Mobile laboratory reveals the circulation of Dengue virus serotype I of Asian origin in Medina Gounass (Guediawaye), Senegal

With the growing success of controlling malaria in Sub-Saharan Africa, the incidence of fever due to malaria is in decline, whereas the proportion of patients with non-malaria febrile illness (NMFI) is increasing. Clinical diagnosis of NMFI is hampered by unspecific symptoms but early diagnosis is a key factor for better patient care and for disease control. The aim of this study was to determine the arboviral aetiologies of NMFI in a low resources settings using a mobile laboratory based on Recombinase Polymerase Amplification (RPA) assays. The panel of tests for this study was expanded to five arboviruses including (Dengue virus (DENV), Zika virus (ZIKV), Yellow fever virus (YFV), Chikungunya virus (CHIKV), and Rift valley fever virus (RVFV). One hundred and four children aged between one month and 115 months were enrolled and screened. Three of 104 blood samples of children < 10 years presenting at an outpatient clinic tested positive for DENV. The results were confirmed by real-time RT-PCR, partial sequencing, and non structural protein 1 (NS1) antigen capture ELISA (Biorad, France). Phylogenetic analysis of the derived DENV-1 sequences clustered them with sequences of DENV-1 isolates from Guangzhou in China in 2014. In conclusion, this mobile setup proved reliable for the rapid identification of the causative agent of NMFI, with results consistent with those obtained in the reference laboratory`s settings

Reemergence of Sylvatic Dengue Virus in Southern Senegal, 2021

As part of the syndromic surveillance of fever in Senegal, the virology department at Institut Pasteur de Dakar (IPD) in collaboration with the Epidemiology Unit and the Senegalese Ministry of Health conducted syndromic surveillance of fever in Senegal. Sample are from all suspected arboviral infections patients attending any of the sentinel sites. Collected blood samples were sent on a weekly basis at WHOCC for arboviruses and hemorrhagic fever viruses for screening of seven medically important arboviruses, including dengue virus (DENV). From January to December 2021, 2010 suspected cases were received among them 124 for confirmed to be DENV+ by RT-qPCR attempt of serotyping led to the detection of atypical DENV case from Sare Yoba area (Kolda region) which is unable to be correctly assigned to a serotype by the available tools (TIB Molbiol Modular Dx Dengue typing kit). Performed genome sequencing et phylogenetic analysis leads to the identification of a sylvatic DENV-2 strain closely related to a virus previously detected in Guinee-Bissau in 2009. This finding constitutes proof of the contemporary circulation of DENV-2 strain belonging to the sylvatic cycle in addition to well-known epidemic strains; this adds a piece of complexity to dengue management in Senegal. Alarmingly, it calls for improved genomic surveillance of DENV to know the genetic diversity of circulating strains in order to strengthen future vaccination policies

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

SELECTA : une approche de construction d'applications par composition de services.

We call composition the mechanism for building software applications by service integration. Service-based applications often require properties like dynamic or non-deterministic service selection that require a new definition of software application, which turns out to be very difficult to perform manually. There is a need to automate this process by providing tools and environments. These tools should allow to build flexible software applications and to ensure the consistency and completeness properties of the composition. This thesis focuses on building software applications, from design to execution. In this thesis, we propose a service composition approach and a prototype named SELECTA that meets the needs and challenges of service composition, such as increasing the abstraction level for application specification, incremental building of composites, consistency management and completeness of composites, definition of service constraints languages or service selection algorithms.On appelle composition le mécanisme permettant la réalisation d'applications logicielles par intégration de services. Les applications à service exigeant souvent des propriétés telles que la sélection dynamique ou non déterministe des services, le concept d'application doit être défini différemment, et le processus de composition est très difficile à réaliser manuellement. Le processus de composition devrait être automatisé par des outils et des environnements logiciels. Ces outils devraient permettre d'une part la construction d'applications flexibles et d'autre part garantir la cohérence et la complétude de la composition. Cette thèse s'intéresse à la construction d'applications depuis leur conception jusqu'à leur exécution. Dans cette thèse, nous proposons une approche de composition de services et un prototype nommé SELECTA permettant de répondre aux besoins et aux défis de la composition de services, tels que l'augmentation du niveau d'abstraction de la spécification de la composition, la construction incrémentale de composites, la gestion de la cohérence et de la complétude de composites, la définition de langages de contraintes de services ou d'algorithmes de sélection de services

Automating Component Selection and Building Flexible Composites for Service-Based Applications

International audienceService Oriented Computing allows defining applications in which components (services) can be available and selected very late during the development process or even "discovered" at execution time. In this context, it is no longer possible to describe an application as a composite entity containing all its components; we need to perform component selection all along the application life-cycle, including execution. It requires describing an application at least partially by its requirements and goals, leaving room for delaying selection; the development system, and the run-time must ensure that the current component selection satisfies, at all time, the application description. In this paper, we propose a concept of composite addressing the needs of advanced and flexible service-based applications, automating component selection and building composites satisfying the application description and enforcing minimality, completeness and consistency properties. We also propose tools and environment supporting these concepts and mechanisms in the different phases of the application life-cycle

