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

Nouveaux auxiliaires organiques pour le pressage de poudres d'alumines atomisées

Les procédés d'élaboration des céramiques avancées nécessitent, de manière générale, l'utilisation d'auxiliaires organiques, dont la vocation est de conférer aux matériaux les propriétés d'écoulement ou de cohésion souhaitées. La coexistence des différents additifs dans la suspension céramique de départ entraîne des interactions non seulement entre les additifs et la poudre mais aussi entre les additifs eux-mêmes. Dans le procédé de granulation des poudres de pressage par atomisation, la faible adsorption du liant, au regard de celle de dispersant engendre une distribution hétérogène de la phase organique dans les céramiques crues. Notre étude a pour objectif la définition et la synthèse de nouveaux polymères, qui portent deux fonctions susceptibles de leur conférer à la fois le rôle de liant et de dispersant. Une attention particulière est portée d'une part, sur la compréhension des phénomènes d'interaction entre ces copolymères et la surface des poudres d'alumine en suspension aqueuse par l'étude des isothermes d'adsorption, des propriétés électrocinétiques et rhéologiques et, d'autre part, sur l'effet de ces interactions sur l'état de dispersion des poudres. Les propriétés mécaniques des pièces crues élaborées par pressage des poudres atomisées en présence des copolymères synthétisés sont ensuite évaluées et discutées en tenant compte de la nature des copolymèresLIMOGES-BU Sciences (870852109) / SudocLIMOGES-ENSCI (870852305) / SudocSudocFranceF

Agrobacterium strains isolated from root nodules of common bean specifically reduce nodulation by Rhizobium gallicum

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699International audienceIn a previous work, we showed that non-nodulating agrobacteria strains were able to colonize root nodules of common bean. Both rhizobia and agrobacteria co-existed in the infected nodules. No impact on symbiosis was found in laboratory conditions when using sterile gravel as a support for growth. In this study, soil samples originating from different geographic and agronomic regions in Tunisia were inoculated with a mixture of agrobacteria strains isolated previously from root nodules of common bean. A significant effect on nodulation and vegetal growth of common bean was observed. Characterization of nodulating rhizobia and comparison with non-inoculated controls showed a biased genetic structure. It seemed that Rhizobium gallicum was highly inhibited, whereas nodulation by Sinorhizobium medicae was favored. Co-inoculation of non-sterile soils with R. gallicum and agrobacteria confirmed these findings. In vitro antibiosis assays indicated that agrobacteria exercised a significant antagonism against R. gallicum

RAFT Polymerization of Bio-Based 1‑Vinyl-4-dianhydrohexitol-1,2,3-triazole Stereoisomers Obtained via Click Chemistry

Four 1-vinyl-4-dianhydrohexitol-1,2,3-triazole stereoisomers are prepared from isomannide, isoidide, and isosorbide using an alkylation/CuAAC-ligation/elimination three-step strategy. After characterization of the monomers by NMR, differential scanning calorimetry (DSC), and high-resolution mass spectrometry (HRMS), the corresponding stereocontrolled poly­(1-vinyl-4-dianhydrohexitol-1,2,3-triazole)­s are obtained by RAFT polymerization using a xanthate chain transfer agent. A systematic investigation of the structure-properties relationship of both the monomers and polymers highlights the significant impact of the dianhydrohexitols stereochemistry on their physical properties (¹H and ¹³C NMR chemical shifts, physical state, <i>T</i>_g, thermal stability and solubility). A particularly original and unexpected behavior is highlighted since the two different isosorbide-based poly­(1-vinyl-4-dianhydrohexitol-1,2,3-triazole) stereoisomers exhibit contrasting solubility in water

2 - Les sanctuaires du forum, du centre de l’agglomération et de la grande rue courbe

On comptait à Dougga dans la seconde moitié du IIe siècle, à l’époque de la plus grande prospérité, plus de trente-cinq sanctuaires païens. Ce second volume en étudie quinze, dont six pour le seul forum, les autres furent implantés dans le centre de la ville, ou proches de lui. Ils ont été choisis en raison de la variété des programmes architecturaux auxquels ils répondaient et de leurs vestiges qui devaient être suffisants pour envisager des restitutions célèbres.L’étude architecturale, soutenue par des sondages archéologiques, a permis de renouveler l’approche et la connaissance de ces monuments, y compris celle du plus célèbre d’entre eux, le capitole. Elle a fait un appel constant aux inscriptions publiques, très nombreuses dans le domaine religieux. On a pu suivre ainsi l’évolution des sanctuaires sous le Haut-Empire, parfois jusqu’à la fin du IIIe siècle. De grandes nouveautés concernent la monumentalisation du forum et les phases de son aménagement désormais établies avec la plus grande précision possible. À l’est du forum, le "Domaine de Mercure", voué au dieu et aux activités du commerce, résulte d’un projet architectural original et ambitieux qui fut réalisé d’un seul jet vers la fin du IIe siècle. Parmi les autres sanctuaires, une attention particulière a été donnée à un grand ensemble auquel fut attaché un vaste théâtre cultuel, et à Dar Laccheb, un monument imposant jusqu’ici énigmatique.Cet ouvrage est le fruit d’une réflexion théorique sur les méthodes d’étude et de restitution des monuments cultuels. Résultat des recherches d’une équipe franco-tunisienne étoffée, réunissant architectes, archéologues, épigraphistes, il témoigne de la richesse qu’a pu apporter l’association de ces disciplines, pour la connaissance de l’un des sites antiques les plus étudiés de la TunisieMore than thirty-five sanctuaries are known in Dougga dating to the most prosperous period of the city. This second volume examines fifteen of these monuments, six linked to the forum, the others being in the vicinity. Selected for the variety of their architectural programs, all are in a sufficient state of preservation to allow credible reconstruction.The architectural study, based on archaeological soundings, has added to existing knowledge of these sanctuaries, including the most famous of all, the Capitole. The study has also exploited the many public inscriptions of Dougga pertaining to religious matters. In doing so, the evolution of the sanctuaries under the High Empire, and sometimes until the end of the 3rd century, has been established. New considerations concerning the phases of the development of the monuments have been confirmed with the highest possible level of certainty. East of the Forum, the precinct of Mercury, devoted to dedicatory and commercial activities, is an original and ambitious architectural project, that developed continuously until the end of the 2nd century. Among other sanctuaries, special attention is given to the architectural complex of a temple behind the large cultic theater and to the imposing "Dar Lachheb", a once-enigmatic religious monument.This book is the result of theoretical reflection on the methods of study and reconstruction of cultural monuments. It represents the culmination of the research efforts of a diverse Franco-Tunisian team of archaeologists, architects, and epigraphers, demonstrating how their interdisciplinary collaboration has enriched our knowledge of one of the most studied sites in TunisiaUsing the world in ancient societies : processes and forms of appropriation of space in Long TimeParis Sciences et LettresCultural and material tranfers, translation, interface

