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

A flexible composition based abstract services for a better adaptation to users' intentions

La méthode de conception des architectures orientées services (SOA) est basée sur des standards et permet de créer une infrastructure informatique intégrée capable de répondre rapidement aux nouveaux besoins d’un utilisateur. Réellement, il n’est pas toujours facile de trouver des services correspondant aux requêtes des utilisateurs. Par conséquent, la composition des services satisfaisant la requête est un besoin grandissant de nos jours. La composition de services implique la capacité de sélectionner, de coordonner, d’interagir, et de faire interopérer des services existants. Elle constitue une tâche complexe. Cette complexité est due principalement au grand nombre de services disponibles et à leur hétérogénéité puisqu’ils sont créés par des organisations différentes. Cette complexité est renforcée quand il s’agit d’intégrer dynamiquement des services à la demande, et les composer automatiquement pour répondre à des exigences qui ne sont pas réalisées par les services existants. En fait, une approche pour la composition de services doit offrir le potentiel de réaliser des applications flexibles et adaptables, en sélectionnant et en combinant les services de manière appropriée sur la base de la requête et du contexte de l’utilisateur. Dans cette perspective, différentes approches ont été développées pour la composition de services. Cependant, la plupart des processus de composition ont tendance à être statique et non flexible dans le sens où ils n’ont pas la capacité de s’adapter aux besoins des utilisateurs. Dans cette thèse, nous proposons une approche de composition dans laquelle la génération du schéma de composition est effectuée en partie au moment de l’exécution en ayant recours aux services abstraits fournis au moment de la conception. L’utilisation des services abstraits permet une certaine flexibilité et adaptabilité sans avoir besoin de construire une composition de services à partir de zéro au moment de l’exécution. Le processus de composition que nous proposons se compose principalement de quatre étapes. La première étape prend une structuration des besoins de l’utilisateur matérialisée par un graphe d’intentions et l’enrichit pour expliciter les relations implicites. Le résultat de cette étape permet de générer un schéma de composition initial en construisant le flux de contrôle déduit du graphe des intentions enrichi, puis en sélectionnant les services abstraits adéquats. Le choix de ces services est basé sur le matching sémantique et le degré d’affinité sémantique entre les services abstraits. La troisième étape consiste à générer le schéma de composition final à l’aide d’un mécanisme de raffinement des services abstraits en utilisant des techniques de matching sémantique et en tenant compte du contexte de l’utilisateur. Enfin, le plan d’exécution est généré en tenant compte des contraintes non-fonctionnelles fournies dans la spécification des intentions.The design approach of service oriented architectures (SOA) is based on standards which gives the possibility of creating an integrated IT infrastructure capable of rapidly responding to new user needs. Actually, it is not always easy to find services that meet user requests.Therefore, the service composition satisfying the user intention is a growing need. The composition of services implies the ability to select, coordinate, interact, and to interoperate existing services. The composition is considered as a complex task. This complexity is mainly due to the large number of available services and their heterogeneity as they are created by different organizations. This complexity is increased when services must be dynamically and automatically composed to meet requirements which are not satisfied by existing services. In fact, an approach for service composition must offer the potential to achieve flexible and adaptable applications, by selecting and combining services based of the request and the context of the user. In this perspective, different approaches have been developed for services composition. However, most of the existing composition approaches tend to be static and not flexible in the sense that they do not have the ability to adapt to user requirements. In this thesis, we propose a composition approach in which the generation of the composition schema is performed at runtime through the use of abstract services provided at design time. The use of abstract services allows flexibility and adaptability without having to build a service composition from scratch at run time. The composition process that we propose consists mainly of four steps. The first step takes a structure of user requirements materialized by a graph of intentions and enriches this graph to explicit the implicit relationships. The enriched graph is used to generate an initial composition scheme by building the control flow and selecting the appropriate abstract services. The selection of these services is based on the semantic matching and the degree of semantic affinity between abstract services. The third step is to generate the final composition schema with a refinement mechanism of abstract services using semantic matching techniques and taking into account user context and constraints. Finally, the execution plan is generated driven by non-functional constraints provided in the intentions specification

Sélection et composition flexible basée services abstraits pour une meilleure adaptation aux intentions des utilisateurs

