhibited bacterial growth, but their effectiveness was varied. Among the essential oils tested, that from M. piperita showed a greater antimicrobial activity against E. coli (8.106 UA mL-1), moderate activity for S. enterica Enteritidis and E. sakazakii (1.706 e 3.200 UA mL-1 respectively) and low activity for L. monocytogenes (106,67 UA mL-1). However, the essential oil from C. citratus presented a greater antimicrobial activity against E. coli (9.386 UA mL-1) and a moderate activity against E. sakazakii, S. enterica Enteritidis and L. monocytogenes (2.773 UA mL-1 for both). The essential oil from O. basilicum showed a greater antimicrobial activity against E. coli and E. sakazakii (6.826 e 8.106 UA mL-1 respectively),moderate activity against S. enterica Enteritidis (1.600 UA mL-1), and was inactive against L, monocytogenes. Origanum majorana, which was also tested in our work, showed a greater antibacterial activity against E. coli, (5.973 UA mL-1) moderate activity against S. enterica Enteritidis and E. sakazakii (1.706 e 2.346 UA mL-1 , respectively), and was inactive against L. monocytogenes