Polymorphism in dhfr/dhps genes, parasite density and ex vivo response to pyrimethamine in Plasmodium falciparum malaria parasites in Thies, Senegal☆

Resistance to sulfadoxine–pyrimethamine (SP) in Plasmodium falciparum malaria parasites is associated with mutations in the dihydrofolate reductase (dhfr) and dihydropteroate synthase (dhps) genes, and these mutations have spread resistance worldwide. SP, used for several years in Senegal, has been recommended for intermittent preventive treatment for malaria in pregnancy (IPTp) and has been widely implemented since 2003 in this country. There is currently limited data on SP resistance from molecular marker genotyping, and no data on pyrimethamine ex vivo sensitivity in Senegal. Molecular markers of SP resistance and pyrimethamine ex vivo sensitivity were investigated in 416 parasite samples collected from the general population, from the Thies region between 2003 and 2011. The prevalence of the N51I/C59R/S108N triple mutation in dhfr increased from 40% in 2003 to 93% in 2011. Furthermore, the prevalence of the dhfr N51I/C59R/S108N and dhps A437G quadruple mutation increased, from 20% to 66% over the same time frame, then down to 44% by 2011. There was a significant increase in the prevalence of the dhfr triple mutation, as well as an association between dhfr genotypes and pyrimethamine response. Conversely, dhps mutations in codons 436 and 437 did not show consistent variation between 2003 and 2011. These findings suggest that regular screening for molecular markers of antifolate resistance and ex vivo drug response monitoring should be incorporated with ongoing in vivo efficacy monitoring in areas where IPTp-SP is implemented and where pyrimethamine and sulfa drugs are still widely administered in the general population

High resolution melting: a useful field-deployable method to measure dhfr and dhps drug resistance in both highly and lowly endemic Plasmodium populations

Background: Emergence and spread of drug resistance to every anti-malarial used to date, creates an urgent need for development of sensitive, specifc and feld-deployable molecular tools for detection and surveillance of validated drug resistance markers. Such tools would allow early detection of mutations in resistance loci. The aim of this study was to compare common population signatures and drug resistance marker frequencies between two populations with diferent levels of malaria endemicity and history of anti-malarial drug use: Tanzania and Sénégal. This was accomplished by implementing a high resolution melting assay to study molecular markers of drug resistance as compared to polymerase chain reaction–restriction fragment length polymorphism (PCR/RFLP) methodology. Methods: Fifty blood samples were collected each from a lowly malaria endemic site (Sénégal), and a highly malaria endemic site (Tanzania) from patients presenting with uncomplicated Plasmodium falciparum malaria at clinic. Data representing the DHFR were derived using both PCR–RFLP and HRM assay; while genotyping data representing the DHPS were evaluated in Senegal and Tanzania using HRM. Msp genotyping analysis was used to characterize the multiplicity of infection in both countries. Results: A high prevalence of samples harbouring mutant DHFR alleles was observed in both population using both genotyping techniques. HRM was better able to detect mixed alleles compared to PCR/RFLP for DHFR codon 51 in Tanzania; and only HRM was able to detect mixed infections from Senegal. A high prevalence of mutant alleles in DHFR (codons 51, 59, 108) and DHPS (codon 437) were found among samples from Sénégal while no mutations were observed at DHPS codons 540 and 581, from both countries. Overall, the frequency of samples harbouring either a single DHFR mutation (S108N) or double mutation in DHFR (C59R/S108N) was greater in Sénégal compared to Tanzania Conclusion: Here the results demonstrate that HRM is a rapid, sensitive, and feld-deployable alternative technique to PCR–RFLP genotyping that is useful in populations harbouring more than one parasite genome (polygenomic infections). In this study, a high levels of resistance polymorphisms was observed in both dhfr and dhps, among samples from Tanzania and Sénégal. A routine monitoring by molecular markers can be a way to detect emergence of resistance involving a change in the treatment policy

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

Prophylaxie pré-exposition (PrEP) pour la prévention du VIH chez les travailleuses du sexe au Bénin