Software Product Line Evolution: The Selecta System

International audienceThe current technology gives little room for the different kinds of evolution needed for any software product line (SPL): evolution of the associated engineering environment, evolution of the market and SPL scope, evolution of the products and variability. The paper describes how these different evolution needs are addressed in the CADSE and Selecta systems. The solution we propose uses metamodeling and generation for the engineering environment evolution, composition for scope and market evolution, a component database and a selection language for the product and variability evolution. The paper presents the Selecta system and shortly discusses the experience

FOCAS: An Enginering Environment for Service-Based Applications

International audienceService composition is an important topic, but so far addressed from a technical and low level perspective. The issue is not (too much) the orchestration formalism, but rather the engineering issues related to the many concerns that must be combined, to the technical complexity, to the heterogeneity and incompatibilities between available services, and the low level formalism and tools. The paper presents FOCAS, a full fledge environment that targets the different categories of stakeholders involved in the design, development, and maintenance of a service-based application. FOCAS first separates the different concerns, both functional and non functional, that made up a service-based application; second, it separates different levels of abstraction, and third it establishes links and mediations between these concerns and levels of abstraction. The paper presents FOCAS its principles, implementation and its evaluation

Opportunistic Computing Experience with the SAM platform

International audienceService-Oriented Computing (SOC) technology allows one to build applications exhibiting opportunistic, non deterministic and dynamic behavior. Unfortunately in SOC technologies these features are uncontrolled and software application is not an explicit concept. The challenge therefore is to provide a well defined application definition (an application model) in which the opportunistic behavior is used only when convenient, and to provide an extended SOC platform which enforces compliant application execution. This paper discuses the issues and shows the solution proposed by the SAM platform

Flexible composites and automatic component selection for service-based applications

International audienceIn traditional Software Engineering approaches, an application is described as a composite entity containing all its components. This approach is no longer relevant in modern Software Engineering, at least when developing service-based applications where some components (services) are selected very late during the development process or even "discovered" at execution. This new context requires describing an application in a more flexible way, leaving room for delayed selection. In turn, if component selection can be performed all along the life-cycle, an application description must explicitly include the application requirements and goals and the system must at least ensure that the selections satisfy the application description. In this work, we propose a concept of composite addressing the needs of the advanced and flexible service-based applications, automating component selection and building composites satisfying the application description and enforcing minimality, completeness and consistency properties. We also propose tools and environment supporting these concepts and mechanisms in the different phases of the application life-cycle

Caractérisation des services écosystémiques fournis par Cordyla pinnata dans la périphérie de la Forêt classée de Patako au Sénégal

Les espèces végétales autochtones permettent d’illustrer la diversité de services écosystémiques fournis par les milieux naturels. Cette étude a pour objectif de caractériser les services écosystémiques de Cordyla pinnata, une espèce autochtone typique de la zone soudanienne sénégalaise. Pour atteindre cet objectif, 97 questionnaires ont été administrés à des chefs de ménage dans la périphérie de la Forêt classée de Patako et les données ont été analysées avec des indicateurs ethnobotaniques. L’étude montre que Cordyla pinnata fournit 20 services écosystémiques appartenant à trois catégories, notamment les services d’approvisionnement, les services de régulation et les services culturels. La Valeur d’usage totale (VUt) de l’espèce est de 7,9 et les VU diffèrent en fonction des sites. Son Facteur de Consensus Informateur (FCI) est supérieur à 0,9 dans les trois catégories et ses Niveaux de Fidélité (NF) sont élevés pour la nourriture, la médecine traditionnelle, le bois, l’ombrage, la fertilisation des terres et l’héritage. Ces résultats permettent de dire que Cordyla pinnata a une grande importance dans plusieurs aspects de la vie des populations locales. Sa VU est plus élevée dans les localités éloignées de la Forêt classée de Patako où la couverture végétale naturelle est plus pauvre. Mais la majorité des services écosystémiques que l’espèce fournit sont perçus et appréciés localement, et sont compromis par la dégradation de son peuplement dans la zone. Ainsi, il conviendrait de mieux conscientiser les populations locales sur l’importance socio-économique et écologique de l’espèce afin qu’elles la préservent davantage et la restaurent dans les agro-systèmes.Local plant species allow illustrate the diversity of ecosystem services provided by natural ecosystems. The present study has the objective to characterize ecosystem services provided by Cordyla pinnata, an indigenous species of the sudanian zone of Senegal. To achieve this objective, 97 questionnaires were conducted with the head of households around Patako Classified Forest and data analysis was based on ethnobotanical indicators. This study shows that Cordyla pinnata provides 20 ecosystem services which belong to three categories : provisioning services, regulation services and cultural services. The total Use Value (UVt) of the species is 7.9 and UV differ among sites. Factor of Informant Consensus (FIC) is greater than 0.9 in all three categories and Fidelity Levels (FL) are high for food, traditional medicine, wood, shade, soil fertilization and inheritance. Results show that Cordyla pinnata is a useful species in many aspects of local people’s lives. Its UV is higher in sites distant from Patako Classified Forest were the natural vegetation is less abundant. However the majority of these ecosystem services provided by the species are locally perceived and enjoyed and is compromised by the degradation of its stand population in the area. Thus, it appropriate to make local population more conscious about the socio-economic and ecological importance of the species for them so that they the preserve it better and restore it in agro-systems