La méthode de conception des architectures orientées services (SOA) est basée sur des standards et permet de créer une infrastructure informatique intégrée capable de répondre rapidement aux nouveaux besoins d’un utilisateur. Réellement, il n’est pas toujours facile de trouver des services correspondant aux requêtes des utilisateurs. Par conséquent, la composition des services satisfaisant la requête est un besoin grandissant de nos jours. La composition de services implique la capacité de sélectionner, de coordonner, d’interagir, et de faire interopérer des services existants. Elle constitue une tâche complexe. Cette complexité est due principalement au grand nombre de services disponibles et à leur hétérogénéité puisqu’ils sont créés par des organisations différentes. Cette complexité est renforcée quand il s’agit d’intégrer dynamiquement des services à la demande, et les composer automatiquement pour répondre à des exigences qui ne sont pas réalisées par les services existants. En fait, une approche pour la composition de services doit offrir le potentiel de réaliser des applications flexibles et adaptables, en sélectionnant et en combinant les services de manière appropriée sur la base de la requête et du contexte de l’utilisateur. Dans cette perspective, différentes approches ont été développées pour la composition de services. Cependant, la plupart des processus de composition ont tendance à être statique et non flexible dans le sens où ils n’ont pas la capacité de s’adapter aux besoins des utilisateurs. Dans cette thèse, nous proposons une approche de composition dans laquelle la génération du schéma de composition est effectuée en partie au moment de l’exécution en ayant recours aux services abstraits fournis au moment de la conception. L’utilisation des services abstraits permet une certaine flexibilité et adaptabilité sans avoir besoin de construire une composition de services à partir de zéro au moment de l’exécution. Le processus de composition que nous proposons se compose principalement de quatre étapes. La première étape prend une structuration des besoins de l’utilisateur matérialisée par un graphe d’intentions et l’enrichit pour expliciter les relations implicites. Le résultat de cette étape permet de générer un schéma de composition initial en construisant le flux de contrôle déduit du graphe des intentions enrichi, puis en sélectionnant les services abstraits adéquats. Le choix de ces services est basé sur le matching sémantique et le degré d’affinité sémantique entre les services abstraits. La troisième étape consiste à générer le schéma de composition final à l’aide d’un mécanisme de raffinement des services abstraits en utilisant des techniques de matching sémantique et en tenant compte du contexte de l’utilisateur. Enfin, le plan d’exécution est généré en tenant compte des contraintes non-fonctionnelles fournies dans la spécification des intentions.The design approach of service oriented architectures (SOA) is based on standards which gives the possibility of creating an integrated IT infrastructure capable of rapidly responding to new user needs. Actually, it is not always easy to find services that meet user requests.Therefore, the service composition satisfying the user intention is a growing need. The composition of services implies the ability to select, coordinate, interact, and to interoperate existing services. The composition is considered as a complex task. This complexity is mainly due to the large number of available services and their heterogeneity as they are created by different organizations. This complexity is increased when services must be dynamically and automatically composed to meet requirements which are not satisfied by existing services. In fact, an approach for service composition must offer the potential to achieve flexible and adaptable applications, by selecting and combining services based of the request and the context of the user. In this perspective, different approaches have been developed for services composition. However, most of the existing composition approaches tend to be static and not flexible in the sense that they do not have the ability to adapt to user requirements. In this thesis, we propose a composition approach in which the generation of the composition schema is performed at runtime through the use of abstract services provided at design time. The use of abstract services allows flexibility and adaptability without having to build a service composition from scratch at run time. The composition process that we propose consists mainly of four steps. The first step takes a structure of user requirements materialized by a graph of intentions and enriches this graph to explicit the implicit relationships. The enriched graph is used to generate an initial composition scheme by building the control flow and selecting the appropriate abstract services. The selection of these services is based on the semantic matching and the degree of semantic affinity between abstract services. The third step is to generate the final composition schema with a refinement mechanism of abstract services using semantic matching techniques and taking into account user context and constraints. Finally, the execution plan is generated driven by non-functional constraints provided in the intentions specification

Automated and flexible composition based on abstract services for a better adaptation to user intentions

International audienceIn recent years, the composition of loosely coupled servies with the aim of satisfying the user intention is a widely followed research topic. The composition of services implies the ability to select, coordinate, interact, and interoperate existing services. This is considered as a complex task. This complexity is mainly due to the large number of available services and their heterogeneity as they are created by different organizations. This complexity is increased when services must be dynamically and automatically composed to meet requirements which are not satisfied by existing services. In fact, an approach for service composition must offer the potential to achieve flexible and adaptable applications, by selecting and combining services based of the request and the context of the user. In this perspective, different approaches have been developed for services composition. However, most of the existing composition approaches tend to be static and not flexible in the sense that they do not have the ability to adapt to user requirements. To overcome these challenges, we propose a composition approach in which the generation of the composition schema is performed at runtime through the use of abstract services provided at design time. The composition process that we propose takes as input a structure of user requirements materialized by a graph of intentions and enriches this graph to explicit the implicit relationships. The enriched graph is used to generate an initial composition schema by building the control flow and selecting the appropriate abstract services. The selection of these services is based on the semantic matching and the degree of semantic affinity between abstract services. Then, the final composition schema is generated using a refinement mechanism of abstract services using semantic matching techniques and taking into account user context and constraints

