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

Le bloc abdominal transverse continu au cours de la chirurgie programmée de l aorte abdominale par laparotomie latérale (essai prospectif, contrôlé, randomisé en double aveugle comparant la ropivacaïne 0.2% au placebo)

INTRODUCTION: La chirurgie de l aorte abdominale par laparotomie est une chirurgie douloureuse et prodiguée à des patients fragiles. Une prise en charge optimale de la douleur postopératoire a montré un bénéfice sur la morbi-mortalité. Le bloc abdominal transverse (TAP bloc) est une technique d anesthésie loco-régionale récente et efficace pour l analgésie de la paroi abdominale s incluant dans le concept d analgésie multimodale. Son utilisation en continu par la pose d un cathéter a peu été évaluée. MATERIELS ET METHODES: Lors d un essai prospectif, randomisé, en double aveugle (ropivacaïne 0,2% versus placebo), nous avons évalué au CHU de Dijon l efficacité du TAP bloc continu durant 48 heures en postopératoire de chirurgie programmée de l aorte abdominale par voie d abord rétropéritonéale. Le cathéter est placé par le chirurgien au moment de la fermeture de la paroi musculaire. Le critère de jugement principal est la consommation de morphine par PCA au cours des 24 premières heures. Les critères secondaires sont la consommation de morphine à 48 heures, les scores de douleur, la durée du séjour hospitalier, la survenue d épisodes de rétention aigue d urine, de nausées vomissements postopératoires et de retard de reprise du transit. RESULTATS: 25 patients ont été inclus dans chaque groupe du 1er septembre 2011 24 Août 2012. La consommation de morphine est inférieure dans le groupe ropivacaïne à 24 heures (30,7 +- 15,9 mg versus 40,7 +- 16,9 mg ; p = 0,019) et à 48 heures (42 +- 26,2 mg versus 63,8 +- 24,5 mg ; p = 0,003). Il n y a pas de différence significative entres les deux groupes sur les autres critères. Aucun incident lié à la technique n est relevé. CONCLUSIONS : Le TAP bloc en continu permet de réduire significativement la consommation de morphine en postopératoire de chirurgie programmée de l aorte abdominale par voie rétropéritonéale. Il doit faire partie de l arsenal analgésique au décours de ce type d intervention. Il se distingue par sa simplicité d apprentissage, de réalisation, de surveillance et son innocuité.DIJON-BU Médecine Pharmacie (212312103) / SudocSudocFranceF

Validity and reliability of a modified short version of a stigma scale for use among Tunisian COVID‐19 patients after quarantine: A cross‐sectional study

Abstract Background and Aim The COVID‐19 is a stigmatizing infectious disease even after healing. Until now, no COVID‐19 stigma scale validated in Tunisian Arabic language among the general population is available. Developing such tools is necessary to detect COVID‐19 stigma and reduce it effectively. Indeed, stigmatization of COVID‐19 patients could increase the spread of this disease and its related mental health issues. We aimed at testing the validity of a translated and modified version of the 12‐item HIV stigma scale among Tunisian COVID‐19 patients. Methods A cross‐sectional study was conducted between November and December 2020 among a representative sample of COVID‐19 patients in the governorate of Sousse, Tunisia, after quarantine. The 12‐item HIV stigma scale was translated in Tunisian Arabic and then modified to be adapted to the Tunisian context. The preliminary modified version was administrated to the participants by pretrained medical doctors during phone calls. It consisted on 20 items covering the four stigma dimensions (personalized stigma, disclosure concerns, concerns with public attitudes, and negative self‐image). The psychometric evaluation of this version included internal consistency as well as principal component analysis (PCA). Results The responses of 346 COVID‐19 patients were obtained. Their median age was 40 years (interquartile range: 30‐54.5). Females represented 60.4% of them. The PCA resulted in a three factor solution with 14 items. This 14‐item scale demonstrated good internal consistency with a global Cronbach's α of 0.91 and values of 0.94, 0.93, and 0.98 for social stigma, negative self‐image, and disclosure concerns, respectively. Conclusion This study provides a reliable and valid instrument for stigma measuring among Tunisian COVID‐19 patients. The use of this scale would contribute in reducing the spread of this new infectious disease and its related mental health issues