Rapidly rising cases with Omicron in Senegal.

•Omicron variant continues to progress in Senegal with the appearance of new contaminations.•IRESSEF detected the first positive case of the Omicron variant on Friday, December 3, 2021.•Since this date, the number of Omicron variant infections has increased over the weeks.•Molecular surveillance of the Omicron variant is carried out in real time to inform the medical authorities.

The potential for quality assurance systems to save costs and lives: the case of early infant diagnosis of HIV.

OBJECTIVES: Scaling up of point-of-care testing (POCT) for early infant diagnosis of HIV (EID) could reduce the large gap in infant testing. However, suboptimal POCT EID could have limited impact and potentially high avoidable costs. This study models the cost-effectiveness of a quality assurance system to address testing performance and screening interruptions, due to, for example, supply stockouts, in Kenya, Senegal, South Africa, Uganda and Zimbabwe, with varying HIV epidemics and different health systems. METHODS: We modelled a quality assurance system-raised EID quality from suboptimal levels: that is, from misdiagnosis rates of 5%, 10% and 20% and EID testing interruptions in months, to uninterrupted optimal performance (98.5% sensitivity, 99.9% specificity). For each country, we estimated the 1-year impact and cost-effectiveness (US$/DALY averted) of improved scenarios in averting missed HIV infections and unneeded HIV treatment costs for false-positive diagnoses. RESULTS: The modelled 1-year costs of a national POCT quality assurance system range from US$ 69 359 in South Africa to US$ 334 341 in Zimbabwe. At the country level, quality assurance systems could potentially avert between 36 and 711 missed infections (i.e. false negatives) per year and unneeded treatment costs between US$ 5808 and US$ 739 030. CONCLUSIONS: The model estimates adding effective quality assurance systems are cost-saving in four of the five countries within the first year. Starting EQA requires an initial investment but will provide a positive return on investment within five years by averting the costs of misdiagnoses and would be even more efficient if implemented across multiple applications of POCT.

OBJECTIFS: L'intensification du dépistage au point des soins (DPS) pour le diagnostic précoce du VIH chez le nourrisson (DPVN) pourrait réduire le grand écart dans le dépistage des nourrissons. Cependant, un DPVN DPS sous-optimal pourrait avoir un impact limité et des coûts évitables potentiellement élevés. Cette étude modélise la rentabilité d'un système d'assurance qualité pour traiter les performances des tests et les interruptions de dépistage, dues par exemple à des ruptures de stock, au Kenya, au Sénégal, en Afrique du Sud, en Ouganda et au Zimbabwe, avec des épidémies variables du VIH et des systèmes de santé différents. MÉTHODES: Nous avons modélisé une qualité de DPVN soulevée par le système d'assurance qualité à partir de niveaux sous-optimaux: c'est-à-dire des taux d'erreurs de diagnostic de 5%, 10% et 20% et des interruptions des tests de DPVN en mois, à des performances optimales ininterrompues (sensibilité de 98,5%, spécificité de 99,9%). Pour chaque pays, nous avons estimé l'impact sur un an et la rentabilité (en USD/DALY évitée) de scénarios améliorés pour éviter les infections à VIH manquées et les coûts inutiles de traitement du VIH pour les diagnostics faux positifs. RÉSULTATS: Les coûts modélisés sur un an d'un système national d'assurance qualité DPS vont de 69.359 USD en Afrique du Sud à 334.341 USD au Zimbabwe. Au niveau des pays, les systèmes d'assurance de la qualité pourraient potentiellement éviter entre 36 et 711 infections manquées (c'est-à-dire des faux négatifs) par an et des coûts de traitement inutiles entre 5.808 et 739.030 USD. CONCLUSIONS: Le modèle estime que l'ajout de systèmes d'assurance qualité efficaces permet de réaliser des économies dans quatre des cinq pays au cours de la première année. Le lancement de l'assurance qualité nécessite un investissement initial, mais fournira un retour sur investissement positif dans les cinq ans en évitant les coûts des diagnostics erronés et serait encore plus efficace s'il était mis en œuvre dans plusieurs applications de DPS.

HIV self-testing in Africa: stakes and challenges.

