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

Elastofibrome à propos de 24 cas. L’expérience du service d’anatomopathologie de l’hôpital Ibn Sina de Rabat.

L’élastofibrome est une lésion fibro-proliférative, bénigne, lentement évolutive des parties molles. Il s’agit d’une étude rétrospective des cas d’élastofibrome colligés au service d’anatomopathologie de l’hôpital Ibn Sina de Rabat de Janvier 2006 à Février 2012 inclus. L’étude a recensé 24 cas d’élastofibrome. Nos patients présentaient tous une localisation thoracique postérieure. L’âge moyen était de 57 ans (44 et 83 ans). Le sexe ratio H/F = 0,41. L’atteinte bilatérale est trouvée chez 8 patients (33 %). L’atteinte unilatérale chez 16 patients (67 %), dont 12 à droite (75%) et 3 à gauche (19 %). Cliniquement, seulement 8 de nos patients (33 %) présentaient des douleurs. Radiologiquement, 19 patients (79,1 %) avaient bénéficié d’une échographie scapulaire, 5 (soit 20,8 %) d’une TDM, et enfin 3 (soit 12,5 %) d’une IRM. La taille moyenne de la lésion était de 9,5 cm, avec une taille qui varie entre 5,5 et 15 cm. Tous nos patients ont bénéficié d’une résection chirurgicale et l’évolution était favorable dans 100 % des cas. L’élastofibrome est une tumeur bénigne dont la pathogénie reste controversée. Il touche préférentiellement les femmes âgées et siège avec prédilection au niveau de la paroi thoracique postérieure. Il est le plus souvent asymptomatique, et de découverte fortuite par le patient. L’aspect en radiologie et en histologie est typique. Quand la lésion est tout à fait typique cliniquement et en imagerie, et qu’elle est asymptomatique, ce qui est le plus fréquent, seul la surveillance est préconisée. Conclusion : L’élastofibrome est une lésion qu’il faut savoir reconnaître afin d’éviter les biopsies inutiles, voire une chirurgie abusive

Predominance of OXA-48 Carbapenemase-Producing Enterobacterales in a Moroccan Hospital

Objective. The emergence of carbapenemase-producing Enterobacterales (CPE) is a major concern that is increasingly reported worldwide. Our study aimed at investigating the resistance of CPE isolates in a Moroccan teaching hospital using phenotypic and genotypic methods. Methods. Enterobacterales strains from March to June 2018 were collected from different clinical samples. The Enterobacterales isolates resistant to third-generation cephalosporins (3GC) and/or carbapenems were subjected to the Carba NP test and an immunochromatographic test for phenotypic detection. Detection of extended-spectrum β-lactamases (ESBL) was also performed following standards. Molecular screening of carbapenemases genes (OXA-48, NDM, blaKPC, blaIMP, blaVIM, and blaOXA-24, blaOXA-23, OXA-51, OXA-58) using conventional multiplex PCR assays was also performed on 143 isolates. Results. Enterobacterales represented 52.7% with a proportion of 21.8% of bacteria resistant to 3GC and/or carbapenems. Within 143 isolates MDR to 3GC, K. pneumoniae, E. coli, and E. cloacae represent 53.1%, 40.6%, and 6.3%, respectively. These strains were isolated mainly from urinary samples (74.8%) in patients admitted to emergency and surgical units. 81.1% of strains are producing ESBL and 29% are carbapenemase producers as confirmed by the Carba NP test, immunochromatographic test, and molecular testing. OXA-48 carriers represent 83.3% of these strains, followed by NDM with 16.7%. blaKPC, blaIMP, blaVIM, and blaOXA-24, blaOXA-23, OXA-51, OXA-58 were not detected in any of these bacteria. Conclusions. A high rate of CPE carrying OXA-48 among Enterobacterales resistant to 3GC and/or carbapenems isolates was found. Strict observance of hospital hygiene measures and more rational use of antibiotics are mandatory. Implantation of carbapenemases detection should be encouraged in our hospital settings to estimate the true burden of the CPE