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

Systèmes éducatifs, orientation et insertion professionnelle en Afrique francophone : quelles articulations à l'ère de la promotion de l'entrepreneuriat et du travail décent ?

Malgré la croissance démographique importante des pays africains et leur population jeune, ces pays parviennent difficilement à tirer pleinement profit de cet avantage en raison du manque d’opportunités d’emploi pour les jeunes. Les systèmes éducatifs sont également considérés comme inadaptés aux besoins du marché du travail. Cet ouvrage examine le système éducatif, l’orientation scolaire et professionnelle ainsi que leur contribution à l’insertion socioprofessionnelle des jeunes dans trois pays d’Afrique francophone (Burkina Faso, Cameroun et Togo), dans le contexte de la promotion de l’entrepreneuriat et du travail décent

Shared or divergent practices of safety integrity level allocation in the railway domain

Les conditions de conception et d'exploitation des systèmes ferroviaires au sein de l'U.E sont régies par des directives, des règlements et des décrets. Cependant, chaque état membre de l'U.E. a développé ses propres règles de sécurité en se basant sur ses propres concepts techniques et opérationnels et aboutissant, au final, à des pratiques divergentes entre états. L'allocation des SIL (Safety Integrity Level) utilisée afin de réduire le risque résiduel ne fait pas exception à ce constat. Le travail présenté résume les points faisant consensus et les points de divergence liés à cette allocation puis propose une méthodologie d'allocation homogène des SIL.In the E.U, safety railway system design and operational terms are governed by directives, regulations and decrees. However, based on its own technical and operational concepts, each state member of the E.U. has developed its own safety rules leading to divergent practices between states. Used to reduce residual risks, the SIL (Safety Integrity Level) concept has the same problem. This research work summarizes shared and divergent points related to the SIL allocation and proposes a homogeneous allocation methodology applied to SIL

Global climate change and vulnerability of African agriculture: implications for resilience and sustained productive capacity

Despite noticeable improvements in recent socio-economic performance in Africa, variations exist across countries and performance is constrained by plethora of factors that inhibit the attainment of Africa’s optimum production potential. Changing climate and environmental factors have contributed to increased transactions costs, lower productivity of factors of production, increased bottlenecks in the production process and investment challenges, especially for small and medium scale farmers in varying degrees across the continent. This paper reviews the impact of climate change on farming activities in Africa. Four countries across the continent are studied, viz. Burkina Faso, Egypt, Kenya and South Africa. We examine how long-term profitability of 4,000 farms vary with local climate, such as temperature and precipitation. To better ascertain the impact of climate variables, the marginal impacts of unit changes in temperatures and precipitation on crop farming activities are studied. Using selected climate scenarios, predictions are made on the extent to which projected climate changes will affect net revenues by the year 2050 and 2100. The findings suggest that climate affects agricultural returns in the four countries. The results further show that there is a non-linear relationship between temperature and crop revenue on the one hand and between precipitation and crop revenue on the other. Overall, the temperature elasticity suggests that global warming is harmful for agriculture across all the countries. These have profound implications for the policy requirements to address the productive capacity and resilience of the agricultural sector. Effort will be required to enhance adaptation at farm, regional and national levels. Policy adjustments will in addition require increased liberalization of the financial system and an implementation of agriculture civil service reforms for better performance of the extension service. This may have further implications for state budgeting and agriculture sector expenditures which will without doubt require new shifts

Atypie semiologique du sujet age : Une alteration de l'etat general d’origine tuberculeuse pulmonaire occasionnant une errance diagnostique et therapeutique

La tuberculose est fréquente chez le sujet âgé (SA) du fait de la baisse de l’immunité. La tuberculose surtout pulmonaire présente une atypie sémiologique d’emprunt cardiaque ou pulmonaire sur terrain  polypathologique en gériatrie. La persistance des symptômes malgré les traitements doit faire réviser les diagnostics. L’évolution est favorable en cas de traitement précoce pour éviter le risque de cachexie, de  grabatisation et de décès. Le théléthorax systématique associé à la bacilloscopie des crachats orientent le diagnostic. La thérapeutique est superposable à celle des sujets adultes en dehors d’une adaptation en fonction de la clairance rénale, hépatique, des pathologies et leurtraitement. Nous rapportons un cas de tuberculose pulmonaire chez une patiente de 85 ans évoluant depuis plus de deux ans justifiant la réalisation systématique du théléthorax pour orienter l’atypie sémiologique en gériatrie.Mots clés : Tuberculose pulmonaire, téléthorax, bacilloscopie, sujet âgé, Togo.  Semiologic atypia in elderly: general state alteration by pulmonary tuberculosis causing diagnostic and therapeutic difficultTuberculosis is common in dysimmune patients. In elderly patients, many factors depress immunity. Tuberculosis, especially pulmonary, presents a semiological atypia with signs of other diseases, especially cardiac and pulmonary in polypathological patients. The symptoms persistence despite different treatments should help to revise  diagnosis. Unfavourable events  occur without treatment such as cachexia, getting bedridden and finally death. Systematic Chest X-Ray associated to sputum microscopy must help to diagnosis. The treatment is generally same than for young patients, although adaptation to renal and hepatic function are necessary. Evolution is favourable if early treatment. We report a 85 years old case of pulmonary tuberculosis. This observation justifies the systematic chest radiography to diagnose tuberculosis in elderly.Keywords: Pulmonary tuberculosis, chest radiography, sputum bacteriology, elderly, Togo