HIV self-testing constitutes a new complementary strategy for HIV testing for general populations as well as "key" populations such as sex workers and their clients, men who have sex with men, and young people; it may help to reach the UNAIDS 90-90-90 objectives by 2020. In Africa, many pilot studies have been conducted, mainly in English-speaking countries, and they have demonstrated the high acceptability, practicability and clinical performance of HIV self-testing. Innovative strategies, including the translation of HIV self-test instructions for use into vernacular languages in association with educational pictograms, should be developed and evaluated in sub-Saharan Africa to implement HIV self-testing.

Does smallpox vaccination modify HIV disease progression among ART-naive people living with HIV in Africa?

We examined the association between a history of smallpox vaccination and immune activation (IA) in a population of antiretroviral therapy-naïve people living with HIV (PLHIV). A cross-sectional study was conducted in Senegal from July 2015 to March 2017. Smallpox vaccination was ascertained by the presence of smallpox vaccine scar and IA by the plasma level of ß-2-microglobulin (ß2m). The association was analysed using logistic regression and linear regression models. The study population comprised 101 PLHIV born before 1980 with a median age of 47 years (interquartile range (IQR) = 42-55); 57·4% were women. Smallpox vaccine scar was present in 65·3% and the median ß2m level was 2·59 mg/l (IQR = 2·06-3·86). After adjustment, the presence of smallpox vaccine scar was not associated with a ß2m level ⩾2·59 mg/l (adjusted odds ratio 0·94; 95% confidence interval 0·32-2·77). This result was confirmed by the linear regression model. Our study does not find any association between the presence of smallpox vaccine scar and the ß2m level and does not support any association between a previous smallpox vaccination and HIV disease progression. In this study, IA is not a significant determinant of the reported non-targeted effect of smallpox vaccination in PLHIV.

Chryseobacterium gleum in a man with prostatectomy in Senegal: a case report and review of the literature.

BACKGROUND: Here we report a rare case of a urinary tract infection due to Chryseobacterium gleum. This widely distributed Gram-negative bacillus is an uncommon human pathogen and is typically associated with health care settings. CASE PRESENTATION: We describe a case of urinary tract infection caused by Chryseobacterium gleum in a 68-year-old man of Wolof ethnicity (an ethnic group in Senegal, West Africa) who presented to our Department of Urology in a university teaching hospital (Hôpital Aristide Le Dantec) in Dakar, Senegal, 1 month after prostatectomy. The strain isolated from a urine sample was identified as Chryseobacterium gleum by mass spectrometry (Vitek matrix-assisted laser desorption/ionization, time-of-flight, bioMérieux) and confirmed by 16S ribosomal ribonucleic acid sequencing. The organism was resistant to a wide range of antibiotics, including carbapenem, due to a resident metallo-ß-lactamase gene that shared 99% of amino-acid identity with Chryseobacterium gleum class B enzym. CONCLUSIONS: Infection by Chryseobacterium gleum is infrequent, and no such case has been previously reported in Africa. Despite its low virulence, Chryseobacterium gleum should be considered a potential opportunistic and emerging pathogen. Further studies on the epidemiology, pathogenicity, and resistance mechanisms of Chryseobacterium gleum are needed for better diagnosis and management.

Usefulness of Dried Blood Spots (DBS) to perform hepatitis C virus genotyping in drug users in Senegal.

The aim of this pilot study was to analyze the Hepatitis C Virus (HCV) genotypes circulating in Senegal among Drug User (DUs), using Dried Blood Spots (DBS) as RNA source for molecular assays. Heroin and/or cocaine users (n = 506) were recruited in Dakar from April to July 2011, using a Respondent Driven Sampling (RDS) method. DBS preparation consisted of five drops of whole blood from finger applied to a Whatman paper card. HCV infection was screened by the detection of anti-HCV antibodies, using a rapid immune-chromatographic test. HCV RNA was quantified on anti-HCV positive DBS, using the Abbott RealTime HCV® Genotyping was performed on DBS with detectable viral load with Versant® HCV Genotype 2.0 Assay (LiPA) and Abbott RealTime HCV Genotype II assay®. Among the 506 participants, 120 were tested as positive for anti-HCV antibodies and their samples were analyzed for HCV RNA viral load and genotype. Out of the 120 DBS tested, HCV RNA was detected on 25 (20.8%). The median viral load was 15,058 IU/ml (ranging from 710 to 766,740 IU/ml). All positive DBS were suitable for the genotyping assay, that showed a predominance of genotype 1 (21/25) including 16 genotypes 1a and 5 genotypes 1b. HCV genotype 1 prevails in a DU population in Dakar. DBS could be useful for HCV RNA genotyping, but optimal storage conditions should required avoiding RNA impairment. Acknowledging this limitation, DBS could be a great interest for detecting and genotyping HCV viremic patients. J. Med. Virol. 89:484-488, 2017. © 2015 Wiley Periodicals, Inc.

