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

A framework to improve fertilizer recommendations for irrigated rice in West Africa

A framework to optimize soil fertility management in irrigated rice, based on soil and climate variability, fertilizer and paddy prices and farmers' objectives is presented. The framework uses three models in succession. The dynamic ecophysiological ORYZAS model simulates potential rice yields under irrigation, based on weather conditions, cultivar choice and sowing date. This yield potential is used in the static FERRIZ model, together with site specific information on recovery efficiency of applied N, P and K, indigenous soil N, P and K supply, and maximum N, P and K accumulation and dilution in rice dry matter. Resulting outputs are required fertilizer doses to obtain different target yields depending on yield potential and soil nutrient supply. The framework allows sensitivity analysis and agro-economic evaluation of different fertilizer options. In a last step, the dynamic decision tool RIDEV is used to simulate optimal timing of different management actions such as fertilizer application, weeding, and harvest. Resulting integrated crop management recommendations ensure high resource use efficiency adapted to local socio-economic and bio-physical conditions. Provided necessary input data are available, this framework can be applied to field, perimeter or regional scale. The framework was applied to the Office du Niger in Mali, using field data of 58 farmers. In the wet season, fertilizer doses adjusted to three soil fertility classes out-performed current uniform recommendations only slightly, except on soils with very low K supply (10 cases). Only on these soils was application of K profitable. Profit-optimizing fertilizer doses had high costs and low value/cost ratios. Target yields close to potential yield increased farmers' risk. Adjusting fertilizer doses to the lower yield potential in the dry season reduced costs and risk without reducing profit, resulting in better value/cost ratios. New simple recommendations for both wet and dry seasons were formulated. (C) 2003 Elsevier Science Ltd. All rights reserved

Prise en charge de la maladie hémorroïdaire en milieu chirurgical à propos d’une série de 258 observations

La maladie hémorroïdaire constitue l'affection proctologique la plus fréquente. Son incidence dans la population est en constante augmentation et le changement de mode vie en est le facteur le plus déterminant. La prise en charge des hémorroïdes de grade III et IV nécessite presque toujours un traitement chirurgical et la procédure de Milligan Morgan est la plus pratiquée dans notre contexte. Il s'est agi d'une étude observationnelle, rétrospective, ayant colligé 258 patients opérés de maladie hémorroïdaire selon la procédure de Milligan Morgan. Notre série était composée de 191 hommes et 67 femmes soit un sex ratio de 3. L'âge moyen était de 36 ans, les extrêmes de 15 et 81 ans. Le motif de consultation le plus courant était la tuméfaction anale suivie des rectorragies et les gênes anales. Les hémorroïdes étaient de grade III chez 62 patients soit 24% et de grade IV chez 166 patients soit 64% des cas. Une anémie de degré variable était notée chez 14 patients. L'endoscopie ne retrouvait aucune lésion suspecte de néoplasie. Au plan thérapeutique, l'exérèse  des 3 paquets hémorroïdaires était réalisée systématiquement. Un quatrième paquet était enlevé chez 17 patients. Les suites post-opératoires étaient marquées par des douleurs intenses et mal soulagées durant la première semaine et la constipation chez 74% des patients avec une première selle souvent mal vécue. Des complications étaient notées dans 13 cas soit 5%. Un saignement persistant noté chez un patient (0,38%) avait nécessité une reprise chirurgicale. Une sténose anale notée chez une patiente (0,38%), avait nécessité des dilatations itératives avec une nette amélioration. L'incontinence au gaz chez 6 patients (2,32%) et aux selles chez 1 patient (0,38%), avait régressé après 2 mois de suivi environ. L'ulcère de stress noté chez un patient était traité médicalement. Aucune récidive n'était notée dans la série. La constipation constitue un facteur essentiel dans la genèse et l'aggravation des symptômes dela maladie hémorroïdaire. Danslesformes avancées comme fréquemment notées dans les services de chirurgie, l'exérèse chirurgicale par la procédure de Milligan Morgan assure des résultats satisfaisants. La morbidité post opératoire demeure cependant nonnégligeable et peut fortement être réduite par un suivi et un traitement spécifique Mots clés : proctologie, anus, hémorroïdes, constipation, Milligan Morgan. Hemorrhoids are the most frequent anal pathology. Its incidence in the population is on a steady rise and lifestyle changes are the most determining factor. The management of stage III and IV hemorrhoids is almost always surgical and the Milligan Morgan procedure is the most commonly performed in our context. This was a retrospective study on 258 patients with hemorrhoids who underwent surgery using the Milligan Morgan procedure. Our series consisted of 191 men and 67 women for a sex ratio of 3. The mean age was 36 years, ranging from 15 to 81 years. The most common presenting complaint was anal swelling followed by rectal pain and  anal discomfort. Hemorrhoids were stage III and IV in 62 (24%) and 166 (64%) patientsrespectively. Anemia of variable degrees was noted in 14 patients. Endoscopy found no apparent neoplastic lesions. Regarding treatment, excision of the 3 haemorrhoidal bundles was systematically performed. A fourth bundle excision was realised in 17 patients. The postoperative progress was marked by postoperative pain in the first week, constipation in 74% of patients with an extremely bad experience during the first bowel  movement.  Complications were noted in 13 cases (5%). Persistent bleeding, noted in one patient (0.38%),required a redo surgery.  Analstenosis noted in one patient (0.38%) was successfully managed with anal dilatations. Flatus and fecal incontinence in 6 (2.32%) and 1 (0.38%) patientsrespectively, reduced after about 2 months of followup. The stress ulcer noted in one patient was treated  medically. No recurrence was identified in the series. Constipation is an important risk factor in the onset and aggravation of the symptoms of hemorrhoids. In advanced stages as frequently noted in surgical units, excision by the Milligan Morgan procedure  produces satisfactory results. However, post-operative morbidity remains significant and can be greatly reduced by specific follow-up and treatment. Keywords: proctology, anus, hemorrhoids, constipation, Milligan Morgan

