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

Modeles dynamiques et commandes en boucle fermee d'un moteur pas a pas

Available from INIST (FR), Document Supply Service, under shelf-number : T 82334 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueSIGLEFRFranc

Méta-heuristiques à base de modèles : applications à l ordonnancement d atelier flow-shop hybride monocritère et multicritère

Nous proposons dans cette thèse l étude de problèmes d ordonnancement monocritère et multicritère sur un atelier de production flow-shop hybride. Nous nous intéressons à la résolution approchée de problèmes qui différent par leur fonction objectif que l on cherche à minimiser : la date d achèvement du travail le plus tardif (makespan), la somme pondérée des pénalités avance/retard et la somme totale des pénalités avance/retard. Notre objectif est d explorer et de justifier l utilisation d algorithmes d optimisation à base de colonie de fourmis pour la résolution de ces problèmes. Le problème multicritère, que nous abordons, considère le makespan et la somme pondérée des pénalités avance/retard comme critères d optimisation. Une approche hybride basée sur un algorithme de colonie de fourmis et la logique floue est développée pour résoudre ce problème. Cette approche permet de générer une multitude de solutions et emploie un module d aide à la décision et d évaluation pour sélectionner une solution parmi les solutions possibles en utilisant comme operateur d agrégation une intégrale de Choquet. Des expérimentations ont été effectuées sur des instances issues de la littérature ou générées aléatoirement, pour chacune des méthodes présentées. Les résultats obtenus sont prometteurs et l intérêt de chaque approche est discuté.In this thesis, we propose the study of mono-criterion and multi-criteria scheduling problems on a hybrid flow-shop factory. We focused on the approximate resolution of the problems that differ by their objective function that we seek to minimize: the makespan, the weighted sum of earliness/tardiness penalties and the total sum of earliness/tardiness penalties. Our objective is to explore and justify the using of algorithms based on ant colony optimization for the considered problems. The multi-criteria problem that we address, considers the makespan and the weighted sum of earliness/tardiness penalties as optimization criteria. A hybrid approach, based on an ant colony algorithm and fuzzy logic, is developed in order to solve this problem. So, this approach enable the generation of multiple solutions and use a module for decision support and evaluation to select a solution among the possible solutions, by using a Choquet integral as aggregation operator. Experimentations were performed on several benchmarks taken from the literature or randomly generated for all proposed methods. The obtained results are promising and their quality is discusses.REIMS-BU Sciences (514542101) / SudocSudocFranceF

Commande robuste des systèmes non linéaires complexes

Le travail de la thèse traite le problème de suivi de trajectoires des systèmes non linéaires incertains,dont le modèle nominal est construit à l aide d un système flou TS (Takagi-Sugeno) de type-2. Cedernier, exploite les modèles locaux du système obtenus par linéarisation autour de certains pointsde fonctionnement. La commande développée est basée sur les modes glissants d ordre deux avecSuper-Twisting. Nous avons proposé deux systèmes flous type-2 adaptatifs, qui ont comme uniqueentrée la surface de glissement, pour résoudre le problème du calcul de la valeur optimale des gainsde la commande. Des résultats de simulation ont permis de comparer les performances de l approcheproposée avec la méthode classique. Ensuite, nous avons introduit le concept de l intégral sliding modepour imposer à priori le temps d arrivée sur la surface de glissement. Les approches proposées sontgénéralisées aux cas des systèmes multivariables. Plusieurs résultats par simulation et implémentationen temps réel sont présentés pour illustrer les performances des approches développéesThis work deals with a fuzzy tracking control design for uncertain nonlinear dynamic system withexternal disturbances and using a TS (Takagi-Sugeno) fuzzy model description. The control is basedon the Super-Twisting algorithm, which is among of second order sliding mode control. Moreover, twoadaptive fuzzy type-2 systems have been introduced to generate the two Super-Twisting signals toavoid both the chattering and the constraint on the knowledge of disturbances and uncertainties upperbounds. These adaptive fuzzy type-2 systems has only one input : the sliding surface, and one output :the optimale values of the control gains, which are hard to compute with the original algorithm.Simulation results are obtained in order to compare the performances of the proposed method tothat given by Levant. Then, we have introduced the integral sliding mode concept to impose inadvance the convergence time and the arrival on the sliding surface. The proposed approaches aregeneralized to the case of multivariable systems. Several results in simulation and in real time usinga benchmark are obtained to validate and to confirm the performances of our contributions.REIMS-SCD-Bib. electronique (514549901) / SudocSudocFranceF

On the modelling of dc-dc converters: an enhanced approach

International audienc

Commande adaptative floue backstepping d une machine asynchrone avec et sans capteur mécanique

REIMS-BU Sciences (514542101) / SudocSudocFranceF

Control of Nonlinear Phenomena in DC-DC Converters: Fuzzy Logic Approach

International audienc

DC-DC power converter: modeling and control survey

International audienc

Fuzzy Controller Synthesis for a Dc-Dc Converter

International audienc

Optimisation of fuzzy controller for tracking the maximum power point in PV systems

International audienc