Malgré tous les efforts de prévention et de traitement réalisés à ce jour, l’infection au virus de l’immunodéficience humaine (VIH) continue d’être un problème de santé publique. Proposer de nouvelles méthodes de prévention pour réduire la transmission du VIH est donc essentiel. L’utilisation des antirétroviraux (ARV) pour prévenir la transmission et l’acquisition de l’infection à VIH semble prometteuse à cette fin. Deux méthodes de prévention, le traitement précoce (early antiretroviral therapy: E-ART) pour les personnes séropositives et la prophylaxie pré-exposition (PrEP) pour les personnes séronégatives ont prouvé leur efficacité dans les essais cliniques mais devraient être évaluées dans les conditions réelles de vie hors du cadre des essais cliniques. Ainsi, l’objectif de cette thèse était d’évaluer la pertinence et la faisabilité d’ajouter ces deux nouvelles méthodes de prévention au paquet de prévention et traitement actuellement offert aux travailleuses du sexe (TS) au Bénin. Dans le projet de démonstration présenté, 361 TS ont été recrutées et suivies pendant 12 à 24 mois dont 105 TS sous E-ART et 256 TS sous PrEP. Dans un premier temps, des indicateurs clés ont été mesurés. L’acceptabilité était de 95,5% pour l’E-ART et 88,3% pour la PrEP. La rétention à la fin de l’étude était de 59,0% pour l’E-ART et 47,3% pour la PrEP. L’observance auto-rapportée à l’E-ART était plus élevée que l’observance auto-rapportée à la PrEP qui a significativement diminué au cours du suivi. Nos résultats ne suggèrent pas de compensation de risque avec la PrEP. Par la suite, nous avons comparé les tendances de trois mesures d’observance à la PrEP avec des équations d’estimation généralisées (GEE). Le dosage du tenofovir (TFV), considéré comme mesure de référence a été comparé aux mesures auto-rapportées et au décompte des pilules. Le dosage du TFV a indiqué que l’observance à la PrEP a significativement diminué durant l’étude. Le décompte des pilules et les mesures auto-rapportées ont surestimé l’observance. Le dosage du TFV est la mesure la plus appropriée pour mesurer l’observance dans cette population à haut-risque mais son coût empêche son utilisation systématique. Finalement, nous avons identifié les prédicteurs de l’observance à la PrEP. Un âge plus avancé, une durée plus courte dans l’étude et une intention élevée de prendre la PrEP au début de l’étude étaient les seuls facteurs associés à l’observance. En conclusion, la PrEP pourrait être intégrée comme choix au paquet de prévention combinée du VIH offert aux TS au Bénin. Toutefois, la PrEP ne protège pas contre les autres infections sexuellement transmissibles. Elle est une méthode de prévention individuelle pour les personnes à haut-risque d’infection au VIH pour qui les moyens de prévention traditionnels n’ont pas fonctionné ou ne sont pas adaptés. L’E-ART par contre pourrait avoir un grand impact pour une meilleure prise en charge clinique du VIH chez les TS et pour la prévention de sa transmission au niveau populationnel. Toutefois, pour la mise en œuvre de la PrEP et de l’E-ART, les interventions doivent tenir compte de la réalité des TS, et en particulier leur mobilité pour assurer une bonne observance et une bonne rétention.HIV infection continues to be a public health burden despite all the prevention and treatment efforts accomplished to date. It is therefore essential to propose new prevention methods to reduce the transmission of HIV. The use of antiretrovirals (ARVs) to prevent the transmission and acquisition of HIV infection seems promising for this purpose. Two prevention methods, early antiretroviral (E-ART) and pre exposure prophylaxis (PrEP) have proven their efficacy in clinical trials but should be evaluated in "real life" outside the framework of clinical trials. The objective of this thesis was therefore to assess the relevance and feasibility of adding these two new prevention methods to the prevention and treatment package currently offered to female sex workers (FSWs) in Benin. In this demonstration project, 361 FSWs were recruited and followed for 12 to 24 months, 105 FSWs for E-ART and 256 FSWs for PrEP. First, key indicators were measured. Uptake was 95.5% for E-ART and 88.3% for PrEP. Retention at the end of the study was 59.0% for E-ART and 47.3% for PrEP. Self-reported adherence to E-ART was higher than self-reported adherence to PrEP, which decreased significantly during follow-up. Additionally, our results do not suggest any risk compensation with PrEP. We then measured PrEP adherence using 3 different measures and compared the trends using generalized estimating equations (GEE). Tenofovir (TFV) concentration in plasma, considered as the gold standard, was compared to self-reports and pill counts. Adherence to PrEP measured by TFV concentration decreased significantly over the course of the study. The pill counts and self-reported measures overestimated adherence. The TFV concentration in plasma appears to be the most appropriate measure for adherence in this high-risk population. However, its high cost limits its systematic use. Finally, we identified the predictors of adherence to PrEP. Older age, shorter duration in the study, and high intention to take PrEP at the start of the study were the only factors associated with adherence. In conclusion, PrEP could be included as a choice in the combined HIV prevention package offered to FSWs in Benin. However, PrEP does not protect against other sexually transmitted infections. It is an individual prevention method for people at high risk of HIV infection for whom traditional means of prevention have not worked or are not adapted. E-ART, on the other hand, could have a great impact for the prevention of HIV at the population level, while significantly improving clinical care for HIV-infected FSWs. However, for the implementation of PrEP and E-ART, the interventions must take into account the reality of FSWs, particularly their mobility to ensure good adherence and retention

