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

Les Zelliges du palais Al-Mansour (XVIIe siècle, Meknès, Maroc) : Données technologiques

International audienceOne of the restoration processes of the buildings covered with glazed ceramics consists in replacing themissing elements. This way of making runs up against the problem of lack of data concerning thematerials and, more generally, their old techniques of manufacture. For this aim, we undertook the studyof a four differently coloured zelliges (green, honey, black and white) and a bleu glazed tile, sampledfrom Al-Mansour palace (17th century, Meknes, Morocco). We made some physico-chemical analysisconcerning the colours, the texture and the composition of the different phases. All the glazes are leadcontaining. The agents, responsible for the colour, are traditional. Moreover, the examination of thetexture interface between glaze and body, in natural light and cathodoluminescence, showed that the bluetile is different from the zelliges by its dimensions, the colour of its ceramic support and the importance ofthe luminescent edging at the glaze-body interface. Two different techniques seem to have been used forthe manufacture of these glazed ceramics. They are characterized by their number of firings (simple ordouble) and by the fact that they are or not cut once finished.L'un des procédés de restauration des édifices recouverts de céramiques glaçurées consiste à remplacerles éléments manquants. Cette façon de faire se heurte au problème du manque de données sur lesmatériaux mis en oeuvre et d'une manière générale, sur les techniques anciennes de fabrication de cescéramiques. Dans cet objectif, nous avons entrepris l’étude d'une série de quatre zelliges de couleursdifférentes (vert, miel, noir et blanc) et d’un carreau bleu, provenant du Palais Al-Mansour (XVIIe siècle,Meknès, Maroc. Les analyses ont porté sur les couleurs, sur la texture et sur la composition desdifférentes phases constitutives. Toutes les glaçures sont plombifères. Les ions chromogènes,responsables de leur coloration, sont classiques. Par ailleurs, l'examen de la texture de l'ensembleglaçure/terre cuite, en lumière naturelle et en cathodoluminescence, montre que le carreau bleu estdifférent des autres zelliges par ses dimensions, la couleur de son support céramique et l'importance duliseré luminescent à l'interface glaçure/terre cuite. Deux techniques semblent avoir été utilisées pour lafabrication de ces céramiques glaçurées, qui se distinguent par le nombre de cuissons (mono oubicuisson) et par le fait qu'elles sont "taillées" ou utilisées sans découpage

Archaeological Zelliges of Meknes (14th-century): Physical measurements of the colour and identification of colouring agents

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New interpretations of the Témara’s caves and their occupations: special focus on small vertebrates and palaeoenvironments

International audienceThe El Harhoura 2 and El Mnasra caves are located in the region of Témara, on the Atlantic coast of Morocco, which was occupied by human populations since the beginning of the Late Pleistocene (around 120 ka BP). The recent excavations yielded human and faunal remains, as well as exceptional archaeological objects associated to anthropological structures. Small vertebrate remains are especially abundant in these sites, which allowed us to realize the first study on these taxa with a pluridisciplinary approach (taxonomy, taphonomy, palaeoecology) for North-African archaeological sites. The continuous sedimentary sequence of these sites covers the last climatic cycle, and is studied in a renewed geologic, stratigraphic, chronological and cultural context. We obtained significant data on the palaeoenvironmental and taphonomic context of the human occupations of the Témara’s caves. Today, there is no equivalent of such regional data for the whole Late Pleistocene in North Africa

Dossier : La fabrique de la mémoire

Le Maghreb est-il, à l’instar des sociétés du Nord, saturé par la fièvre des entreprises mémorielles ? Certes, il est invité – et s’invite – en France dans les conflits résultant de l’affrontement des mémoires autour de la question coloniale. Mais la fabrique de la mémoire au Maghreb n’est pas uniquement le résultat des interactions entre le Nord et le Sud de la Méditerranée. Elle est aussi le fruit d’un « travail de mémoire » interne qui se déploie depuis les indépendances avec d’autant plus de force qu’il s’est agi pour les États de l’Afrique du Nord de construire rapidement des nations à la fois ancrées dans le passé et porteuses d’un vouloir-vivre ensemble. Comme le note Jean-Philippe Bras coordinateur de ce dossier de recherche, ce processus de production d’une mémoire nationale édifiante se heurte à l’émergence de mémoires concurrentielles qui s’inscrivent dans les conflits les plus contemporains des sociétés maghrébines. C’est aujourd’hui la nécessité de surmonter les déchirements politiques ayant affecté le tissu social qui débouche, comme le montre bien l’exemple marocain, sur l’émergence d’un nouveau « registre mémoriel » fondé, cette fois-ci, sur la conciliation et la réparation. Un débat de recherche essentiel à côté duquel on retrouve les rubriques habituelles de L’Année du Maghreb : Chroniques politiques, Gros Plans, Études thématiques, ainsi que des sujets à la pointe de l’actualité portant sur l’islamisme ou les relations Maghreb-Europe en matière de sécurité et de défense. Éric Gobe, rédacteur en che