Next-generation sequencing survey of acute febrile illness in Senegal (2020-2022).

Introduction: Acute febrile illnesses (AFI) in developing tropical and sub-tropical nations are challenging to diagnose due to the numerous causes and non-specific symptoms. The proliferation of rapid diagnostic testing and successful control campaigns against malaria have revealed that non-Plasmodium pathogens still contribute significantly to AFI burden. Thus, a more complete understanding of local trends and potential causes is important for selecting the correct treatment course, which in turn will reduce morbidity and mortality. Next-generation sequencing (NGS) in a laboratory setting can be used to identify known and novel pathogens in individuals with AFI. Methods: In this study, plasma was collected from 228 febrile patients tested negative for malaria at clinics across Senegal from 2020-2022. Total nucleic acids were extracted and converted to metagenomic NGS libraries. To identify viral pathogens, especially those present at low concentration, an aliquot of each library was processed with a viral enrichment panel and sequenced. Corresponding metagenomic libraries were also sequenced to identify non-viral pathogens. Results and Discussion: Sequencing reads for pathogens with a possible link to febrile illness were identified in 51/228 specimens, including (but not limited to): Borrelia crocidurae (N = 7), West Nile virus (N = 3), Rickettsia felis (N = 2), Bartonella quintana (N = 1), human herpesvirus 8 (N = 1), and Saffold virus (N = 1). Reads corresponding to Plasmodium falciparum were detected in 19 specimens, though their presence in the cohort was likely due to user error of rapid diagnostic testing or incorrect specimen segregation at the clinics. Mosquito-borne pathogens were typically detected just after the conclusion of the rainy season, while tick-borne pathogens were mostly detected before the rainy season. The three West Nile virus strains were phylogenetically characterized and shown to be related to both European and North American clades. Surveys such as this will increase the understanding of the potential causes of non-malarial AFI, which may help inform diagnostic and treatment options for clinicians who provide care to patients in Senegal.

Liver Disease and Treatment Needs of Asymptomatic Persons Living With Hepatitis B in Senegal.

The prevalence of active hepatitis B among asymptomatic persons remains unclear in Africa. Of 1206 newly diagnosed persons in Senegal, 12.3% had significant fibrosis and 31.3% had hepatitis B virus (HBV) DNA levels >2000 IU/mL. Overall, 128 (12.9%) were eligible for antiviral therapy. Generalized HBV screening allowed the identification of a large population requiring HBV care.

Hepatitis E Virus Seroprevalence and Associated Risk Factors in Pregnant Women Attending Antenatal Consultations in Senegal.

In West Africa, research on the hepatitis E virus (HEV) is barely covered, despite the recorded outbreaks. The low level of access to safe water and adequate sanitation is still one of the main factors of HEV spread in developing countries. HEV infection induces acute or sub-clinical liver diseases with a mortality rate ranging from 0.5 to 4%. The mortality rate is more alarming (15 to 25%) among pregnant women, especially in the last trimester of pregnancy. Herein, we conducted a multicentric socio-demographic and seroepidemiological survey of HEV in Senegal among pregnant women. A consecutive and non-redundant recruitment of participants was carried out over the period of 5 months, from March to July 2021. A total of 1227 consenting participants attending antenatal clinics responded to a standard questionnaire. Plasma samples were collected and tested for anti-HEV IgM and IgG by using the WANTAI HEV-IgM and IgG ELISA assay. The overall HEV seroprevalence was 7.8% (n = 96), with 0.5% (n = 6) and 7.4% (n = 91) for HEV IgM and HEV IgG, respectively. One of the participant samples was IgM/IgG-positive, while four were declared indeterminate to anti-HEV IgM as per the manufacturer's instructions. From one locality to another, the seroprevalence of HEV antibodies varied from 0 to 1% for HEV IgM and from 1.5 to 10.5% for HEV IgG. The data also showed that seroprevalence varied significantly by marital status (p < 0.0001), by the regularity of income (p = 0.0043), and by access to sanitation services (p = 0.0006). These data could serve as a basis to setup national prevention strategies focused on socio-cultural, environmental, and behavioral aspects for a better management of HEV infection in Senegal.