Recurrent symptomatic ischemic stroke in a 46-year-old African male revealing Angio-Behçet with severe cardiovascular involvement

Behçet’sdisease (BD) is a chronic, multisystem vasculitis. It is categorized under variable vessel vasculitis in the new Chapel Hill nomenclature as it involves blood vessels of any type and size. It is characterized by relapsing aphthous ulcers commonly occurring in the oral mucosa and genitalia with ocular involvement. Other organ systems may be involved any time throughout the course of the disease. The exact cause is unknown. However, combination of genetic and environmental factors is likely to play a role. Cardiac involvement may occur in the form of intracardiac thrombus, endocarditis, myocarditis, pericarditis, endomyocardial fibrosis, coronary arteritis, myocardial infarction, and valvular disease. We present a case of Angio-Behçet in a 46-year-old African male with severe cardiovascular involvement including pulmonary artery hypertension (PAH), right ventricular failure and left ventricular diastolic dysfunction diagnosed after 2 episodes of symptomatic ischemic stroke resulting from complete occlusion of the right internal carotid artery (ICA) up to its intracranial portion. Immunosuppressive and anticoagulant therapies have induced improvement in cardiac manifestations. Nevertheless, prompt recognition of the primarily vascular manifestation of BD without mucocutaneous manifestations was responsible for considerable delay that did not afford surgical therapy for the carotid occlusion

Factors influencing the use of malaria prevention strategies by women in Senegal: a cross-sectional study

Background: The World Health Organization (WHO) recommends the use of insecticide-treated nets (ITNs) and intermittent preventive treatment in pregnancy (IPTp) as a cost-effective intervention for the prevention of malaria during pregnancy in endemic areas. This study was conducted to investigate: (1) the extent of use of both IPTp and ITNs, and (2) conduct multinomial regression to identify factors affecting the optimal usage of IPTp and ITNs among women with a recent pregnancy in Senegal. Methods: Data was drawn from the 2013–2014 Demographic and Health Survey. A total of 4616 women aged 15–49 years old, who had a recent pregnancy were analyzed. Multinomial logistic regression model was used to assess factors associated with optimal uptake of malaria preventive strategies (both IPTp and ITN use). Results: Amongst women who had a recent pregnancy, less than half of them used ITNs (46.84%) however, 80.35% reported taking IPTp during their last pregnancy. Overall, 37.51% reported using the optimal malaria preventive strategies. Women aged 35–49 years and living in the richer or middle wealth quintile were more likely to use optimal prevention methods. Pregnant women living in Diourbel, Saint-Louis, Thies, Louga, Fatick and Matam were more likely to use both IPTp-SP and ITNs compared to those living in Dakar. Additionally, women who initiated antenatal care in at least at 6 weeks of pregnancy or who attended four antenatal visits or more were more likely to use optimal malaria preventive methods during pregnancy. Conclusions: This study has shown important factors that influence the uptake of malaria prevention methods during pregnancy in Senegal. These findings highlight the need for targeted preventive strategies when designing and implementing policies aimed at improving the uptake of these measures during pregnancy in Senegal