Implementation of an in-house quantitative real-time polymerase chain reaction method for Hepatitis B virus quantification in West African countries.

Hepatitis B virus (HBV) is a major cause of chronic liver disease worldwide. HBV infection is diagnosed by serological tests, while real-time polymerase chain reaction (qRT-PCR) assays are used to quantify viral load, which is a crucial parameter to determine viral replication and to monitor antiviral treatments. However, measuring viral load in resource-limited countries remains nonsystematic, due to the high cost of commercial kits. Here, we describe the development, validation and implementation of a low-cost, in-house qRT-PCR assay to monitor HBV viral load in chronic carriers enrolled in the PROLIFICA programme in the Gambia and Senegal. Over 1500 HBsAg-positive patients, including 210 chronically infected HBV patients, who were given antiviral treatment (tenofovir), were monitored by qRT-PCR using the SYBR Green- and HBV-specific primers. Twenty-four tenofovir-treated patients were followed up and their viral load was tested every 3 months over the 12-month experimental time course. Compared to commercial assays, our in-house assay was shown to be (i) highly reliable, with good intra- and interassay reproducibility over a wide range (45-4.5 × 108 copies mL-1 ), (ii) very similar in the viral loads detected (R2  = .90), (iii) highly sensitive, as it detected loads as low as 30 copies mL-1 (~5 IU mL-1 ), (iv) cheaper (2- to 3-fold), (v) easier to implement and (vi) more rapid. Based on our experience, we recommend this assay as a reliable alternative to commercial assays, for monitoring HBV viraemia in resource-limited, highly endemic countries to reduce the cost and technical obstacles associated with commercial kits.

[The challenges of training in medical laboratories in Africa]. / Le défi de la formation dans le domaine du laboratoire de biologie clinique en Afrique.

Sub-Saharan Africa has a considerable deficit in laboratory facilities. For a decade, international and national public and private initiatives have multiplied to expand both the supply and quality of medical laboratories in Africa. By 2020, the World Health Organization, with as its main operator the African Society for Laboratory Medicine, will have provided training for 30,000 laboratory personnel and encouraged 2,500 laboratories to begin the accreditation process. In addition, the World Health Organization recommendations for treatment and care of HIV-infected individuals in resource-limited settings, revised in 2013, emphasize the need for laboratory monitoring to guide antiretroviral therapy. The University Diploma in Biological Retrovirology at the Cheikh Anta Diop University in Dakar, Senegal, offers multidisciplinary training in French at the postgraduate level in the complex and diverse field of biological monitoring of HIV infection in Africa. In nearly 10 years, more than 200 African biologists have been trained.

Schistosome infection is associated with enhanced whole-blood IL-10 secretion in response to cercarial excretory/secretory products.

Infection of the human host by schistosome parasites follows exposure of skin to free-swimming cercariae and is aided by the release of excretory/secretory (E/S) material, which is rich in proteases and glycoconjugates. This material provides the initial stimulus to cells of the innate immune system. The study presented here is the first to examine human innate/early immune responsiveness to cercarial E/S in subjects from an area co-endemic for Schistosoma mansoni and S. haematobium. We report that in infected participants, stimulation of whole-blood cultures with cercarial E/S material (termed 0-3 hRP) caused the early (within 24 h) release of greater quantities of regulatory IL-10, compared with uninfected controls. Elevated levels of IL-10 but not pro-inflammatory TNFα or IL-8 were most evident in participants co-infected with S. mansoni and S. haematobium and were accompanied by a higher 0-3 h RP-specific IL-10: TNFα ratio. We also report that glycosylated components within 0-3 h RP appear to be important factors in the stimulation of IL-8, TNFα and IL-10 production by whole-blood cells.

