A prospective, multi-site, cohort study to estimate incidence of infection and disease due to Lassa fever virus in West African countries (the Enable Lassa research programme)–Study protocol

Background Lassa fever (LF), a haemorrhagic illness caused by the Lassa fever virus (LASV), is endemic in West Africa and causes 5000 fatalities every year. The true prevalence and incidence rates of LF are unknown as infections are often asymptomatic, clinical presentations are varied, and surveillance systems are not robust. The aim of the Enable Lassa research programme is to estimate the incidences of LASV infection and LF disease in five West African countries. The core protocol described here harmonises key study components, such as eligibility criteria, case definitions, outcome measures, and laboratory tests, which will maximise the comparability of data for between-country analyses. Method We are conducting a prospective cohort study in Benin, Guinea, Liberia, Nigeria (three sites), and Sierra Leone from 2020 to 2023, with 24 months of follow-up. Each site will assess the incidence of LASV infection, LF disease, or both. When both incidences are assessed the LASV cohort (nmin = 1000 per site) will be drawn from the LF cohort (nmin = 5000 per site). During recruitment participants will complete questionnaires on household composition, socioeconomic status, demographic characteristics, and LF history, and blood samples will be collected to determine IgG LASV serostatus. LF disease cohort participants will be contacted biweekly to identify acute febrile cases, from whom blood samples will be drawn to test for active LASV infection using RT-PCR. Symptom and treatment data will be abstracted from medical records of LF cases. LF survivors will be followed up after four months to assess sequelae, specifically sensorineural hearing loss. LASV infection cohort participants will be asked for a blood sample every six months to assess LASV serostatus (IgG and IgM). Discussion Data on LASV infection and LF disease incidence in West Africa from this research programme will determine the feasibility of future Phase IIb or III clinical trials for LF vaccine candidates

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

Évaluation de performance d’architecture de contrôle-commande en réseau dans un contexte incertain d’avant-vente

This PhD dissertation, supported by CIFRE convention between the company Schneider-Electric and the University of Lorraine through the CRAN laboratory, deals with the assessment of temporal performances for a networked distributed control system. The industrial need was the development of a quotation and sizing tool of industrial control architecture during pre-sales stage. This stage is characterized by limited information about the process and the customers’ needs. The underlying scientific problematic was the ability to generate automatically models serving as support for the evaluation. In fact, performance assessment is realized for a wide range of architecture during a small amount of time, which is not compliant with a manual definition of the models. Our contribution is mainly based on a formal definition of a “builder” model with Colored and Timed Petri Nets which embeds mechanisms for configuration, instantiation and parameters setting of the architecture models. Several algorithms have been proposed for firstly build automatically the architecture Petri Nets model from a formal description of the topology and from a component model library and, secondly, for generating performance observers. Theses algorithms have been implemented on a tool gathering a user interface developed by Schneider –Electric and the Petri Nets simulator called CPN Tools which provides the performance assessment through Monte-Carlo simulation. The added value of this approach has been illustrated through case studies provided by Schneider-ElectricCe mémoire, réalisé dans le cadre d’une thèse sous convention CIFRE avec la société Schneider-Electric et l’Université de Lorraine à travers le laboratoire du CRAN, porte sur l’évaluation des performances temporelles des architectures de contrôle-commande distribuées sur un réseau de communication. Le besoin industriel s’exprime sous la forme d’un outil d’aide au dimensionnement des architectures en phase d’avant-vente caractérisée par une connaissance partielle de ces dernières. Le problème scientifique sous-jacent est relatif à la génération automatique des modèles servant de support à l’évaluation. En effet, l’évaluation des performances doit être réalisée pour un ensemble important d’architectures, dans un temps court, difficilement compatible avec une construction manuelle des modèles. Notre contribution porte sur la définition formelle, à l’aide de réseaux de Petri colorés et temporisés, d’un modèle « constructeur » d’architectures embarquant des mécanismes de configuration, d’instanciation et de paramétrage. Plusieurs algorithmes sont proposés pour, d’une part, construire automatiquement le modèle d’une architecture donnée, à partir d’une description formelle de sa topologie et d’une librairie de modèles d’équipements de contrôle-commande, et, d’autre part, pour générer les observateurs requis à partir d’une description formelle des performances à évaluer. Ces différents algorithmes ont été implantés dans un outil interfacé, d’une part avec l’outil Schneider de description des architectures, et, d’autre part avec le simulateur de l’outil CPN Tools qui fournit une estimation des performances via des simulations de Monte-Carlo. L’intérêt de cette approche a été illustrée sur la base de quelques architectures types fournies par la société Schneider-Electri

Performance assessment of Networked Control System (NCS) during uncertain pre-sales context

