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

Epidémiologie de l’infection chez les brûles hospitalises à l’unité des brûlés de l’hôpital Militaire d’instruction Mohamed V de Rabat

Objectif : déterminer le profil bactériologique des patients de l’unité des brûlés de l’hôpital Militaire de Rabat et décrire la sensibilité aux antibiotiques des bactéries prédominantes issues des plaies. Matériel et méthode : l’étude prospective comprise entre juillet 2009 et mars 2011 a été menée à l’hôpital militaire de Rabat, au sein du laboratoire de bactériologie en collaboration avec l’unité des brûlés. Un questionnaire récoltant les données relatives au patient a été rempli à l’admission du brûlé. Les prélèvements bactériologiques ont été réalisés à l’admission du patient et à chaque changement de pansement. L’identification des bactéries s’est faite en se basant sur les caractères culturo-morphologiques et biochimiques. La sensibilité aux antibiotiques a été déterminée par méthode de diffusion sur milieu gélosé en suivant les recommandations de la société française de microbiologie. L’étude statistique s’est faite à l’aide du logiciel SPSS version 13 (Statistical Package for the Social Sciences). Résultat : 58 patients ont été inclus dans l’étude. L’âge moyen de la population a été de 38,2 ± 15,5 ans avec un taux de létalité par brûlure de 13,8% et une prévalence d’infection de 43,1%. Sur les 112 prélèvements réalisés, 126 souches bactériennes non redondantes ont été identifiées avec la prédominance d’Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumoniae, Entérobacter cloacae et staphylocoque. Lorsque les résultats sont rapportés au nombre de semaines après la brûlure, les staphylocoques sont les germes les plus isolés durant la première semaine d’admission pour les prélèvements de pus superficiel alors que pour ceux d’hémocultures ce sont les A.baumannii qui dominent. Conclusion : une vigilance avec une application rigoureuse des mesures d’hygiène et une surveillance épidémiologique des bactéries sont nécessaires, à l’échelle de l’unité des brûlés et de l’hôpital, pour mieux guider l’antibiothérapie probabiliste

Determinants associated with low dietary diversity among migrants to Morocco: a cross sectional study

Abstract Low dietary diversity (LDD) is prevalent among vulnerable populations, posing a morbidity risk. Few studies have been conducted on the dietary diversity of migrants. The objectives of this study are to determine the prevalence of LDD among migrants in Morocco and the risk factors associated with it. In the Oriental region, we conducted a cross-sectional study with migrants between November and December 2021. The sampling method used was convenience sampling. A face-to-face, structured questionnaire was used to collect sociodemographic, behavioral, and clinical data. We calculated a dietary diversity score based on a 24-h food recall and assessed food intake. The risk factors associated with LDD were identified using multivariate logistic regression. A total of 445 migrants was enrolled. The prevalence of LDD was 31.7%. Risk factors associated with LDD were: being homeless (adjusted Odds Ratio (AOR) of 6.32; CI% [3.55–11.25]), a lack of social support (AOR of 2.30; CI% [1.33–03.98]), and low monthly income (AOR of 8.21; CI% [3.39–19.85]). Public policies must focus on social and environmental determinants. Nutrition training programs should be set up for the migrant population

Prevalence of uncontrolled blood pressure in Meknes, Morocco, and its associated risk factors in 2017.

BackgroundUncontrolled high blood pressure (UBP) can lead to various cardiovascular complications causing an estimated nine million deaths per year worldwide. In Meknes, epidemiologic data on UBP are scarce, depriving programs from evidence-based information that would allow a better management of hypertension. Hence, we aimed to assess UBP prevalence in hypertensive patients treated in Meknes and identify UBP-associated risk factors.MethodsBetween November and December 2017, we conducted a cross-sectional study enrolling 922 hypertensive patients managed at Meknes's primary health care facilities using the multistage sampling method. We interviewed patients face to face to collect their socio-demographic-characteristics, lifestyle behaviours, clinical parameters and the triad care system-patient-physician. Another questionnaire was self-administered by physicians to characterize therapeutic inertia. A multivariate logistic regression analysis highlighted the risk factors associated with UBP.ResultsUBP prevalence was 73% with a mean age of 61±11 years (mean±standard deviation) and a male/female ratio of 1/3. Risk factors associated with UBP were: therapeutic inertia (adjusted odds ratio to other variables (AOR) = 18.2, 95% CI [8.35-39.84]), drug non-adherence (AOR = 1.8, 95% CI [1.07-3.04]), obesity/overweight (AOR = 1.6, 95% CI [1.03-2.58]), unemployment (AOR = 1.9, 95% CI [1.09-3.01]), low income (AOR = 2.6, 95% CI [1.01-6.86]), family history of hypertension (AOR = 1.5, 95% CI [1.07-2.08]) and male sex (AOR = 1.6, 95% CI [1.04-2.58]).ConclusionUBP prevalence is high in Meknes. Prevention should firstly focus on raised awareness of hypertensive patients' self-care management. Secondly, health professionals should better comply to the guidelines of anti-hypertensive treatments. Lastly, health professionals should frequently be reminded to reach therapeutic goals to overcome therapeutic inertia

Self-reported depression and its risk factors among hypertensive patients, Morocco: a cross-sectional study

Abstract Hypertensive patients are at an elevated risk of developing mental diseases such as depression, which can impair their quality of life. The purpose of this study is to measure the prevalence of self-reported depression among hypertensive patients treated at primary health care facilities in Marrakech. Between May 2021 and December 2022, a cross-sectional study of 1053 hypertensive patients attending primary health care facilities in Marrakech was conducted. A face-to-face questionnaire was used to collect socio-demographic, behavioral, and clinical data, as well as hypertension treatment characteristics and the care-patient-physician triad. The Patient Health Questionnaire-9 was used to assess self-reported depression. To identify self-reported depression risk factors, multivariate logistic regression was used. Depressive symptoms were reported by 56.1% of hypertensive patients. The patients' average age was 63.2 ± 9.5 years, and 508 (85.9%) were female. Female sex, stress, a low-salt diet, pain and physical discomfort, an urban living environment, a lack of self-monitoring of hypertension, an unsatisfactory relationship with the healthcare system, a family history of hypertension, and the perception of adverse effects of the antihypertensive drug were all associated with self-reported depression. Self-reported depression is prevalent among hypertensive patients in Marrakech. The mental health component should be emphasized while addressing hypertensive patients in primary health care facilities