Association between herpes simplex virus type 2 and HIV-1 in a population of married couples from Dakar, Senegal.

Numerous studies suggest that herpes simplex virus type 2 (HSV-2) increases the risk of HIV-1 infection but recent clinical trials of HSV-2 suppressive therapy failed to show an effect. We assessed the putative association between HSV-2 and HIV-1 in a population of HIV-concordant-negative, HIV-1-discordant and HIV-1-concordant-positive married couples from Dakar, Senegal. In agreement with previous studies, we observed a strong overall association between HSV-2 and HIV-1 (odds ratio 4.61; P < 0.001). However, this association was mainly determined by a low HSV-2 prevalence in HIV-concordant-negative couples compared with HIV-1-discordant and HIV-1-concordant-positive couples (23% versus 59% and 66%, respectively; P < 0.001). We observed no further differences in HSV-2 prevalence between HIV-1-discordant and HIV-1-concordant-positive couples (59% and 66%, respectively; P = 0.483). Neither the index (59% versus 62%, P = 1.000) nor recipient partners (41% versus 63%, P = 0.131) in HIV-1-discordant and HIV-1-concordant-positive couples showed significant differences in HSV-2 prevalence. HSV-2 does not constitute a clear risk factor for HIV-1 infection in this population.

RNA versus DNA (NucliSENS EasyQ HIV-1 v1.2 versus Amplicor HIV-1 DNA test v1.5) for early diagnosis of HIV-1 infection in infants in Senegal.

The objective of this study was to compare the performance of the NucliSENS EasyQ HIV-1 v1.2 platform (bioMérieux, France) to the Amplicor HIV-1 DNA test v1.5 (Roche Molecular Systems, Switzerland) in detecting HIV-1 infection in infants using venipuncture-derived whole blood in tubes and dried blood spots. A total of 149 dried blood spots and 43 EDTA-anticoagulated peripheral blood samples were collected throughout Dakar and other areas in Senegal from infants and children aged 3 weeks to 24 months who were born to HIV-1-infected mothers. Samples were tested using the NucliSENS and Amplicor technologies. The NucliSENS and Amplicor results were 100% concordant using either EDTA-anticoagulated peripheral blood or dried blood spots. Compared to Amplicor, the sensitivity and specificity of the NucliSENS test were 100%. The NucliSENS EasyQ HIV-1 RNA assay performed as well as the Amplicor HIV-1 DNA test in detecting HIV-1 infection in infants. In addition, this platform can give an indication of the viral load baseline. The NucliSENS EasyQ platform is a good alternative for early infant diagnosis of HIV-1 infection.

Efficacy and safety of unboosted atazanavir in combination with lamivudine and didanosine in naive HIV type 1 patients in Senegal.

The use of ritonavir as a protease inhibitor boost is rare in sub-Saharan Africa because a heat-stable formula is not available. We report the results of an open-label pilot trial with unboosted atazanavir in combination with lamivudine and didanosine as first-line therapy conducted in Senegal. Treatment-naive HIV-1 infected adult patients without active opportunistic disease were included. The primary endpoint was the proportion of patients with plasma HIV-1 RNA <400 copies/ml at week 48. Forty patients (12 men and 28 women; mean age +/- SD: 40 +/- 9 years) were included. Treatment was changed during the study for two patients (pregnancy, tuberculosis); one patient was lost to follow-up and one patient died (gastroenteritis with cachexia). At week 48, 78% [95% confidence interval (CI): 65-90%] and 68% (95% CI: 53-82%) of the patients had HIV-1 RNA <400 and <50 copies/ml, respectively (intent-to-treat analysis; not completer = failure). Among the seven patients with HIV-1 RNA >or=400 copies/ml at week 48, five were not compliant; genotyping analysis (n = 4) did not reveal a major mutation for protease inhibitors. The mean CD4 cell count change from baseline to week 48 was +238 +/- 79 cells/mm(3). The combination of unboosted atazanavir with lamivudine and didanosine was efficient and well tolerated in HIV-1-infected patients with results similar to those observed in Northern countries. These results suggest that unboosted atazanavir with its high genetic barrier could be a valuable alternative to NNRTIs in resource-limited countries in some HIV-1-infected patients in case of compliance issues with NNRTIs, intolerance to NNRTIs, resistance mutations to NNRTIs, in women with childbearing potential, or as a maintenance therapy in patients with virological suppression.