Critical Limit of Extractable Phosphorous in a Gleysol for Rice Production in the Senegal River Valley of West Africa

Soil-test correlation and calibration, a useful tool for fertilizer recommendations, has been little used in West Africa. Soils from a long-term fertility experiment have been used to study the relationship between rice yields and soil extractable phosphorus (P) with Bray 1 and Olsen methods. The Cate and Nelson graphical method was used for critical limits of soil P determination. The critical limits of soil extractable P at 95% relative grain yield were 9 mg P for the Bray 1P and 17 mg P kg21 for Olsen P. The Olsen P was more correlated (r ¼ 0.63) with rice grain yields than Bray P (r ¼ 0.50), but a strong correlation (r ¼ 0.92) was also observed between the values of the two methods. Results indicate that at levels less than these critical levels of extractable P, P fertilizers should be applied to increase rice yields

New clustering of the spikes morphology based on dynamic clouds in partial epilepsy

International audienceThe acquisition of EEG signals can be done during days. In this paper, the signals of depth Stereo-Electroencephalography (SEEG) are used. In SEEG signal, several inter-ictal paroxystic events (IPE) are found, they appear between the crises. To analyze their distribution, they should initially be detected by separating them from the basic activity. After the detection step, we implement a clustering process to distinguish IPE or spike according to their morphology. Results of detection and clustering would characterize a link between space-time distribution of IPE and the arrival of the crises. It would be thus a contribution on the diagnosis of the partial epilepsies. © 2016 IEEE

Classification model of spikes morphology using principal components analysis in drug-resistant epilepsy

International audienceEpilepsy is one of the diseases that are more subject to consultation in neurological clinics. To help neurologists to accurately diagnose this disease, several technological tools have been developed. Electroencephalography (EEG) of scalp or deep is a signal acquisition tool from electrical discharges of the brain areas. These signals are often accompanied by transient events commonly called interictal paroxystic events (IPE) or spikes of short durations. Analysis of these IPE could help with the diagnosis of drug-resistant epilepsy. With this intention, we will first of all seek to detect IPE, by separating them from the basic activity of signal EEG. In this paper, we propose spike detection method based on Smoothed Nonlinear Energy Operator (SNEO) using adaptive threshold. Then we will implement a new approach using principal components analysis (PCA) before classification to separate the events detected according to their morphologies. The objective in the long term is to characterize their space-time distribution over all the duration of the EEG signal. ©ICST Institute for Computer Sciences, Social Informatics and Telecommunications Engineering 2018

Bilateral Spermatocyte Seminoma: A Case Report

Spermatocyte seminoma is rare pathologic presentation of testicular cancer. We report a case of bilateral testicular seminoma in an 18-year-old man with thoracolumbar metastases. He presented with large, bilateral painless scrotal masses with a normal appearance of the scrotal skin. He also had thoracolumbar gibbus, and flaccid paraplegia that has been evolving for a month. Bilateral orchiectomy was performed but the patient died before adjuvant treatment