The effect of extended cold storage on the functional quality attributes of different potato genotypes

Potato (Solanum tuberosum L.) is a staple food widely consumed in Tunisia and represents a source of various secondary metabolites with human health benefits. However, cold storage of potato tuber affects their bioactive properties and functional quality. Despite the importance of this fact, few studies have examined the effects of extended cold storage on potato tubers quality. Therefore, the objective of the present work was to evaluate the effect of cold storage on the main quality traits of different potato genotypes grown in Tunisia. This investigation focused on four cultivated potato varieties including three commercial (Selena, Elbeidha, and Naima) and a selected clone CL27 grown under late cropping season conditions with planting at the beginning of autumn and a winter tuberization. The tubers from this trial were stored for 90 days at 8 degrees C. The results obtained showed that quality traits of potato tubers were strongly influenced by storage at 8 degrees C throughout 90 days. Additionally, disregarding the genotype, total carotenoids, phenolics, and flavonoids contents increased significantly following 90 days storage at 8 degrees C. However, genotypic differences underlying the antioxidant activity in both hydrophilic and lipophilic fractions were detected suggesting their sensibility to cold storage. This study might be useful for breeders working on potato genotypes suitable for extended storage duration and for growers storing their material for extended period under low temperature.The effect of storage varies according to the considered genotype.Stored tubers at 8 degrees C for 90 days exhibited higher nutritional quality with respect to fresh samples.Appropriate storage can contribute to maintain high-quality potato tubers

A genome wide SNP genotyping study in the Tunisian population: specific reporting on a subset of common breast cancer risk loci

International audienceBackground: Breast cancer is the most common cancer in women worldwide. Around 50% of breast cancer familial risk has been so far explained by known susceptibility alleles with variable levels of risk and prevalence. The vast majority of these breast cancer associated variations reported to date are from populations of European ancestry. In spite of its heterogeneity and genetic wealth, North-African populations have not been studied by the HapMap and the 1000Genomes projects. Thus, very little is known about the genetic architecture of these populations.Methods : This study aimed to investigate a subset of common breast cancer loci in the general Tunisian population and to compare their genetic composition to those of other ethnic groups. We undertook a genome-wide haplotype study by genotyping 135 Tunisian subjects using the Affymetrix 6.0-Array. We compared Tunisian allele frequencies and linkage disequilibrium patterns to those of HapMap populations and we performed a comprehensive assessment of the functional effects of several selected variants.Results : Haplotype analyses showed that at risk haplotypes on 2p24, 4q21, 6q25, 9q31, 10q26, 11p15, 11q13 and 14q32 loci are considerably frequent in the Tunisian population (> 20%). Allele frequency comparison showed that the frequency of rs13329835 is significantly different between Tunisian and all other HapMap populations. LD-blocks and Principle Component Analysis revealed that the genetic characteristics of breast cancer variants in the Tunisian, and so probably the North-African populations, are more similar to those of Europeans than Africans

L’aire sacrée de Baal Hammon-Saturne à Dougga. In: Aounallah S., Brouquier-Reddé V. (dir.), Dossier "Dougga, la périphérie nord (résultats des campagnes 2017-2019)"

International audienc

Mutational founder effect in recessive dystrophic epidermolysis bullosa families from Southern Tunisia

Dystrophic epidermolysis bullosa (DEB) is a group of heritable bullous skin disorders caused by mutations in the COL7A1 gene. One of the most severe forms of DEB is the severe generalized [recessive dystrophic epidermolysis bullosa (RDEB-SG)] subtype, which is inherited in an autosomal recessive manner. This subtype is most often due to COL7A1 mutations resulting in a premature termination codon on both alleles. We report here, the molecular investigation of 15 patients belonging to 14 nuclear families from the city of Sfax in Southern Tunisia, with clinical features of RDEB-SG complicated by squamous cell carcinoma in 3 patients. We identified two novel mutations, p.Val769LeufsX1 and p.Ala2297SerfsX91, in addition to one previously reported mutation (p.Arg2063Trp). The p.Val769LeufsX1 mutation was shared by 11 families and haplotype analysis indicated that it is a founder mutation. The p.Ala2297SerfsX91 mutation was a private mutation found in only one family. Together with the previously described recurrent mutations in Tunisia, screening for the founder p.Val769LeufsX1 mutation should provide a rapid molecular diagnosis tool for mutation screening in RDEB patients from Southern Tunisia and possibly from other Mediterranean populations sharing the same genetic background