Osteonecrosis of the humeral head in a human immunodeficiency virus-infected patient under tenofovir disoproxil fumarate-emtricitabine-lopinavir/ritonavir for 10 years: a case report.

BACKGROUND: Human immunodeficiency virus-infected patients are 100 times more likely to develop aseptic osteonecrosis compared with the general population. While 90% of cases concern the femoral head, the involvement of humeral bone remains rare. CASE PRESENTATION: We report a case of aseptic osteonecrosis of the left humeral head complicating antiretroviral therapy in a female, 46-year-old, Bissau-Guinean human immunodeficiency virus-infected patient received in a context of progressive pain in the left shoulder followed by limitation of articular movements. Standard x-ray of the shoulder allowed us to make the diagnosis by showing a typical image of osteonecrosis. The treatment was medical combined with physiotherapy. CONCLUSIONS: Aseptic osteonecrosis should be systematically looked for in human immunodeficiency virus patients on antiretroviral treatment. In addition to femoral head aseptic necrosis, the involvement of the humeral bone should also be considered.

Severe dengue in adults and children, Ouagadougou (Burkina Faso), West Africa, October 2015-January 2017.

Introduction: Although dengue is the most common arbovirus infection worldwide, studies of severe dengue in Africa are lacking, and risk factors for severe dengue have been insufficiently described. This study was conducted in the context of the 2016 dengue epidemic in Burkina Faso to determine the prevalence of severe dengue, identify factors associated with severe dengue, and perform mapping of dengue cases in the country's capital, Ouagadougou. Methods: This cross-sectional study was conducted from November 2015 to January 2017. Data were collected in 15 public and private health centres, and included sociodemographic, clinical and patient outcome variables. Dengue was diagnosed using SD Bioline Dengue Duo rapid diagnostic tests. Data were analysed using Epi-Info Version 7. Logistic regression was used to identify predictors of severe dengue. P<0.05 was considered significant. Dengue case mapping was performed using Geographic Information System software (ArcGIS). Results: Of the 811 patients who tested positive for dengue, 609 (75%) had early dengue (AgNS1 positive) and 272 (33.5%) had severe dengue. Patient age ranged from 1 to 83 years (median 30.5 years) and 393 (48.3%) were female. Renal failure (13.1%) and severe bleeding (10.6%) were the most common signs of severe dengue. Risk factors for severe dengue included age, male sex, haemoglobin S, diabetes, hypertension, and primary dengue. Dengue cases were more concentrated  in sectors located in the centre of the city and close to the health centres. Conclusion: Dengue is increasingly common in Africa and factors associated with severity should be sought systematically as soon as a patient tests positive. Additional studies are needed to determine if the factors found to be associated with severity can be used to identify patients at risk for dengue-related complications, and to provide early and specialized management to reduce morbidity and mortality related to dengue in Africa.

[Disseminated cysticercosis affecting the brain, the eye and the skin on a Senegalese patient]. / Cysticercose disséminée à localisation neurologique, oculaire et cutanée chez une patiente sénégalaise.

Cysticercosis is a neglected tropical disease set as health priority by WHO. Most of the reported cases included isolated types of cysticercosis affecting the skin, the eyes or the brain . Disseminated types, however, are rare. We here report a case of disseminated cysticercosis affecting the brain, the eyes and the skin in a Senegalese female patient aged 66 years admitted with headaches and chronic seizures. Clinical examination showed cerebellar syndrome associated with generalized and painless nodular subcutaneous lesions. Diagnosis was confirmed based on histopathological examination of skin biopsy which showed cysticerci. Patient's outcome was good under albendazole therapy.

Hepatitis B-related hepatocellular carcinoma in a 36-year-old pregnant woman: prognosis and management dilemma.

Management of chronic hepatitis B infection complicated by hepatocellular carcinoma (HCC) in pregnancy poses a treatment dilemma as the pregnancy accelerates disease progression and narrows the diagnostic tools and therapeutic choices. Studies have reported higher maternal and fetal losses. We share our experience with a 36-year-old pregnant woman who presented at 35 weeks' gestation with a large painful nodular liver and significant weight loss. She tested HBsAg-positive and had both clinical and laboratory features of severe liver decompensation. The abdominal ultrasound rightly described HCC on a cirrhotic background. The fetus was delivered by cesarean section but the mother died soon after.