Cardiovascular disease and ABO blood-groups in Africans. Are blood-group A individuals at higher risk of ischemic disease?: A pilot study

Background: Since the discovery of the ABO blood group system by Karl Landsteiner in 1901, several reports have suggested an important involvement of the ABO blood group system in the susceptibility to thrombosis. Assessing that non-O blood groups in particular A blood group confer a higher risk of venous and arterial thrombosis than group O. Epidemiologic data are typically not available for all racial and ethnics groups. The purpose of this pilot study was to identify a link between ABO blood group and ischemic disease (ID) in Africans, and to analyze whether A blood group individuals were at higher risk of ischemic disease or not. Methods: A total of 299 medical records of patients over a three-year period admitted to the cardiology and internal medicine department of military hospital of Ouakam in Senegal were reviewed. We studied data on age, gender, past history of hypertension, diabetes, smoking, sedentarism, obesity, hyperlipidemia, use of estrogen-progestin contraceptives and blood group distribution. In each blood group type, we evaluated the prevalence of ischemic and non-ischemic cardiovascular disease. The medical records were then stratified into two categories to evaluate incidence of ischemic disease: Group 1: Patients carrying blood-group A and Group 2: Patients carrying blood group non-A (O, AB and B). Results: Of the 299 patients whose medical records were reviewed, 92 (30.8%) were carrying blood group A, 175 (58.5%) had blood group O, 13 (4.3%) had blood group B, and 19 (6.4%) had blood group AB. The diagnosis of ischemic disease (ID) was higher in patients with blood group A (61.2%) than in other blood groups, and the diagnosis of non-ischemic disease (NID) was higher in patients with blood group O (73.6%) compared to other groups. In patients with blood group B or AB compared to non-B or non-AB, respectively there was no statistically significant difference in ID incidence. Main risk factor for ID was smoking (56.5%), hypertension (18.4%) and diabetes (14.3%). In our study, there was no statistical difference between blood group A and non-A in myocardial infarction (MI) incidence (p = 0.09, 95% CI = 0.99–2.83) but a statistically significant difference between blood group A and non-A in stroke and coronary artery disease (CAD) incidence (p < 0.0001, 95% CI = 1.80–3.37 and p < 0.0001 95% CI = 1.82–3.41 respectively) was found. The incidence of ID in men was significantly higher in blood group A (95% CI = 2.26–4.57, p < 0.0001) compared with non-A group, while there was no statistically significant difference in women (p = 0.35). However, an overall effect was detected to be statistically significant regardless of gender (p < 0.0001). Conclusion: Our study suggests an association between blood group A and ID in sub-Sahara Africans. In African countries, where most of health facilities are understaffed, more rigorous studies with a larger population are needed to give a high level of evidence to confirm this association in order to establish the need to be more aggressive in risk factor control in these individuals

Genomic Epidemiology of SARS-CoV-2 in Urban Settings in Senegal

We used whole genome sequencing to identify and analyze mutations in SARS-CoV-2 in urban settings during the deadliest wave of the COVID-19 epidemic—from March to April 2021—in Senegal. Nasopharyngeal samples testing positive for SARS-CoV-2 were sequenced on the Illumina NovaSeq 6000 sequencing system using the COVIDSeq protocol. A total of 291 genotypable consensus genome sequences were obtained. Phylogenetic analyses grouped the genomes into 16 distinct PANGOLIN lineages. The major lineage was B.1.1.420, despite circulation of the Alpha variant of concern (VOC). A total of 1125 different SNPs, identified relative to the Wuhan reference genome, were detected. These included 13 SNPs in non-coding regions. An average density of 37.2 SNPs per 1000 nucleotides was found, with the highest density occurring in ORF10. This analysis allowed, for the first time, the detection of a Senegalese SARS-CoV-2 strain belonging to the P.1.14 (GR/20J, Gamma V3) sublineage of the Brazilian P.1 lineage (or Gamma VOC). Overall, our results highlight substantial SARS-CoV-2 diversification in Senegal during the study period