[HIV sentinel surveillance of pregnant women in Mauritania from 2001 to 2007]. / Surveillance sentinelle du VIH chez les femmes enceintes en Mauritanie entre 2001 et 2007.

According to the 2008 report on global AIDS epidemic, 33 millions of people are living with HIV/AIDS. Subsaharian Africa is the most affected part of the world. The first case of AIDS in Mauritania was reported in 1987. The national prevalence of HIV/AIDS in the country is estimated at less than 1%. The HIV serosurveillance among pregnant women started in country in 2001. This work has focused on HIV sentinel surveillance among pregnant women in antenatal clinics, attending health centres in different wilayas (regions) of the country in order to assess evolution of prevalence between 2001 and 2007. An anonymous and non-correlated method is used for this survey. A questionnaire was administered and venous sampling made for eligible women. Analyses were performed with an algorithm based on two screening tests (ELISA) and another test for confirmation (New Lav Blot). Despite some disparities between the sites considered, the results have shown a low prevalence rate (between 0.1 and 1.48). The average prevalence of HIV infection samples collected increased from 0.57% [0.34-0.80] in 2001 to 0.61% [0.40-0.82] in 2007 with 95% confidence interval. Statistical analysis showed no significant changes between 2001 and 2007 at all these sites. HIV1 is the most frequent type with a proportion of 93.5% in 2007. After several years of classic HIV sentinel surveillance, and to better understand disparities between sites, we recommend a second generation sentinel surveillance (behavioural and serological) approach.

Concentrated and linked epidemics of both HSV-2 and HIV-1/HIV-2 infections in Senegal: public health impacts of the spread of HIV.

The objective of this article is to report seroprevalences on HIV and herpes simplex virus 2 (HSV-2) in female sex workers (FSW) and in two sentinel populations of pregnant women living in Senegal. Serosurveys of HIV and HSV-2 were conducted in two unselected sentinel populations from Dakar, Senegal, and its provinces, including in 2003 only pregnant women and 2006 pregnant women and FSW. The population study involved 888 pregnant women and 604 FSW. In pregnant women, HIV and HSV-2 seroprevalences were, respectively, 1.01% and 15.65%. There was no association between HSV-2 and HIV infection, whatever the age. In contrast, the seroprevalence of HIV infection in the group of FSW was high, reaching 22.9% in women over 30 years old. FSW above 20 years of age harboured much higher HSV-2 seroprevalences that those found in pregnant women of similar age groups. In FSW, strong associations between HSV-2 and age, and among HSV-2 and HIV-1 as well HIV-2, were evidenced. In conclusion, HIV epidemic remains concentrated in high-risk groups of the Senegalese population, such as the FSW population in which the seroprevalence of HSV-2 infection is very high. Intervention against STI including HSV-2 is urgently needed to prevent the spreading of HIV epidemic.

[Screening for HIV, syphilis, Chlamydia trachomatis and Neisseria gonorrhoreae during a combined survey conducted in Malicouna, a Senegalese rural area]. / Dépistage du VIH, de la syphilis, des infections dues à Chlamydia trachomatis et à Neisseria gonorrhoreae au cours d'une enquête combinée conduite à Malicounda, une zone rurale du Sénégal.

To implement a second-generation HIV surveillance, through a prevention programme of HIV and sexually transmitted infections (STIs), Senegal conducted a combined survey from 2003 September 2 to October 5 in Malicounda located in the region of Thiès in the center of Senegal. The objectives of this study were to collect data on sexual behaviours and prevalence of HIV gonorrhoea, Chlamydia infections and syphilis in the community. After obtaining their informed consent, 679 people were interviewed among whom 617 accepted blood sampling and 619 accepted urine sampling, that is to say an acceptance rate of 90% and 91% respectively. Women reported having fewer sexual risk behaviours than men. However, when having sexual risk behaviour men only reported using condoms. Overall, the prevalence of HIV as well as the prevalence of STI are low: 0.5% for HIV, 0.9% for syphilis, 0.3% for Chlamydia trachomatis and 0.2% for Neisseria gonorrhoea. In this study, the small numbers of cases of infection identified did not allow to analyse the influence of sexual behaviour at risk on the occurrence of these infections.

