La commercialisation de la viande bovine au Sénégal

Ce document décrit les différents stades actuels de la commercialisation de la viande bovine au Sénégal. Après en avoir analysé les insuffisances à tous les niveaux, il propose les améliorations à entreprendre et la fixation de nouveaux prix de la viande. Des statistiques concernant l'évolution des abattages et celle de la consommation de viande bovine sont jointes en annex

A Comparison of Methods for Poverty Estimation in Developing Countries

Small area estimation is a widely used indirect estimation technique for micro-level geographic profiling. Three unit level small area estimation techniques-the ELL or World Bank method, empirical best prediction (EBP) and M-quantile (MQ) - can estimate micro-level Foster, Greer, & Thorbecke (FGT) indicators: poverty incidence, gap and severity using both unit level survey and census data. However, they use different assumptions. The effects of using model-based unit level census data reconstructed from cross-tabulations and having no cluster level contextual variables for models are discussed, as are effects of small area and cluster level heterogeneity. A simulation-based comparison of ELL, EBP and MQ uses a model-based reconstruction of 2000/2001 data from Bangladesh and compares bias and mean square error. A three-level ELL method is applied for comparison with the standard two-level ELL that lacks a small area level component. An important finding is that the larger number of small areas for which ELL has been able to produce sufficiently accurate estimates in comparison with EBP and MQ has been driven more by the type of census data available or utilised than by the model per se

Report on biological and ecological data in FFDB pilot version 1

Task 2.3 of work package 2 (Advancing biological knowledge and evaluation of current stock assessment models) focuses on the compilation of biological, ecological and fisheries dependent and fisheries independent data that is required for other FarFish WPs. During the first year of FarFish, some modifications in the objectives occurred, resulting in changes in the species. For example, in the Cape Verde and Seychelles CSs, the focus is now on by-catch species that are not assessed by the Regional Management Fisheries Organizations (RMFO): the International Commission for the Conservation of Atlantic Tunas (ICCAT) and the Indian Ocean Tuna Commission (IOTC). Lists of species for each CS have now been drawn up, sources of data identified, contacts have been made with RMFOs and DG MARE, and data is being compiled. Data compilation has been largely driven by the FarFish Data Base (FFDB) template developed in WP 6 (see deliverables D6.1 and D6.4). On the other hand, other data required for visualization purposes, especially time series, is also being compiled or requested. A formal data request is being prepared for DG MARE, while coastal state CS participants will be requested to provide data for the FFDB. Talks are also ongoing with RFMOs, especially CECAF, regarding data acquisition and how FarFish can contribute or add value to assessment and management. Actions that need to be taken by Task 2.3 participants include the provision of data and uploading of data to the FFDB. Task 2.3 is ongoing (Report on biological and ecological data in FFDB pilot version 2, due in Month 26 (July 31, 2019)

Autoantibodies against type I IFNs in patients with life-threatening COVID-19

Interindividual clinical variability in the course of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is vast. We report that at least 101 of 987 patients with life-threatening coronavirus disease 2019 (COVID-19) pneumonia had neutralizing immunoglobulin G (IgG) autoantibodies (auto-Abs) against interferon-w (IFN-w) (13 patients), against the 13 types of IFN-a (36), or against both (52) at the onset of critical disease; a few also had auto-Abs against the other three type I IFNs. The auto-Abs neutralize the ability of the corresponding type I IFNs to block SARS-CoV-2 infection in vitro. These auto-Abs were not found in 663 individuals with asymptomatic or mild SARS-CoV-2 infection and were present in only 4 of 1227 healthy individuals. Patients with auto-Abs were aged 25 to 87 years and 95 of the 101 were men. A B cell autoimmune phenocopy of inborn errors of type I IFN immunity accounts for life-threatening COVID-19 pneumonia in at least 2.6% of women and 12.5% of men

GloPID-R report on chikungunya, o'nyong-nyong and Mayaro virus, part 2: Epidemiological distribution of o'nyong-nyong virus

The GloPID-R (Global Research Collaboration for Infectious Disease Preparedness) chikungunya (CHIKV), o'nyong-nyong (ONNV) and Mayaro virus (MAYV) Working Group has been established to identify gaps of knowledge about the natural history, epidemiology and medical management of infection by these viruses, and to provide adapted recommendations for future investigations. Here, we present a report dedicated to ONNV epidemiological distribution. Two large-scale ONNV outbreaks have been identified in Africa in the last 60 years, interspersed with sporadic serosurveys and case reports of returning travelers. The assessment of the real scale of ONNV circulation in Africa remains a difficult task and surveillance studies are necessary to fill this gap. The identification of ONNV etiology is made complicated by the absence of multiplex tools in co-circulati

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

Global, regional, national, and selected subnational levels of stillbirths, neonatal, infant, and under-5 mortality, 1980�2015: a systematic analysis for the Global Burden of Disease Study 2015

