A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

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

Strengthening psychosocial support and emergency response in Senegal : lessons from a tragic traffic accident: Strengthening Psychosocial Support and Emergency Response in Senegal: Lessons from a Tragic Traffic Accident

International audienceOn January 8, 2023, Senegal experienced a tragic traffic accident that claimed the lives of 42 people and left approximately 100 injured. During such events, the victims, their families, the first responders to arrive on the scene and the frontline personnel must benefit from medical and psychological care. Promptly, the Emergency Health Operations Center (EOC) acted, activating the Kaolack mobile psycho-social intervention and Support Team in addition to deploying mental health professionals in Kaffrine. On-site in Kaffrine, a medical-psychological emergency cell was established. This cell efficiently organized immediate and post-immediate care, offering individual and group counseling sessions tailored to the specific needs of each person affected. Approximately sixty direct or indirect victims received psychological assistance. Beyond the challenges inherent in managing such events and considering their increasing occurrence in our country, a vital lesson emerged-the necessity of formalizing Mobile Intervention and Psychosocial Support Teams in every region for the effective management of medical-psychological emergencies.Cet article rend compte du processus de création d’un dispositif d’urgence innovant au Sénégal, l’Équipe mobile d’intervention et de soutien psychosocial, en rappelant comment au début des années 2000 une tragédie bouleverse le pays et amorce la réflexion sur le suivi psychosocial dans un contexte politique assujetti à l’idiome de la résilience. La création de l’EMIS semble paradoxale, puisqu’elle requiert et valorise des compétences en psychologie et en psychiatrie qui en temps ordinaire sont peu soutenues par les politiques sociales et de santé

Investigation of the Potential of Energy Recovery from Poultry Droppings in a Semi-Industrial Farm in the Sangalkam, Senegal

The poultry sector has grown significantly in the recent years. Certainly, the rise in the global population, particularly in developing nations, has prompted the expansion of the poultry farm sector to fulfill the growing demand for food. The activity produces organic waste and the management of which can pose problems in the farms. Poultry farming requires energy for the production processes. It is in this context this study aims to examine the energy potential of poultry waste depending where it came from (factory farm or domestic farm). The methanogenic potential of these wastes was determined using the Biochemical Methane Potential (BMP) test on poultry droppings from factory farms or domestic farms and other wastes as controls, such as cow and horse dung. The tests showed that the poultry droppings from factory farms had higher gas content and methane (CH4) than the controls. The link between biogas production and the chemical composition of the poultry droppings, was also demonstrated. These findings suggested that poultry droppings from factory farms can be used to produce biogas and/or energy. The latter can be reused for the needs of the farm itself

Methanogenic and fertilizing potential of aquaculture waste: towards freshwater farms energy self‐sufficiency in the framework of blue growth

International audienceThe fisheries sector, particularly aquaculture, is a fundamental source of nutrition for humans, particularly in developing countries. The modern development of fish farming requires energy for production systems. This study investigates the potential of using organic wastes derived from fish fattening to produce on-farm energy through the process of methanization. Oreochromis niloticus faeces methanogen potential was determined with (IFF) and without (UIFF) methanizer microbial inoculum. At the end of the manure methanation trials, the resulting digestates were tested as organic fertilizers for agriculture. The tests showed that inoculated fish faeces had faster biogas kinetics production compared with uninoculated fish faeces. In both cases, the produced biogas contained more than 60% methane (CH4) from the second week of incubation, indicating that it was of good quality. Furthermore, the total CH4 volume was twice as larger in IFF compared with UIFF. Biofertilizer tests showed no significant differences for most of the growth parameters in onion and tomato when compared to the unfertilized control, except in one case for tomato plants, which significantly increased its aboveground biomass. The results show that fish faeces are good methanogenic substrates conducive to energy recovery that could facilitate farm autonomy; however, valorization of the digestates as biofertilizer still requires extensive agronomic optimization. Based on our results, we estimate that equivalents of energy need of almost ten millions of people could be covered using the aquaculture potential in freshwater fish faeces biogas worldwide or that at least aquaculture farm energy self-sufficiency could be fostered

The use of green macroalgae (<em>Ulva lactuca</em> and <em>Codium tomentosum</em>) that have a high methane potential, as a source of biogas in Senegal

