ABSTRACT
Africa faces both a disproportionate burden of infectious diseases coupled with unmet needs in bioinformatics and data science capabilities which impacts the ability of African biomedical researchers to vigorously pursue research and partner with institutions in other countries. The African Centers of Excellence in Bioinformatics and Data Intensive Science are collaborating with African academic institutions, industry partners, the Foundation for the National Institutes of Health (FNIH) and the National Institute of Allergy and Infectious Diseases (NIAID) at the National Institutes of Health (NIH) in a public-private partnership to address these challenges through enhancing computational infrastructure, fostering the development of advanced bioinformatics and data science skills among local researchers and students and providing innovative emerging technologies for infectious diseases research.
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Introduction: While real-time reverse transcription PCR (RT-PCR) is the recommended laboratory method to diagnose severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) infection, its use in resource limited settings can be difficult to maintain due to high testing demand and shortage of reagents. The aim of this study was to evaluate the performances of Realy Tech™ and Standard Q™ in comparison to RT-PCR in a relatively low COVID-19 prevalence setting, Mali. Methods: We conducted a cross-sectional study between January and April 2021 in Bamako and Kati regions to evaluate both rapid tests during a large SARS-CoV-2 prevalence study in Mali. Results: Of the 390 samples tested, the sensitivity and specificity of Realy Tech™ and Standard Q™ were 57.1% (95%CI: 44.1-69.2), 95.8% (95%CI: 93.1-97.5); 61.9% (95%CI: 46.8-75.0), and 94.1% (95%CI: 89.5-96.8) respectively. Using RT-PCR, the global prevalence of SARS-CoV-2 was 14.4% (56/390). In both rapid antigen tests, the performance was better when used in suspected patients compared to positive patients under treatment. Moreover, higher viral loads equivalent to Ct < 25 were associated with better detection rates. Conclusion: While waiting for more complete data, these preliminary studies suggest that Realy Tech™ and Standard Q™ should not be used alone for COVID-19 diagnosis in Mali.
Subject(s)
COVID-19 , SARS-CoV-2 , Sensitivity and Specificity , Humans , Mali/epidemiology , COVID-19/diagnosis , COVID-19/epidemiology , Cross-Sectional Studies , SARS-CoV-2/isolation & purification , COVID-19 Serological Testing/methods , Antigens, Viral/analysis , Female , Male , Adult , COVID-19 Nucleic Acid Testing/methods , Prevalence , Real-Time Polymerase Chain Reaction , COVID-19 Testing/methods , Resource-Limited SettingsABSTRACT
Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks. One-Sentence SummaryExpanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.
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The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, 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 following 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 breeding ground for new variants.
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Background: The diagnosis of tuberculosis (TB) has mostly been relied on a long-used method called sputum smear microscopy. In 2010, Xpert MTB/RIF assay was approved by the World Health Organization for simultaneous TB diagnosis and detection of resistance. Our current study was undertaken to compare the diagnostic performance of Xpert MTB/RIF assay to auramine staining-based light-emitting diode-Fluorescence Microscopy (LED-FM) considering culture as the gold standard method for pulmonary and extrapulmonary TB. Method: Pulmonary and extrapulmonary specimens of suspected TB patients were examined in this study. From January 2016 to June 2019, sputum, urine, superficial swabs, gastric aspirates, and pleural infusion specimens were collected from new and previously treated TB individuals. Specimens were examined using Xpert MTB/RIF, LED-FM, and Mycobacterium culture techniques to evaluate their performance. Results: A total of 697 suspected TB samples were included in this analysis, and of these, 469 (67.29%) were positive for all three used methods. The overall sensitivities, specificities, and positive and negative predictive values were 99.6%, 62.0%, 88.4%, and 98.2% for Xpert MTB/RIF and 88.0%, 95.6%, 99.0%, and 60.7% for LED-FM, respectively, compared to culture method. Conclusion: The sensitivity of Xpert MTB/RIF assay was observed to be higher than the LED-FM method, thus suggesting this molecular technique as a promising tool for the diagnosis of pulmonary and extrapulmonary TB, which will help in the management of TB infections in developing countries such as Mali.
