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

Moderate endurance exercise is not a risk for rhabdomyolysis or renal failure in sickle cell trait carriers

International audienceThis study tested the hypothesis that trained sickle cell trait (SCT) carriers are not subjected to greater risk of rhabdomyolysis or renal failure in response to moderate submaximal exercise than subjects with normal hemoglobin (CONT). Blood markers in 11 trained SCT carriers and 12 control counterparts were measured before and after 40 min of exercise at 55% of peak power output (Ppeak) conducted in thermoneutral environment. Body weights decreased with exercise in the same proportion in the two groups (from 65.1 ± 7.0 kg to 64.1 ± 7.0 kg and from 70.2 ± 6.6 to 68.6 ± 6.6 kg at the end of exercise in SCT and CONT, respectively). Heart rate and rectal temperature increased in the two groups in response to exercise, but the groups remained closely matched. Serum urea, CRP, CK and LDH were similar in the two groups and remained unchanged in response to exercise. Creatinine, Na + , K + , Cl − and myoglobin concentrations increased above baseline in response to exercise, with changes of the same magnitude in the two groups. In summary, the results of the present study suggest that moderate submaximal exercise is not unsafe from a biochemical point of view for sportsmen carrying SCT

Prévalence des dyslipidémies au laboratoire de biochimie du CHU Aristide le Dantec de Dakar, Sénégal

Introduction: l'objectif de cette étude était d'évaluer la prévalence des dyslipidémies chez les patients reçus au laboratoire de Biochimie de l'Hôpital Aristide Le Dantec pour le dosage d'un paramètre lipidique au cours de l'année 2013. Méthodes: il s'agit d'une étude rétrospective portant sur 1356 patients âgés de 10 à 94 ans reçus au laboratoire de Biochimie du CHU Le Dantec de janvier à décembre 2013. Etaient inclus dans l'étude, tous les patients ayant au moins un paramètre du bilan lipidique dont les résultats étaient enregistrés dans le registre du laboratoire. Le cholestérol total, le cholestérol HDL, le cholestérol LDL ainsi que les triglycérides ont été dosés grâce à des méthodes enzymatiques sur un automate de Biochimie de type Cobas Integra 400 (Roche Diagnostics). Résultats: la prévalence des dyslipidémies dans notre population d'étude est de 39,30%. Les prévalences de l'hypercholestérolémie, l'hypoHDLémie, l'hyperLDLémie, l'hypertriglycéridémie et l'hyperlipidémie mixte étaient respectivement : 30,89% ; 7,30% ; 31,19% ; 0,51% ; 7,22%. Les sujets de 40 à 59 ans semblaient être plus exposés et on note une prédominance féminine en ce qui concerne l'hypercholestérolémie (54,17% vs 45,82%), l'hypoHDLémie (54,54% vs45, 45%), et l'hyperlipidémie mixte (51,08% vs 48,97%). Enfin les dyslipidémies étaient fortement corrélées à l'HTA et l'obésité. Conclusion: la forte prévalence des dyslipidémies retrouvée dans notre étude démontre l'intérêt d'étudier la prévalence des facteurs de risque cardio-vasculaires en particulier les dyslipidémies dans la population sénégalaise.The Pan African Medical Journal 2016;2