International audienceAnaerobic digestion is a biochemical process that occurs naturally in the absence of oxygen. It is used commonly in developing countries to produce both energy and biofertilizers. Objective: The purpose of this work was to study the anaerobic digestion of green macroalgae (Ulva lactuca and Codium tomentosum), which cause severe environmental problems in Dakar-Senegal, and elsewhere along Africa's Atlantic coast. Methodology and Results: These green macroalgae were characterized in terms of physicochemical properties and biochemical methane potential (BMP). Their characteristics were compared to those of other locally available feedstock, such as cow manure and Jatropha curcas cake. The results showed that volatile solids of macroalgae were about 500 g VS/kg and twice that of cow manure. Furthermore, the methane potential of macroalgae was twice (216.4 L CH4/kg VS) that of cow manure (100.3 L CH4/kg VS). The green macroalgae achieved a heating value potential of 2151 kWh/t VS. The methane potential of Jatropha cake as a substrate for anaerobic digestion was intermediate (133.6 L CH4/kg VS) but contained a large quantity of lignin (34%), a slowly biodegradable organic substance. Conclusions and application of findings: This study results showed that green macroalgae could be used as a substrate for the production of renewable energy the biogas in Senegal

The use of green macroalgae (Ulva lactuca and Codium tomentosum) that have a high methane potential, as a source of biogas in Senegal

Anaerobic digestion is a biochemical process that occurs naturally in the  absence of oxygen. It is used commonly in developing countries to produce both energy and biofertilizers.Objective: The purpose of this work was to study the anaerobic digestion of green macroalgae (Ulva lactuca and Codium tomentosum), which cause severe environmental problems in Dakar-Senegal, and elsewherealong Africa's Atlantic coast.Methodology and Results: These green macroalgae were characterized in terms of physicochemical properties and biochemical methane potential (BMP). Their characteristics were compared to those of other locally available feedstock, such as cow manure and Jatropha curcas cake. The results showed that volatile solids of macroalgae were about 500 g VS/kg and twice that of cow manure. Furthermore, the methane potential ofmacroalgae was twice (216.4 L CH4/kg VS) that of cow manure (100.3 L CH4/kg VS). The green macroalgae achieved a heating value potential of 2151 kWh/t VS. The methane potential of Jatropha cake as a substrate foranaerobic digestion was intermediate (133.6 L CH4/kg VS) but contained a large quantity of lignin (34%), a slowly biodegradable organic substance.Conclusions and application of findings: This study results showed that green macroalgae could be used as a substrate for the production of renewable energy the biogas in Senegal.Keywords: Biogas, renewable energy, biochemical methane potential, macroalgae, Jatropha curcas

Characteristics of HIV-2 and HIV-1/HIV-2 Dually Seropositive Adults in West Africa Presenting for Care and Antiretroviral Therapy: The IeDEA-West Africa HIV-2 Cohort Study.

HIV-2 is endemic in West Africa. There is a lack of evidence-based guidelines on the diagnosis, management and antiretroviral therapy (ART) for HIV-2 or HIV-1/HIV-2 dual infections. Because of these issues, we designed a West African collaborative cohort for HIV-2 infection within the framework of the International epidemiological Databases to Evaluate AIDS (IeDEA).We collected data on all HIV-2 and HIV-1/HIV-2 dually seropositive patients (both ARV-naive and starting ART) and followed-up in clinical centres in the IeDEA-WA network including a total of 13 clinics in five countries: Benin, Burkina-Faso Côte d'Ivoire, Mali, and Senegal, in the West Africa region.Data was merged for 1,754 patients (56% female), including 1,021 HIV-2 infected patients (551 on ART) and 733 dually seropositive for both HIV-1 and HIV 2 (463 on ART). At ART initiation, the median age of HIV-2 patients was 45.3 years, IQR: (38.3-51.7) and 42.4 years, IQR (37.0-47.3) for dually seropositive patients (p = 0.048). Overall, 16.7% of HIV-2 patients on ART had an advanced clinical stage (WHO IV or CDC-C). The median CD4 count at the ART initiation is 166 cells/mm(3), IQR (83-247) among HIV-2 infected patients and 146 cells/mm(3), IQR (55-249) among dually seropositive patients. Overall, in ART-treated patients, the CD4 count increased 126 cells/mm(3) after 24 months on ART for HIV-2 patients and 169 cells/mm(3) for dually seropositive patients. Of 551 HIV-2 patients on ART, 5.8% died and 10.2% were lost to follow-up during the median time on ART of 2.4 years, IQR (0.7-4.3).This large multi-country study of HIV-2 and HIV-1/HIV-2 dual infection in West Africa suggests that routine clinical care is less than optimal and that management and treatment of HIV-2 could be further informed by ongoing studies and randomized clinical trials in this population