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

Interaction ion‐surface : simulation de l'interaction plasma‐paroi (ITER)

The wall materials of magnetic confinement in fusion machines are exposed to an aggressive environment; the reactor blanket is bombarded with a high flux of particles extracted from the plasma, leading to the sputtering of surface material. This sputtering causes wall erosion as well as plasma contamination problems. In order to control fusion reactions in complex reactors, it is thus imperative to well understand the plasma-wall interactions. This work proposes the study of the sputtering of fusion relevant materials. We propose to simulate the charged particles influx by few keV single-charged ion beams. This study is based on the catcher method; to avoid any problem of pollution (especially in the case of carbon) we designed a new setup allowing an in situ Auger electron spectroscopy analysis. The results provide the evolution of the angular distribution of the sputtering yield as a function of the ion mass (from helium to xenon) and its energy (from 3 keV to 9 keV).Les matériaux de couverture des réacteurs à fusion nucléaire par confinement magnétique subissent un environnement agressif ; le flux intense de particules extraites du plasma attaque les parois du réacteur, engendrant la pulvérisation de la matière en surface. Cette pulvérisation est à l'origine de l'érosion des parois mais aussi de la pollution du plasma, ainsi, afin de maitriser la réaction de fusion dans des réacteurs de plus en plus complexes, il est impératif de bien comprendre les phénomènes d'interaction plasma-paroi. Cette thèse a pour but l'étude de la pulvérisation des matériaux des réacteurs de fusion nucléaire (carbone et tungstène), pour cela nous proposons de simuler le flux de particules chargées du plasma par des faisceaux d'ions monochargés d'énergies inférieures à la dizaine de keV. Cette étude est basée sur la méthode du collecteur, aussi afin de s'affranchir des problèmes liés aux polluants (notamment pour l'étude du carbone), nous avons conçu et réalisé un nouveau dispositif permettant l'analyse des collecteurs in situ par spectroscopie des électrons Auger. Les résultats obtenus donnent accès à l'évolution de la distribution angulaire en fonction des paramètres d'irradiation comme la masse du projectile (de hélium au xénon) ou l'énergie (de 3 keV à 9 keV)

Projet Terres de Sources AMI-TIGA Développement d’un modèle économique Etude des coûts évités Rapport complet

Projet Terres de Sources AMI-TIGA Développement d’un modèle économique Etude des coûts évités Rapport comple

Influence of pH and malate-glucose ratio on the growth kinetics of Leuconostoc oenos

International audienceGrowth, substrate utilization and product formation were studied in batch cultures of a Leuconostoc oenos strain. The effect of various culture conditions, i.e. pH-control at different values and various initial concentrations of malate and glucose, on growth and metabolism were investigated. Addition of malate resulted in a marked stimulation of growth, with only a slight increase in final biomass but a high conversion yield of glucose. Under pH control this stimulation was much greater than could be accounted for from changes in pH profile resulting from malate utilization. The specific rate of malate utilization was maximal at pH 4.0 whereas the specific rate of glucose consumption was highest at pH 5.5. During co-metabolism of malic acid and glucose, substrate utilization and product formation agreed with the stoichiometric relationships of the malo-lactic reaction and the heterolactic fermentation of glucose

Nanostructured surface coatings for titanium alloy implants

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Enhanced osseointegration of titanium implants with nanostructured surfaces: An experimental study in rabbits

International audienceTitanium and its alloys are commonly used for dental implants because of their good mechanical properties and biocompatibility. The surface properties of titanium implants are key factors for rapid and stable bone tissue integration. Micro-rough surfaces are commonly prepared by grit-blasting and acid-etching. However, proteins and cells interact with implant surfaces in the nanometer range. The aim of this study was to compare the osseointegration of machined (MA), standard alumina grit-blasted and acid-etched (MICRO) and nanostructured (NANO) implants in rabbit femurs. The MICRO surface exhibited typical random cavities with an average roughness of 1.5 lm, while the NANO surface consisted of a regular array of titanium oxide nanotubes 37 ± 11 nm in diameter and 160 nm thick. The MA and NANO surfaces had a similar average roughness of 0.5 lm. The three groups of implants were inserted into the femoral condyles of New Zealand White rabbits. After 4 weeks, the pull-out test gave higher values for the NANO than for the other groups. Histology corroborated a direct apposition of bone tissue on to the NANO surface. Both the bone-to-implant contact and bone growth values were higher for the NANO than for the other implant surfaces. Overall, this study shows that the nanostructured surface improved the osseointegration of titanium implants and may be an alternative to conventional grit-blasted and acid-etched surface treatments

Electrogenic malate uptake and improved growth energetics of the malolactic bacterium Leuconostoc oenos grown on glucose-malate mixtures

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Comparative bone tissue integration of nanostructured and microroughened dental implants

International audienceAIM:The aim was to compare osteointegration of nanostructured implants to a microsurface widely used for titanium dental implants.MATERIALS & METHODS:Commercial titanium dental implants with smooth or microroughened surfaces were nanostructured. Implants were inserted into the femoral condyles of rabbits. After 2 and 4 weeks, histomorphometry calculation was performed.RESULTS:Nanotubes measuring 60 nm in diameter were observed on both S-NANO (roughness: 0.05 μm) and R-NANO (roughness: 0.40 μm) surfaces. The MICRO surface exhibited typical random cavities (roughness: 2.09 μm). At 4 weeks, bone-to-implant contact values were significantly higher for the R-NANO than for the MICRO surface while no differences were observed at 2 weeks.CONCLUSION:Overall, this study shows that the nanostructured surfaces improved osteointegration similar or higher than the MICRO