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

Reclaiming African leadership to end FGM/C

By exploring the history of the fight against FGM/C, this SRHM blog aims to inspire African changemakers to reclaim the legacy of past generations. Celebrating past initiatives led by Africans will strengthen their rightful role as leaders in the forefront of continuous endeavors to enable change in their communities and beyond

Four-Month High-Dose Rifampicin Regimens for Pulmonary Tuberculosis

BACKGROUND Shorter but effective tuberculosis treatment regimens would be of value to the tuberculosis treatment community. High-dose rifampicin has been associated with more rapid and secure lung sterilization and may enable shorter tuberculosis treatment regimens. METHODS We randomly assigned adults who were given a diagnosis of rifampicin-susceptible pulmonary tuberculosis to a 6-month control regimen, a similar 4-month regimen of rifampicin at 1200 mg/d (study regimen 1 [SR1]), or a 4-month regimen of rifampicin at 1800 mg/d (study regimen 2 [SR2]). Sputum specimens were collected at regular intervals. The primary end point was a composite of treatment failure and relapse in participants who were sputum smear positive at baseline. The noninferiority margin was 8 percentage points. Using a sequence of ordered hypotheses, noninferiority of SR2 was tested first. RESULTS Between January 2017 and December 2020, 672 patients were enrolled in six countries, including 191 in the control group, 192 in the SR1 group, and 195 in the SR2 group. Noninferiority was not shown. Favorable responses rates were 93, 90, and 87% in the control, SR1, and SR2 groups, respectively, for a country-adjusted absolute risk difference of 6.3 percentage points (90% confidence interval, 1.1 to 11.5) comparing SR2 with the control group. The proportions of participants experiencing a grade 3 or 4 adverse event were 4.0, 4.5, and 4.4% in the control, SR1, and SR2 groups, respectively. CONCLUSIONS Four-month high-dose rifampicin regimens did not have dose-limiting toxicities or side effects but failed to meet noninferiority criteria compared with the standard 6-month control regimen for treatment of pulmonary tuberculosis. (Funded by the MRC/Wellcome Trust/DFID Joint Global Health Trials Scheme; ClinicalTrials.gov number, NCT02581527.

How to implement medical and patient associations in low‐income countries: A proposition from the African French Alliance for the Treatment of Haemophilia (AFATH)

International audienceIntroduction: There is a lack of joint recommendations by healthcare professionals (HCP) and patient organizations when a partnership between high and low-income countries in the field of haemophilia is planned.Aim: To draft recommendations to clarify the methodology when a partnership between low- and high-income countries is planned with the objective of a long-term implication. This methodology is to be implemented for fulfilling both medical and associative aims.Methods: Based on the available literature, a first document was written, then diffused to AFATH (Alliance Franco-Africaine pour le Traitement de l'Hémophilie) members, and after a one-day meeting and further amendments, a second draft was approved by all members before submission for publication.Results: Based on 6 years experience, several recommendations regarding the joint and separate roles of patient association and HCP for a first mission in French-speaking sub-Saharan African countries have been established. The proposed methodology for establishing preliminary contacts, the first visit and the key points for diagnostic action, medical follow-up, patient education and advocacy strategy outlines a model of partnership between patients and HCP.Conclusion: This paper written jointly by patients and physicians underlines the importance of reciprocal expert guidance and a partnership based on complementary inputs

Abstracts of the 1st International Colloquium in Mine & Society

This book presents the abstracts of the selected contributions to the First International Colloquium on Mines and Society (CIMS) organized by The Higher Institute of Mining and Geology of Boke. The theme of this colloquium was "Mining and Sustainable Development, a major challenge for an Emerging Africa" which aims to bring together teachers, researchers, and Professionals from different backgrounds in order to exchange the results of their research work, share their points of view on the issue of mining and sustainable development. It also aims to define, in a collaborative and inclusive manner, research prospects or future projects between all the actors involved in this field. Colloquium Title: 1st International Colloquium in Mine & SocietyTheme: Mining and Sustainable Development, A Major Challenge for an Emerging AfricaColloquium Date: 20-22 May 2022Colloquium Location: A L’Hôtel Rio Nunez de BokeColloquium Organizer: The Higher Institute of Mining and Geology of Bok