Experiments Results and Large Scale Measurement Data for Web Services Performance Assessment

International audienceService provisioning is a challenging research area for the design and implementation of autonomic service-oriented software systems. It includes automated QoS management for such systems and their applications. Monitoring and Measurement are two key features of QoS management. They are addressed in this paper as elements of a main step in provisioning of self-healing web services. In a previous work [1], we defined and implemented a generic architecture applicable for different services within different business activities. Our approach is based on meta-level communications defined as extensions of the SOAP envelope of the exchanged messages, and implemented within handlers provided by existing web service containers. Using the web services technology, we implemented a complete prototype of a service-oriented Conference Management System (CMS). We experienced our monitoring and measurement architecture using the implemented application and assessed successfully the scalability of our approach under the French grid5000. In this paper, experimental results are analyzed and concluding remarks are given

Experiments Results and Large Scale Measurement Data for Web Services Performance Assessment

International audienceService provisioning is a challenging research area for the design and implementation of autonomic service-oriented software systems. It includes automated QoS management for such systems and their applications. Monitoring and Measurement are two key features of QoS management. They are addressed in this paper as elements of a main step in provisioning of self-healing web services. In a previous work [1], we defined and implemented a generic architecture applicable for different services within different business activities. Our approach is based on meta-level communications defined as extensions of the SOAP envelope of the exchanged messages, and implemented within handlers provided by existing web service containers. Using the web services technology, we implemented a complete prototype of a service-oriented Conference Management System (CMS). We experienced our monitoring and measurement architecture using the implemented application and assessed successfully the scalability of our approach under the French grid5000. In this paper, experimental results are analyzed and concluding remarks are given

In Vitro Cryopreservation of Date Palm Caulogenic Meristems

Cryopreservation is the technology of choice not only for plant genetic resource preservation but also for virus eradication and for the efficient management of large-scale micropropagation. In this chapter, we describe three cryopreservation protocols (standard vitrification, droplet vitrification, and encapsulation vitrification) for date palm highly proliferating meristems that are initiated from vitro-cultures using plant growth regulator-free MS medium. The positive impact of sucrose preculture and cold hardening treatments on survival rates is significant. Regeneration rates obtained with standard vitrification, encapsulation-vitrification, and droplet-vitrification protocols can reach 30, 40, and 70%, respectively. All regenerated plants from non-cryopreserved or cryopreserved explants don't show morphological variation by maintaining genetic integrity without adverse effect of cryogenic treatment. Cryopreservation of date palm vitro-cultures enables commercial tissue culture laboratories to move to large-scale propagation from cryopreserved cell lines producing true-to-type plants after clonal field-testing trials. When comparing the cost of cryostorage and in-field conservation of date palm cultivars, tissue cryopreservation is the most cost-effective. Moreover, many of the risks linked to field conservation like erosion due to climatic, edaphic, and phytopathologic constraints are circumvented.status: publishe

2,4-D induction of somaclonal variations in in vitro grown date palm (Phoenix dactylifera L. cv Barhee)

International audienceKey message: Results demonstrate that the 2,4-D can affect physiological and molecular parameters of vitrocultures when used at high concentrations without hampering their morphogenetic capacities. It was found to be efficient at inducing genetic and epigenetic variations.Abstract: The present study is a part of a program designed at improving the date palm, Phoenix dactylifera L. cv. Barhee, through induced somaclonal variation. In this work, caulogenic cultures were subcultured on MS media supplemented with 0, 1, 5, 10, 20 and 40 mg L-1 2,4-D in order to induce genetic and epigenetic variations. The highest doses of 2,4-D were found to induce severe negative effects on in vitro cultures, although some tissues were able to survive and to produce calli with high morphogenetic capacities. Our analysis showed some significant effect of 2,4-D on several physiological parameters. Indeed, chlorophyll and growth rates were found to drastically decrease while proline content increased from 535 to 2973 nmol g(-1) FW when 40 mg L-1 2,4-D were used. In vitro cultures showed several signs of oxidative stress, such as high levels of hydrogen peroxide and malondialdehyde; likewise, the specific activity of several antioxidant enzyme was found to increase. Plant regeneration from in vitro cultures treated with 2,4-D was obtained after subculturing explants onto PGR-free media. The ISSR analysis of 2,4-D-treated material showed that this plant growth regulator (PGR) induced measurable genetic variations. The global DNA methylation rates (GMR) as estimated through the HPLC analysis of nucleosides also confirmed the presence of epigenetic changes caused by 2,4-D as GMRs increased from 13.8 to 18.93%