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

Détection fortuite de cmy-2 et dha-1 chez des isolats d’Escherichia coli producteurs de BLSE au Sénégal

International audienc

Prévalence des entérobactéries productrices de bêtalactamases à spectre étendu isolées des hémocultures sur le continent Africain et les gènes impliqués chez les souches BLSE : revue de la littérature

Introduction: Les entérobactéries productrices de bêta-lactamases à spectre étendu ont été trouvées partout dans le monde. Des études de surveillance sont présentes en Europe, en Amérique, et en Asie, mais en Afrique, il n'y a pas eu de recherche récapitulative montrant la prévalence et la répartition de BLSE sur ce continent.But: Cette revue de la littérature a pour but de décrire la prévalence des entérobactéries productrices de bêta-lactamases à spectre étendu (E-BLSE) isolées des hémocultures en Afrique et les gènes BLSE impliqués dans la résistance.Matériel et méthodes: Une recherche de la littérature a été effectuée sur PubMed. Les articles publiés sur le domaine entre 1996 et 2014 ont été examinés et lus en texte intégral dans le but d’observer l’intérêt et la pertinence de la publication. Dans notre contexte, les articles qui étaient pertinents ont été évalués et inclus dans l'étude.Résultats: La prévalence des E-BLSE chez les patients hospitalisés et dans les communautés, varie largement entre les pays et pouvant atteindre souvent jusqu’à 77,8%. Plusieurs types d’échantillons ont été étudiés pour estimer la prévalence des EBLSE, mais le cas particulier des hémocultures reste vraiment limité. Les BLSE (classe  A et D) et AmpC plasmidique (pAmpC) ont régulièrement été trouvées, le gène CTXM- 15 de la classe A est prédominant sur le continent africain.Conclusion: Les entérobactéries productrices de bêta-lactamases à spectre étendu en milieux hospitaliers et communautaires sont courantes en Afrique. La majorité des études se sont réalisées au Nord et à l’Est, laissant presqu’un vide sur les autres parties du continent.Mots-clés: Afrique ; Bêta-lactamases à spectre étendu ; Entérobactérie ; Hémoculture ; PrévalenceEnglish Title: Prevalence of extended spectrum beta lactamases producing enterobacteria isolated from blood cultures on African continent and the involved genes in ESBL strains: literature reviewEnglish AbstractIntroduction: Extended-spectrum beta-lactamases producing Enterobacteria have been found worldwide. Surveillance studies are present in Europe, America, and Asia, but in Africa, there has been no research summary showing prevalence and distribution of extended-spectrum beta-lactamases on this continent.Aim: This literature review aims to describe the prevalence of Extended-spectrum betalactamases producing Enterobacteria (ESBL-E) isolated from blood cultures in Africa and the involved ESBL genes in resistance.Method: A literature search was performed in PubMed. Published articles in the field between 1996 and 2014 were reviewed and read in full text in order to observe the interest and relevance of the publication. In our context, articles that were relevant were assessed and included in the study.Results: Prevalence of ESBL-E in hospitalized patients and in communities varies largely between countries and often can reach up to 77.8%. Several types of samples were studied to estimate prevalence of ESBL-E, but the particular case of blood cultures is really limited. ESBLs (class A and D) and plasmid-encoded AmpC (pAmpC) have regularly been found, CTX-M-15 gene of the class A is predominant in AfricaConclusion: Extended-spectrum beta-lactamases producing Enterobacteria in hospital and communities areas are common around in Africa. Majority of studies were conducted in the North and in the East, leaving almost empty on other parts of the continent.Keywords: Africa; Blood culture; Enterobacteria; Extended spectrum beta-lactamases; Prevalenc