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

Prévalence des dyslipidémies au laboratoire de biochimie du CHU Aristide le Dantec de Dakar, Sénégal

Introduction: l'objectif de cette étude était d'évaluer la prévalence des dyslipidémies chez les patients reçus au laboratoire de Biochimie de l'Hôpital Aristide Le Dantec pour le dosage d'un paramètre lipidique au cours de l'année 2013. Méthodes: il s'agit d'une étude rétrospective portant sur 1356 patients âgés de 10 à 94 ans reçus au laboratoire de Biochimie du CHU Le Dantec de janvier à décembre 2013. Etaient inclus dans l'étude, tous les patients ayant au moins un paramètre du bilan lipidique dont les résultats étaient enregistrés dans le registre du laboratoire. Le cholestérol total, le cholestérol HDL, le cholestérol LDL ainsi que les triglycérides ont été dosés grâce à des méthodes enzymatiques sur un automate de Biochimie de type Cobas Integra 400 (Roche Diagnostics). Résultats: la prévalence des dyslipidémies dans notre population d'étude est de 39,30%. Les prévalences de l'hypercholestérolémie, l'hypoHDLémie, l'hyperLDLémie, l'hypertriglycéridémie et l'hyperlipidémie mixte étaient respectivement : 30,89% ; 7,30% ; 31,19% ; 0,51% ; 7,22%. Les sujets de 40 à 59 ans semblaient être plus exposés et on note une prédominance féminine en ce qui concerne l'hypercholestérolémie (54,17% vs 45,82%), l'hypoHDLémie (54,54% vs45, 45%), et l'hyperlipidémie mixte (51,08% vs 48,97%). Enfin les dyslipidémies étaient fortement corrélées à l'HTA et l'obésité. Conclusion: la forte prévalence des dyslipidémies retrouvée dans notre étude démontre l'intérêt d'étudier la prévalence des facteurs de risque cardio-vasculaires en particulier les dyslipidémies dans la population sénégalaise.The Pan African Medical Journal 2016;2

The Spatiotemporal Distribution and Molecular Characterization of Circulating Dengue Virus Serotypes/Genotypes in Senegal from 2019 to 2023

Dengue virus is becoming a major public health threat worldwide, principally in Africa. From 2016 to 2020, 23 outbreaks were reported in Africa, principally in West Africa. In Senegal, dengue outbreaks have been reported yearly since 2017. Data about the circulating serotypes and their spatial and temporal distribution were limited to outbreaks that occurred between 2017 and 2018. Herein, we describe up-to-date molecular surveillance of circulating DENV serotypes in Senegal between 2019 to 2023 and their temporal and spatial distribution around the country. For this purpose, suspected DENV-positive samples were collected and subjected to dengue detection and serotyping using RT-qPCR methods. Positive samples were used for temporal and spatial mapping. A subset of DENV+ samples were then sequenced and subjected to phylogenetic analysis. Results show a co-circulation of three DENV serotypes with an overall predominance of DENV-3. In terms of abundance, DENV-3 is followed by DENV-1, with scarce cases of DENV-2 from February 2019 to February 2022. Interestingly, data show the extinction of both serotype 1 and serotype 2 and the only circulation of DENV-3 from March 2022 to February 2023. At the genotype level, the analysis shows that sequenced strains belong to same genotype as previously described: Senegalese DENV-1 strains belong to genotype V, DENV-2 strains to the cosmopolitan genotype, and DENV-3 strains to Genotype III. Interestingly, newly obtained DENV 1–3 sequences clustered in different clades within genotypes. This co-circulation of strains belonging to different clades could have an effect on virus epidemiology and transmission dynamics. Overall, our results highlight DENV serotype replacement by DENV-3, accompanied by a wider geographic distribution, in Senegal. These results highlight the importance of virus genomic surveillance and call for further viral fitness studies using both in vitro and in vivo models, as well as in-depth phylogeographic studies to uncover the virus dispersal patterns across the country

Tette

Lyrical songs with solo and chorus accompanied by keyboard, percussion and guitars, in traditional Senegalese music style mixed with international influence

L'Afrique d'avant

A homage to women in general and rural women in particular, for courageously and stoically facing their arduous socetal burde

Le projet majeur africain de la Grande Muraille Verte

L’initiative de la Grande Muraille Verte (GMV), projet transcontinental, est une réponse de l’Afrique à la désertification, à la pauvreté et au changement climatique. Elle repose sur une approche concertée, multisectorielle, mettant en synergie des actions de lutte contre ces trois fléaux majeurs pour le continent africain. La particularité de la GMV est, tout en créant et consolidant une ligne de défense par des activités de reboisement et d’aménagement, de contribuer efficacement au développement intégré des zones rurales et d’aider à la lutte contre la pauvreté dans le cadre d’un développement durable. Il s’agit de l’installation et de la mise en valeur intégrée d’espèces végétales à valeur économique adaptées aux terres arides et aux particularités locales, de bassins de rétention, de systèmes de production agricoles et autres activités génératrices de revenus. La GMV intègre ainsi plusieurs systèmes des plantations artificielles anciennes ou nouvelles, des unités agro-sylvo-pastorales. Des zones de parcours villageoises ou intercommunautaires, des parcs animaliers, des réserves communautaires et des couloirs de migration de faune. Cet édifice transcontinental est une référence de modèle d’intégration sous-régional mettant en exergue une initiative originale initiée par des pays fortement assujettis aux phénomènes de désertification et de changement climatique Il constitue un Modèle Multisectoriel de Développement Intégré des Zones Andes (MDI/ZA). Dédié à la lutte contre tes effets et l’avancée de la désertification, à la restauration et la mise en valeur des zones dégradées et au mécanisme de développement propre dû à sa forte capacité de séquestration de carbone. L’ouvrage vise un large public, notamment les scientifiques, enseignants, décideurs, techniciens charges de la mise en œuvre de la GMV et permet d’apprécier l’originalité du projet dans son approche concertée et multisectorielle et ses résultats dans le développement intégré des zones arides a semi-arides