Ce mémoire, réalisé dans le cadre d’une thèse sous convention CIFRE avec la société Schneider-Electric et l’Université de Lorraine à travers le laboratoire du CRAN, porte sur l’évaluation des performances temporelles des architectures de contrôle-commande distribuées sur un réseau de communication. Le besoin industriel s’exprime sous la forme d’un outil d’aide au dimensionnement des architectures en phase d’avant-vente caractérisée par une connaissance partielle de ces dernières. Le problème scientifique sous-jacent est relatif à la génération automatique des modèles servant de support à l’évaluation. En effet, l’évaluation des performances doit être réalisée pour un ensemble important d’architectures, dans un temps court, difficilement compatible avec une construction manuelle des modèles. Notre contribution porte sur la définition formelle, à l’aide de réseaux de Petri colorés et temporisés, d’un modèle « constructeur » d’architectures embarquant des mécanismes de configuration, d’instanciation et de paramétrage. Plusieurs algorithmes sont proposés pour, d’une part, construire automatiquement le modèle d’une architecture donnée, à partir d’une description formelle de sa topologie et d’une librairie de modèles d’équipements de contrôle-commande, et, d’autre part, pour générer les observateurs requis à partir d’une description formelle des performances à évaluer. Ces différents algorithmes ont été implantés dans un outil interfacé, d’une part avec l’outil Schneider de description des architectures, et, d’autre part avec le simulateur de l’outil CPN Tools qui fournit une estimation des performances via des simulations de Monte-Carlo. L’intérêt de cette approche a été illustrée sur la base de quelques architectures types fournies par la société Schneider-ElectricThis PhD dissertation, supported by CIFRE convention between the company Schneider-Electric and the University of Lorraine through the CRAN laboratory, deals with the assessment of temporal performances for a networked distributed control system. The industrial need was the development of a quotation and sizing tool of industrial control architecture during pre-sales stage. This stage is characterized by limited information about the process and the customers’ needs. The underlying scientific problematic was the ability to generate automatically models serving as support for the evaluation. In fact, performance assessment is realized for a wide range of architecture during a small amount of time, which is not compliant with a manual definition of the models. Our contribution is mainly based on a formal definition of a “builder” model with Colored and Timed Petri Nets which embeds mechanisms for configuration, instantiation and parameters setting of the architecture models. Several algorithms have been proposed for firstly build automatically the architecture Petri Nets model from a formal description of the topology and from a component model library and, secondly, for generating performance observers. Theses algorithms have been implemented on a tool gathering a user interface developed by Schneider –Electric and the Petri Nets simulator called CPN Tools which provides the performance assessment through Monte-Carlo simulation. The added value of this approach has been illustrated through case studies provided by Schneider-Electri

Determinants de l’adoption des semences certifiees de varietes ameliorees du riz au Benin

Au Bénin, la diffusion des variétés à haut rendement de riz s’est accélérée en réponse à une demande croissante de cette denrée. Ces variétés évaluées par la recherche, favorisent l’augmentation du rendement de la production rizicole. Pour cela, la semence de ces variétés nécessite un renouvellement périodique dans les structures garantissant la certification. De ce fait, il existe une différence entre les riziculteurs qui utilisent les semences non certifiées des variétés améliorées et ceux qui utilisent des semences certifiées des variétés améliorées. Malheureusement, cette différentiation n’est pas prise en compte dans la plupart des études de l’adoption des variétés à haut rendement. Cette étude prend alors en compte cet aspect en explicitant les déterminants de l’adoption et de l’intensité d’adoption des semences certifiées des variétés améliorées. Les données ont été collectées auprès d’un échantillon aléatoire de 272 ménages agricoles au Bénin. Les modèles Probit et Tobit sont respectivement utilisés pour identifier les variables affectant l’adoption et de l’intensité d’adoption des semences certifiées des variétés améliorées. Les résultats montrent que 81% des variétés utilisées sont améliorées et 19% sont des variétés traditionnelles. Parmi les adoptants des variétés améliorées, 37% utilisent des semences certifiées. Malgré un faible taux d’adoption des semences certifiées, l’intensité moyenne d’utilisation est de 30%. Les résultats montrent que l’appartenance à une association, le type de crédit, l’activité secondaire et la quantité d’engrais chimiques influencent l’adoption des semences certifiées au niveau des riziculteurs. Par ailleurs, les variables telles que la superficie agricole, l’activité secondaire et le sexe sont décisives sur l’intensité d’adoption. Les résultats suggèrent que pour accroître le taux d’adoption des semences certifiées, les octrois de crédit et les sensibilisations des riziculteurs à travers les associations sont recommandés.Mots clés: Adoption, semence certifiée, riz, déterminants, tobit, probitEnglish Title: Determinants of adoption of certified seeds of improved rice varieties in BeninEnglish AbstractIn Benin, the dissemination of high yield varieties of rice increased in response to the growing demand for this crop. These varieties assessed by the research favor the increase of rice yield. To this end, the seed of these varieties requires a periodical renewal in the structures guarantying the certification. From this fact, there exists in one hand, rice producers who use non certified seeds of the improved varieties and on the other hands, those who use certified seeds of these varieties. Unfortunately, this differentiation is not  taken into account in the adoption studies on seeds of high yield varieties. This study takes into account this aspect in clarifying the adoption determinants as well as the certified seeds adoption intensity. The data were collected from a random sample of 272 farming households. Probit and Logit models are respectively used to identify the variables that affect the adoption and the intensity of adoption of the certified seeds of the improved varieties. The results show that 81% of the varieties used are improved while 19% are traditional varieties. Among the adopters of the improved seeds, 37% use certified seeds. Despite this low percentage of adoption of certified seeds, the mean intensity of use of certified seeds is 30%. The results reveal that being member of a cooperative, the type of credit, the off-rice production activity and the quantity of chemical inputs influence adoption of certified seeds of the improved varieties. Moreover, the variables such as farm lands area, the off-rice production activities and gender are decisive on the adoption intensity. Therefore, in order to increase the certified seeds adoption rate, credit supply and the rice farmers’ awareness through the cooperatives are recommended.Keywords: adoption, certified Seeds, rice, determinants, tobit, probi