Subject(s)
Mycobacterium tuberculosis , Tuberculosis, Pulmonary , Humans , Mali , Microscopy, Fluorescence , Rifampin , Sensitivity and Specificity , Sputum , TuberculosisABSTRACT
INTRODUCTION: Côte d'Ivoire's status as a polio-free country requires high quality surveillance of acute flaccid paralysis. Our study aims to determine the prevalence of non-poliovirus enteroviruses found in the surveillance of Acute Flaccid Paralysis (AFP) in Côte d'Ivoire and to study their distribution according to individual characteristics and associated factors. METHOD: We conducted an exhaustive descriptive and analytical cross-sectional retrospective study on 3597 cases of acute flaccid paralysis notified in the context of surveillance of AFP from 2007 to 2016 in Côte d'Ivoire. RESULTS: The mean annual rate of non-poliovirus enterovirus over the period was 11.3% over the study period with extremes of 9.2% and 15.9%. The absence of fever at the onset of illness and early age were factors associated with the occurrence of acute flaccid paralysis due to non-poliovirus enterovirus. CONCLUSION: Our study found a downward trend in non-poliovirus enteroviruses detected in AFP surveillance in Côte d'Ivoire, and identified the absence of fever and the age of the subject as being the factors associated with their occurrence. It is therefore necessary to type all cases of non-poliovirus enteroviruses detected in AFP surveillance to assess the risks of vaccine-derived polioviruses.
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INTRODUCTION: Côte d'Ivoire's status as a polio-free country requires high quality surveillance of acute flaccid paralysis. Our study aims to determine the prevalence of non-poliovirus enteroviruses found in the surveillance of Acute Flaccid Paralysis (AFP) in Côte d'Ivoire and to study their distribution according to individual characteristics and associated factors. METHOD: We conducted an exhaustive descriptive and analytical cross-sectional retrospective study on 3597 cases of acute flaccid paralysis notified in the context of surveillance of AFP from 2007 to 2016 in Côte d'Ivoire. RESULTS: The mean annual rate of non-poliovirus enterovirus over the period was 11.3% over the study period with extremes of 9.2% and 15.9%. The absence of fever at the onset of illness and early age were factors associated with the occurrence of acute flaccid paralysis due to non-poliovirus enterovirus. CONCLUSION: Our study found a downward trend in non-poliovirus enteroviruses detected in AFP surveillance in Côte d'Ivoire, and identified the absence of fever and the age of the subject as being the factors associated with their occurrence. It is therefore necessary to type all cases of non-poliovirus enteroviruses detected in AFP surveillance to assess the risks of vaccine-derived polioviruses.
Subject(s)
Enterovirus Infections/diagnosis , Enterovirus/isolation & purification , Paralysis/epidemiology , Poliomyelitis/epidemiology , Poliovirus , Population Surveillance/methods , Cote d'Ivoire/epidemiology , Cross-Sectional Studies , Disease Notification , Enterovirus/classification , Enterovirus Infections/epidemiology , Humans , Infant , Poliomyelitis/virology , Prevalence , Retrospective StudiesABSTRACT
The increasingly increasing resistance of the parasites of malaria to chloroquine pushed all the African countries almost to adopt the ACTs like treatment of first intention of uncomplicated malaria. However, correct use of the ACTs proves to be imperative to guarantee their effectiveness and to even delay the spread resistant parasites to these molecules. Thus, we have conducted this study in order to assess the quality of the prescription and the dispensation of ACTs in randomly selected health centers across Bamako. Our study was a cross-sectional study conducted between April and July 2008 with interview of patients received in clinic for malaria, a questionnaire was administered to physicians and other health workers who give prescription of antimalarials, and pharmacists and other people working in pharmacy or drugs deposit. In total, 52 prescribers, 72 dispensers and 92 patients were included. Our study has shown that the ACT constituted the treatment of first choice of malaria within prescribers (75%) and dispensers (78.8%). However, 57.61% of the prescriptions against malaria did not contain any ACTs. The ACTs recommended by the National Malaria Program (NMCP) were known by 59.7% of dispensers and 73.1% of prescribers. The majority of the prescribers (71.15%) and of the dispensers (84.72%) were favorable to the NMCP's recommendations. Many patients (41.30%) did not understand at all the dose of the prescribed ACTs. Almost all of the prescription containing ACT was a generic drug prescribed (97.72%; n = 44). The prices of the ACTs varied between 140 and 3,380 FCFA with an average of 750 FCFA. According to prescribers and dispensers, the ACT constitutes their first choice (75% of prescribers and 78.8% of the dispensers). However, 57.61% of the prescriptions against malaria did not contain any ACTs. The majority of prescribers (71.15%) and dispensers (84.72%) were favorable to the NMCP's recommendations of malaria treatment in Mali. The average cost of prescriptions containing ACT was 750 FCFA with the extreme ones going from 140 to 3,680 FCFA.
