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

Repetitive transarterial chemoembolization in patients with hepatocellular carcinoma

International audienc

Sturge Weber syndrome, when brain CT is enough for diagnosis: about a case

One of the main manifestations of Sturge Weber syndrome is seizures. We report the case of a child received in the context of generalized seizures and in whom a cerebral contrast CT was sufficient to make the diagnosis of Sturge Weber syndrome

Apport de l’IRM dans la prise en charge des compressions médullaires lentes non traumatiques

Les compressions médullaires lentes sont dues au développement dans le canal médullaire d’une lésion expansive. C’est une pathologie très fréquente dont le diagnostic est essentiellement clinique. L’imagerie par résonnance magnétique occupe une place incontournable dans le diagnostic de localisation et la recherche étiologique. En Europe l’étiologie tumorale est prépondérante. Le but de cette étude était de décrire les aspects IRM des compressions médullaires lentes et de déterminer le profil étiologique. Il s’agit d’une étude rétrospective portant sur 97 observations colligées au service de radiologie du CHUN de Fann sur une période de 30 mois (du 08/03/10 au 29/09/12). On été inclus dans l’étude, tous les patients adressés pour un tableau de compression médullaire lente survenu dans un contexte non traumatique. L’âge moyen des patients était de 42,6 ans avec des extrêmes compris entre 04 mois et 85 ans. Nous avons étudié la topographie des lésions (étage rachidien, compartiments canalaires) leur rehaussement et les critères d’orientation étiologique. Le protocole d’examen permettait la réalisation de séquence pondérées T1 sans avec injection de gado, T2, STIR et T2 DRIVE centrées sur les niveaux lésionnels ou les zones suspectes. L’IRM a permis de préciser le siège exact et l’étendue des lésions. L’atteinte du rachis dorsal représentait 42% des cas, suivi du rachis cervical avec 32% des cas. Les atteintes lombo-sacrées et pluri-étagées représentaient respectivement 18% et 08% des cas. Les lésions extradurales représentaient 87% des cas, suivi des lésions intradurales extramédullaires avec 08% des cas et des lésions intramédullaires dans 05% des cas. La particularité du profil étiologique de notre étude est la prédominance des épidurites infectieuses et la fréquence relative des épidurites métastatiques comparée aux séries occidentales. L’IRM vertébro-médullaire occupe une place capitale dans le diagnostic positif, topographique et étiologique des compressions médullaires.Pan African Medical Journal 2016; 2

Postoperative morbidity and mortality from aortic valve replacements in 25 cases in Senegal

The purpose is to study the short- and medium-term morbidity and mortality linked to the implantation of an aortic prosthesis during cardiac surgery. This is a longitudinal, retrospective and descriptive study which takes place over a period from January 2017 to March 2020 (38 months) at the level of the thoracic and cardiovascular surgery clinic of the University Hospital Center of Fann in Dakar. All patients who underwent aortic valve replacement during this period were included in the study. A number of the series was 25 patients with a sex ratio of 2.66. The average age of the patients was 29.5 years (8-51 years). In the patients’ history, 19 patients (76%) had a notion of recurrent angina. Exercise dyspnea was the most common functional symptomatology present in 24 patients (96%). In the series, there were 22 cases (88%) of aortic insufficiency of various grades (2 to 4) with 7 cases (28%) associated with mitral insufficiency. We had 3 cases (12%) of aortic stenosis. All patients received surgical management under cardiopulmonary bypass. The average duration of cardiopulmonary bypass was 132 minutes ± 41.21 (53-226 minutes). The average duration of aortic clamping was 101 minutes ± 31.87 (53-164 minutes). The surgical procedures consisted in replacing the aortic valve with a biological prosthesis in one patient (4%) and a mechanical prosthesis in 24 patients (96%). The average length of hospital stay in intensive care was 5 days ± 4.03 (2-20 days). The average length of hospital stay was 20.76 days ± 13.19 (9 to 64 days). The average duration of follow-up was 8.2 months ± 4.57 (1 week - 32 months). During the follow-up, only one patient (4%) had developed infectious endocarditis on prosthesis and only one patient (4%) had a complication related to anticoagulant therapy (antivitamin K) such as gingivorrhagia and melena. We had recorded a single case of death at 6 months, a late mortality of 4%. Aortic valve replacement surgery, by median sternotomy gives satisfactory short- and medium-term results with negligible morbidity and negligible operative mortality

Homozygous sickle cell disease related mortality in Senegal (2011–2020)

Abstract Homozygous sickle cell disease (HSCD) is characterized by multiorgan morbidity and an increased risk of early death. We aim to describe the mortality rate, causes, and risk factors of death in HSCD between 2011 and 2020. We conducted a retrospective study with a duration of 10 years in the cohort of 2348 HSCD patients. The mortality rate was determined by reporting the number of deaths to the total number of patients followed in the year. Sociodemographic, clinical, biological data and causes of death were studied. Death risk factors were determined by a bivariate analysis comparing deceased and living HSCD patients. The mean age of death was 26 years (3–52). The sex ratio was 1.2. The mortality rate was 2.76%. The death rate was high in 2011 (3.2%) and low in 2020 (0.17%). We observed a significant reduction of mortality of 94.6%. Most of the common causes of death were acute anemia (40%), acute chest syndrome (24.6%), and infections (20%). Risk factors of death were age, vaso‐occlusive crises ≥3, acute chest syndrome, blood transfusion, and chronic complications. Mortality among HSCD has significantly decreased over the past 10 years in Senegal, and the main causes of death were acute anemia, acute chest syndrome, and infections

Chemical Constituents and Antimicrobial and Antioxidant Activities of Essential Oil from Dried Seeds of Xylopia aethiopica

The study aimed to investigate the chemical composition and antimicrobial and antioxidant activities of the essential oil from dried seeds of Xylopia aethiopica. The essential oil was obtained by hydrodistillation and analyzed by GC/FID and GC/MS. The essential oil yield was 1.35%. Forty-nine compounds were identified in the essential oil with 1,8-cineole (16.3%), β-pinene (14.8%), trans-pinocarveol (9.1%), myrtenol (8.3%), α-pinene (5.9%), and terpinen-4-ol (5.6%) as major components. The antimicrobial activity of this essential oil was studied using disk diffusion and broth microdilution methods on four bacteria (Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, and Pseudomonas aeruginosa) and one fungus (Candida albicans). The essential oil exhibited excellent activity against S. aureus, E. faecalis, and C. albicans and moderate activity against E. coli. Among all strains tested, C. albicans showed the best sensitivity with a MIC of 50 mg/mL. The antioxidant activity was examined using a DPPH-free radical scavenging assay. The essential oil of X. aethiopica showed low antioxidant activity (IC50 = 784.604 ± 0.320 mg/mL) compared to that of ascorbic acid and the reference compound (IC50 = 0.163 ± 0.003 mg/mL). The results indicate that consumption of X. aethiopica seeds can reduce the virulence of food-borne pathogens and their resistance to antibiotics