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

Asthme aigu grave de l’enfant : caractéristiques épidémiologiques, cliniques, thérapeutiques et évolutifs au Sénégal : Severe acute asthma of the child: epidemiological, clinical, therapeutic and evolutive characteristics in Senegal

Context and objective. The lethality of asthma is related to the occurrence of severe acute asthma which is a crisis that does not yield under initial bronchodilator therapy. The objective of this study was to describe the epidemiological, diagnostic, therapeutic and evolutionary characteristics of children hospitalized for a severe acute asthma attack. Methods. We conducted a retrospective study of 11 years (from January 1st, 2005 and December 31st, 2015) at the Pediatric Emergency and Respiratory Department of the Albert Royer Children's Hospital (CHNEAR). 89 Children aged 0 to 15 years hospitalized for severe asthma or severe acute asthma were included. Results. The hospital prevalence of severe asthma attacks was 0.18%. The average age of the children was 44.21 months and the sex ratio was 1.69. The hospitalizations peaks have been registered during the months of July and December. 6.6% of patients were undergoing treatment and 17.9% had already been hospitalized for severe asthma attacks. The main biological abnormalities were: hypoxemia (79.7%), anemia (66.29%) and leukocytosis (44.9%). Radiological abnormalities were dominated by pulmonary over distension (60.7%) and bronchial syndrome (36%). All patients were under oxygen, salbutamol and corticosteroids. One death was encountered. The average hospital length of stay was 3.75 days. The complications were pneumo-mediastinum / cervico-mediastinal emphysema in 4 cases, pneumothorax in 2 cases and atelectasis in 1 case. Conclusion. Severe acute asthma is a relatively rare condition, but it is always associated with a significant morbidity. Contexte et objectif. La létalité de l’asthme est liée à la survenue d’asthme aigu grave qui est une crise qui ne cède pas sous traitement bronchodilatateur initial. L’objectif de cette étude était de décrire les caractéristiques épidémiologiques, diagnostiques, thérapeutiques et évolutives des enfants hospitalisés pour une crise d’asthme aigu grave. Méthodes. Nous avons conduit une étude documentaire portant sur une période de 11 ans (1 janvier 2005-31 décembre 2015) et réalisée aux services des urgences pédiatriques et de pneumologie du centre hospitalier national d’enfants Albert Royer (CHNEAR). Etaient inclus, 89 enfants de 0 à 15ans hospitalisés pour crise d’asthme sévère ou asthme aigu grave. Résultats. La prévalence hospitalière des crises d’asthmes sévère était de 0,18%. Leur âge moyen était de 44,2 mois et le sexe ratio 1,6. Les pics d’hospitalisations ont été enregistrés durant les mois de Juillet et Décembre. 6,6% des patients étaient sous traitement de fond et 17,9% avaient déjà été hospitalisés pour crises d’asthmes sévères. L’hypoxémie (79,7%), l’anémie (66,2%) et l’hyperleucocytose (44,9%) étaient les principales anomalies biologiques. Les signes radiologiques étaient dominés par l’hyperinflation pulmonaire (60,7%) et le syndrome bronchique (36%). Tous les patients étaient ont bénéficié de l’oxygène, le salbutamol et les corticoïdes. Sous cette attitude thérapeutique, un décès avait été déploré. La durée moyenne de l’hospitalisation était de 3,75 jours. Les complications enregistrées étaient le pneumo-médiastin/emphysème cervico-médiastinal dans 4 cas, le pneumothorax dans 2 cas, la rupture trachéale dans 1 cas et l’atélectasie dans 1 cas. Conclusion. L’asthme aigu grave semble peu fréquent mais reste toujours associée à une morbidité non négligeable