Background Established in 2000, Millennium Development Goal 4 (MDG4) catalysed extraordinary political, financial, and social commitments to reduce under-5 mortality by two-thirds between 1990 and 2015. At the country level, the pace of progress in improving child survival has varied markedly, highlighting a crucial need to further examine potential drivers of accelerated or slowed decreases in child mortality. The Global Burden of Disease 2015 Study (GBD 2015) provides an analytical framework to comprehensively assess these trends for under-5 mortality, age-specific and cause-specific mortality among children under 5 years, and stillbirths by geography over time. Methods Drawing from analytical approaches developed and refined in previous iterations of the GBD study, we generated updated estimates of child mortality by age group (neonatal, post-neonatal, ages 1�4 years, and under 5) for 195 countries and territories and selected subnational geographies, from 1980�2015. We also estimated numbers and rates of stillbirths for these geographies and years. Gaussian process regression with data source adjustments for sampling and non-sampling bias was applied to synthesise input data for under-5 mortality for each geography. Age-specific mortality estimates were generated through a two-stage age�sex splitting process, and stillbirth estimates were produced with a mixed-effects model, which accounted for variable stillbirth definitions and data source-specific biases. For GBD 2015, we did a series of novel analyses to systematically quantify the drivers of trends in child mortality across geographies. First, we assessed observed and expected levels and annualised rates of decrease for under-5 mortality and stillbirths as they related to the Soci-demographic Index (SDI). Second, we examined the ratio of recorded and expected levels of child mortality, on the basis of SDI, across geographies, as well as differences in recorded and expected annualised rates of change for under-5 mortality. Third, we analysed levels and cause compositions of under-5 mortality, across time and geographies, as they related to rising SDI. Finally, we decomposed the changes in under-5 mortality to changes in SDI at the global level, as well as changes in leading causes of under-5 deaths for countries and territories. We documented each step of the GBD 2015 child mortality estimation process, as well as data sources, in accordance with the Guidelines for Accurate and Transparent Health Estimates Reporting (GATHER). Findings Globally, 5·8 million (95 uncertainty interval UI 5·7�6·0) children younger than 5 years died in 2015, representing a 52·0% (95% UI 50·7�53·3) decrease in the number of under-5 deaths since 1990. Neonatal deaths and stillbirths fell at a slower pace since 1990, decreasing by 42·4% (41·3�43·6) to 2·6 million (2·6�2·7) neonatal deaths and 47·0% (35·1�57·0) to 2·1 million (1·8-2·5) stillbirths in 2015. Between 1990 and 2015, global under-5 mortality decreased at an annualised rate of decrease of 3·0% (2·6�3·3), falling short of the 4·4% annualised rate of decrease required to achieve MDG4. During this time, 58 countries met or exceeded the pace of progress required to meet MDG4. Between 2000, the year MDG4 was formally enacted, and 2015, 28 additional countries that did not achieve the 4·4% rate of decrease from 1990 met the MDG4 pace of decrease. However, absolute levels of under-5 mortality remained high in many countries, with 11 countries still recording rates exceeding 100 per 1000 livebirths in 2015. Marked decreases in under-5 deaths due to a number of communicable diseases, including lower respiratory infections, diarrhoeal diseases, measles, and malaria, accounted for much of the progress in lowering overall under-5 mortality in low-income countries. Compared with gains achieved for infectious diseases and nutritional deficiencies, the persisting toll of neonatal conditions and congenital anomalies on child survival became evident, especially in low-income and low-middle-income countries. We found sizeable heterogeneities in comparing observed and expected rates of under-5 mortality, as well as differences in observed and expected rates of change for under-5 mortality. At the global level, we recorded a divergence in observed and expected levels of under-5 mortality starting in 2000, with the observed trend falling much faster than what was expected based on SDI through 2015. Between 2000 and 2015, the world recorded 10·3 million fewer under-5 deaths than expected on the basis of improving SDI alone. Interpretation Gains in child survival have been large, widespread, and in many places in the world, faster than what was anticipated based on improving levels of development. Yet some countries, particularly in sub-Saharan Africa, still had high rates of under-5 mortality in 2015. Unless these countries are able to accelerate reductions in child deaths at an extraordinary pace, their achievement of proposed SDG targets is unlikely. Improving the evidence base on drivers that might hasten the pace of progress for child survival, ranging from cost-effective intervention packages to innovative financing mechanisms, is vital to charting the pathways for ultimately ending preventable child deaths by 2030. Funding Bill & Melinda Gates Foundation. © 2016 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY license

Antimicrobial susceptibility profile of community-acquired urinary tract infection in adults: A seven months prospective cross-sectional study in Dakar Town, Senegal

Introduction: With the increasing trend of antibiotic resistance, the management of urinary tract infection (UTI) is likely to become complicated, and there is a need for continuous surveillance of antibiotic susceptibility of uropathogens.Objective: This study aimed to assess the current antimicrobial susceptibility pattern in the common uropathogens isolated from outpatients and hospitalized (<72 h).Subjects and methods: This was a prospective observational study examining urinary isolates from patients aged ≥18 years. Urine samples were collected from 494 consecutive outpatient adults, clinically-suspected cases of urinary tract infections. Bacterial identification and antimicrobial susceptibility testing were carried out using the VITEK® 2 Compact kit of bioMérieux.Results: The observed prevalence of UTI was (132/494) 26.7%, 95% CI [22.9%; 30.9%]. Among the 147 organisms isolated from 132 patients, more than 90% (133) were Gram-negative bacteria. Imipenem appeared as the most active drug, with less than 3% resistance of isolates. Amikacin and cefotaxim were in general active with susceptibility rate of 70% and 67% of isolates, respectively. However cefixim was the most active oral drug tested (61%). Trimethoprim /sulfamethoxazole, nalidixic acid and fluoroquinolons were the less active drug displaying a resistance rate of 73%, 69% and 60% respectively.Conclusion: Trimethoprim/sulfamethoxazole, nalidixic acid and fluoroquinolons should no longer be used as empirical treatments of UTI in Dakar. Alternatives must be recommended, such as cefixim the most active oral drugs available in this country.Keywords: Urinary tract infections; Antibiotic susceptibility; Community-acquired infections; Developing countr