Prevalence, predictors, and management of advanced HIV disease among individuals initiating ART in Senegal, West Africa.

BACKGROUND: The WHO guidelines for the management of advanced HIV disease recommend a package of care consisting of rapid initiation of antiretroviral therapy (ART), enhanced screening and diagnosis of tuberculosis (TB) and cryptococcal meningitis, co-trimoxazole prophylaxis, isoniazid preventive therapy (IPT), fluconazole pre-emptive therapy, and adherence support. The goals of this study were to determine the prevalence of advanced HIV disease among individuals initiating ART in Senegal, to identify predictors of advanced disease, and to evaluate adherence to the WHO guidelines. METHODS: This study was conducted among HIV-positive individuals initiating ART in Dakar and Ziguinchor, Senegal. Clinical evaluations, laboratory analyses, questionnaires and chart review were conducted. Logistic regression was used to identify predictors of advanced disease. RESULTS: A total of 198 subjects were enrolled; 70% were female. The majority of subjects (71%) had advanced HIV disease, defined by the WHO as a CD4 count < 200 cells/mm3 or clinical stage 3 or 4. The median CD4 count was 185 cells/mm3. The strongest predictors of advanced disease were age ≥ 35 (OR 5.80, 95%CI 2.35-14.30) and having sought care from a traditional healer (OR 3.86, 95%CI 1.17-12.78). Approximately one third of subjects initiated ART within 7 days of diagnosis. Co-trimoxazole prophylaxis was provided to 65% of subjects with CD4 counts ≤350 cells/mm3 or stage 3 or 4 disease. TB symptom screening was available for 166 subjects; 54% reported TB symptoms. Among those with TB symptoms, 39% underwent diagnostic evaluation. Among those eligible for IPT, one subject received isoniazid. No subjects underwent CrAg screening or received fluconazole to prevent cryptococcal meningitis. CONCLUSIONS: This is the first study to report an association between seeking care from a traditional healer and presentation with WHO defined advanced disease in sub-Saharan Africa. Given the widespread use of traditional healers in sub-Saharan Africa, future studies to further explore this finding are indicated. Although the majority of individuals in this study presented with advanced disease and warranted management according to WHO guidelines, there were numerous missed opportunities to prevent HIV-associated morbidity and mortality. Programmatic evaluation is needed to identify barriers to implementation of the WHO guidelines and enhanced funding for operational research is indicated.

[Factors associated with immunovirologic dissociation in HIV-1-infected patients under highly active antiretroviral therapy in the Ambulatory Treatment Center (ATC) in Dakar]. / Facteurs associés à la dissociation immunovirologique chez les patients infectés par le VIH-1 sous traitement antirétroviral hautement actif au Centre de Traitement Ambulatoire (CTA) de Dakar.

INTRODUCTION: The objective of this work is to evaluate the different factors associated with immunovirologic dissociation despite highly active and effective antiretroviral treatment. METHODS: We conducted a retrospective, cohort, descriptive and analytical study of the medical records of HIV-1 infected patients having received at least 12 months of antiretroviral therapy, followed in the ATC cohort from 2001 to 2011 and with undetectable viral load in the last 6 months. RESULTS: During this 10-year study period, the prevalence of IVD was 19.3%. Female sex was predominant, with a sex ratio of 1.9. Immunovirologic dissociation was more frequent in male patients (29.7% vs 14.1%) with a statistically significant difference (p = 0,00006). The average age was 44 years ± 10 years. A history of tuberculosis was found in about a third of the cases (31.4%). Immunovirologic dissociation was significantly more frequent in patients with a history of tuberculosis (p = 0.00005). Most patients (68%) had AIDS at WHO clinical stages 3 or 4. Patients with immunovirologic dissociation were more often in WHO clinical stages 3 and 4 (p = 0.0001). More than half of the cases (56.2%) were found to be malnourished and immunovirologic dissociation was prevalent in malnourished patients (p=0.005). The mean CD4+ T lymphocytes counts was 86.7± 83 cells / mm3. Immunovirologic dissociation was more frequent in patients with initial low CD4+ T lymphocyte counts and with a statistically significant difference (p = 0.00000). By multivariate analysis, only age greater than or equal to 43 years, CD4 initial counts < 100 c/mm3 and male sex were significantly associated with this immunovirologic dissociation. CONCLUSION: Our study assessed the main factors associated with immunovirologic dissociation. Other studies of this nature would also merit consideration in order to highlight the impact of this partial immune response on the emergence of opportunistic infections or the implementation of a specific tritherapy for the sole purpose of producing fully successful immune restoration.