Tenofovir-emtricitabine-efavirenz in HIV-I-infected adults in Senegal: a 96-week pilot trial in treatment-naive patients.

We report the results of a pilot open-label trial of a tenofovir (TDF)/emtricitabine (FTC)/efavirenz (EFV) combination conducted in Dakar, Senegal. Forty HIV-1-infected patients, naive of antiretroviral treatment and without active opportunistic disease, were included and followed through 96 weeks. At weeks 48 and 96, respectively, 82.5% and 85% of patients had HIV-1 RNA <400 copies/mL (72.5% and 77.5% with HIV-1 RNA <50 copies/mL). Between baseline and week 96, the mean (SD) CD4 count increased from 126 (102) to 338 (155) cells/mm(3). The mean (SD) creatinine clearance decreased from 92 (36) to 73 (19) mL/min (P = .001). Treatment adherence was at least 94% at all scheduled visits. The efficacy and tolerability of a TDF/FTC/EFV combination were high and similar to those observed in Northern countries. This drug combination can be recommended in limited-resource countries, as did the World Health Organization (WHO) and should be made readily available as a fixed-dose combination.

Erythrocyte invasion profiles are associated with a common invasion ligand polymorphism in Senegalese isolates of Plasmodium falciparum.

Plasmodium falciparum parasites use multiple ligand-receptor interactions to invade human erythrocytes. Variant expression levels of members of the PfRh and PfEBA ligand families are associated with the use of different erythrocyte receptors, defining invasion pathways. Here we analyse a major polymorphism, a large sequence deletion in the PfRh2b ligand, and erythrocyte invasion profiles in uncultured Senegalese isolates. Parasites vary considerably in their use of sialic acid-containing and protease-sensitive erythrocyte receptors for invasion. The erythrocyte selectivity index was not related to invasion pathway usage, while parasite multiplication rate was associated with enhanced use of a trypsin-resistant invasion pathway. PfRh2b protein was expressed in all parasite isolates, although the PfRh2b deletion was present in a subset (approximately 68%). Parasites with the PfRh2b deletion were found to preferentially utilize protease-resistant pathways for erythrocyte invasion. Sialic acid-independent invasion is reduced in parasites with the PfRh2b deletion, but only in isolates derived from blood group O patients. Our results suggest a significant role for PfRh2b sequence polymorphism in discriminating between alternative erythrocyte receptors for invasion and as a possible determinant of virulence.

[Decentralization of the immunological monitoring of people living with HIV/AIDS in a limiting setting with a low HIV seroprevalence: the experience of Senegal]. / Décentralisation du suivi immunologique des personnes vivant avec le VIH dans un pays à ressources limitées et à prévalence faible: expérience du Sénégal.

Our work aimed to propose a manual method of counting CD4 T lymphocytes which is an alternative magnetic immunoseparation followed by a reading with a fluorescence microscope as an alternative to the automated flow cytometry. This alternative technique is easier for use, less expensive and could answer the difficulties encountered for the monitoring CD4 T cells count in developing countries. The specific objectives were: 1) to train the technicians of the peripheral sites in order to make the numeration of the CD4 T lymphocytes more accessible at the peripheral level; 2) to equip the sites with necessary facilities for the T lymphocytes CD4 count; 3) to put in place a system of quality control permitting the reliability of the results. A hundred and fifty patients have been enrolled in three care services for people living with HIV/AIDS in Dakar. This population was constituted of 119 seropositive and 31 seronegative patients acting as control group to have some patients with high rates of T lymphocytes CD4. For the follow-up at peripheral level, the patients were constituted of the active line of the patients living with HIV/AIDS supported in the targeted sites. The measurements allowed studying concordances for different rates of lymphocytes: 0 to 199, 200 to 499 and over 500 cells by mm3. The results showed also a very good correlation (r = 0.97 or r = 0.98 according to the operator) between the two methods for CD4 rates inferior to 500 cells by mm3 among both the negative group and the HIV positive patients. We also discussed the profit of decentralization for the program and the patient, as well as the setting up of an external quality control to validate the alternative technique. According to the results, the Dynabeads is well correlated with the Facscount. It is a technique that can be used as an alternative in the zones with limited resources, low prevalence and for a small number of samples.