Evaluation of Senegal’s prevention of mother to child transmission of HIV (PMTCT) program data for HIV surveillance

Abstract Background With the expansion of Prevention of Mother to Child Transmission (PMTCT) services in Senegal, there is growing interest in using PMTCT program data in lieu of conducting unlinked anonymous testing (UAT)-based ANC Sentinel Surveillance. For this reason, an evaluation was conducted in 2011–2012 to identify the gaps that need to be addressed while transitioning to using PMTCT program data for surveillance. Methods We conducted analyses to assess HIV prevalence rates and agreements between Sentinel Surveillance and PMTCT HIV test results. Also, a data quality assessment of the PMTCT program registers and data was conducted during the Sentinel Surveillance period (December 2011 to March 2012) and 3 months prior. Finally, we also assessed selection bias, which was the percentage difference from the HIV prevalence among all women enrolled in the antenatal clinic and the HIV prevalence among women who accepted PMTCT HIV testing. Results The median site HIV prevalence using routine PMTCT HIV testing data was 1.1% (IQR: 1.0) while the median site prevalence from the UAT HIV Sentinel Surveillance data was at 1.0% (IQR: 1.6). The Positive per cent agreement (PPA) of the PMTCT HIV test results compared to those of the Sentinel Surveillance was 85.1% (95% CI 77.2–90.7%), and the percent-negative agreement (PNA) was 99.9% (95% CI 99.8–99.9%). The overall HIV prevalence according to UAT was the same as that found for women accepting a PMTCT HIV test and those who refused, with percent bias at 0.00%. For several key PMTCT variables, including “HIV test offered” (85.2%), “HIV test acceptance” (78.0%), or “HIV test done” (58.8%), the proportion of records in registers with combined complete and valid data was below the WHO benchmark of 90%. Conclusions The PPA of 85.1 was below the WHO benchmarks of 96.6%, while the combined data validity and completeness rates was below the WHO benchmark of 90% for many key PMTCT variables. These results suggested that Senegal will need to reinforce the quality of onsite HIV testing and improve program data collection practices in preparation for using PMTCT data for surveillance purposes

Evaluation of the LumiraDx SARS-CoV-2 antigen assay for large-scale population testing in Senegal

Purpose: Real-time reverse-transcription polymerase chain reaction (RT-PCR)-based testing remains the gold standard for the diagnosis of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Due to the high diagnosis demand of SARS-CoV-2 and the limited resources for RT-PCR testing, especially in Low-Income Countries (LICs), antigen-based methods are being considered as an option. The aim of this study was to assess the performance of LumiraDx SARS-CoV-2 antigen assay for large population screening compared to RT-PCR.Methods: This evaluation was conducted on 4146 participants including travelers and participants under household survey and vaccine evaluation studies before injection of the first dose. Oropharyngeal and nasopharyngeal swaps were collected from each participant into 2 mL of viral transport medium (VTM) and 400 &mu;l of VTM were used to assess the performance of LumiraDx SARS-CoV-2 antigen assay, compared to RT-PCR.&nbsp;Results: The prevalence of SARS-CoV-2 of the cohort was 4.5% with RT-PCR and 4.1% with LumiraDx antigen test. Compared to the RT-PCR, the sensitivity and specificity of the LumiraDx antigen SARS-CoV-2 test were 82,7% [95% CI 74.1-89,7] and 99.9% [95% CI 99.6-99.9] respectively. Given the RT-PCR threshold cycle (Ct) range, the sensitivity was 92.1% [95% CI 84.6-96.3] when the Ct value was below or equal 33 cycles, and 38.1% [95% CI 18.9-61.3] when it was above 33 cycles. The inter-rater reliability showed a kappa coefficient of 0.88 when considering all the patients and 0.94 for Ct values below 33 cycles.&nbsp;Conclusion: Our data have shown that the LumiraDx platform can be considered for large-scale testing of SARS-CoV-2