Mobile phone data highlights the role of mass gatherings in the spreading of cholera outbreaks.

The spatiotemporal evolution of human mobility and the related fluctuations of population density are known to be key drivers of the dynamics of infectious disease outbreaks. These factors are particularly relevant in the case of mass gatherings, which may act as hotspots of disease transmission and spread. Understanding these dynamics, however, is usually limited by the lack of accurate data, especially in developing countries. Mobile phone call data provide a new, first-order source of information that allows the tracking of the evolution of mobility fluxes with high resolution in space and time. Here, we analyze a dataset of mobile phone records of ∼150,000 users in Senegal to extract human mobility fluxes and directly incorporate them into a spatially explicit, dynamic epidemiological framework. Our model, which also takes into account other drivers of disease transmission such as rainfall, is applied to the 2005 cholera outbreak in Senegal, which totaled more than 30,000 reported cases. Our findings highlight the major influence that a mass gathering, which took place during the initial phase of the outbreak, had on the course of the epidemic. Such an effect could not be explained by classic, static approaches describing human mobility. Model results also show how concentrated efforts toward disease control in a transmission hotspot could have an important effect on the large-scale progression of an outbreak.

Daily consumption of ready-to-use peanut-based therapeutic food increased fat free mass, improved anemic status but has no impact on the zinc status of people living with HIV/AIDS: a randomized controlled trial.

BACKGROUND: Food insecurity in sub-Saharan Africa and malnutrition constitute the main obstacles for successful treatment of people living with HIV/AIDS (PLWH). The aim of this study was to assess the effect of consuming daily 100 g RUTF (ready-to-use therapeutic food) as supplement, on body composition, anemia and zinc status of hospitalized PLWH in Senegal. METHODS: A Controlled clinical trial was conducted in 65 PLWH randomly allocated to receive either standard hospital diet alone (Control group: n = 33), or the standard diet supplemented with 100 g RUTF/day (RUTF group: n = 32). Supplementation was continued at home during 9 weeks. Individual dietary intakes were measured and compared to the Recommended Dietary Allowances. Body composition was determined using Bio-Impedance Analysis. Hemoglobin was measured by HemoCue and plasma zinc (PZ) concentration by atomic absorption spectrometry. PZ was adjusted to infection (CRP and α1-AGP). All measures were conducted on admission, discharge and after 9 weeks home-based follow up. RESULTS: 34 and 24% of the patients in RUTF and Control groups were suffering from severe malnutrition (BMI < 16 kg/m(2)), respectively. In both groups, more than 90% were anemic and zinc deficiency affected over 50% of the patients. Food consumed by the Control group represented 75, 14 and 55% of their daily recommended intake (DRI) of energy, iron and zinc, respectively. When 100 g of RUTF was consumed with the standard diet, the DRI of energy and zinc were 100% covered (2147 kcal, 10.4 mg, respectively), but not iron (2.9 mg). After 9 weeks of supplementation, body weight, and fat-free mass increased significantly by +11% (p = 0.033), and +11.8% (p = 0.033) in the RUTF group, but not in the Control group, while percentage body fat was comparable between groups (p = 0.888). In the RUTF group, fat free mass gain is higher in the patients on ART (+11.7%, n = 14; p = 0.0001) than in those without ART (+6.2%, n = 6; p = 0.032). Anemia decreased significantly with the supplementation, but zinc status, measured using plasma zinc concentration, remained unchanged. CONCLUSION: Improving PLWH' diet with 100 g RUTF for a long period has a positive impact on muscle mass and anemia but not on the zinc status of the patients. TRIAL NUMBER: NCT02433743, registered 29 April 2015.