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Overexpression of HPV-oncoproteins E6 and E7 is necessary for HPV-driven cervical carcinogenesis. Hence, these oncoproteins are promising disease-specific biomarkers. We assessed the technical and operational characteristics of the 8-HPV-type OncoE6/E7 Cervical Test in different laboratories using cervical samples from HPV-positive women living with (WLWH) and without HIV. The 8-HPV-type OncoE6/E7 Test (for short: "OncoE6/E7 test") was performed in 2833 HIV-negative women and 241 WLWH attending multicentric studies in Latin America (ESTAMPA study), and in Africa (CESTA study). Oncoprotein positivity were evaluated at each testing site, according to HIV status as well as type-specific agreement with HPV-DNA results. A feedback questionnaire was given to the operators performing the oncoprotein test to evaluate their impression and acceptability regarding the test. The OncoE6/E7 test revealed a high positivity rate heterogeneity across all testing sites (I 2 : 95.8%, p < .01) with significant lower positivity in WLWH compared to HIV-negative women (12% vs 25%, p < .01). A similar HPV-type distribution was found between HPV DNA genotyping and oncoprotein testing except for HPV31 and 33 (moderate agreement, k = 0.57). Twenty-one laboratory technicians were trained on oncoprotein testing. Despite operators' concerns about the time-consuming procedure and perceived need for moderate laboratory experience, they reported the OncoE6/E7 test as easy to perform and user-friendly for deployment in resource-limited settings. The high positivity rate variability found across studies and subjectivity in test outcome interpretation could potentially results in oncoprotein false positive/negative, and thus the need for further refinements before implementation of the oncoprotein testing in screen-triage-and-treat approaches is warranted., (© 2024 The Authors. International Journal of Cancer published by John Wiley & Sons Ltd on behalf of UICC.)

Background: In endemic areas, vertical transmission of hepatitis B virus (HBV) remains a major source of the global reservoir of infected people. Eliminating mother-to-child transmission (MTCT) of HBV is at the heart of World Health Organization's goal of reducing the incidence of HBV in children to less than 0.1% by 2030. Universal screening for hepatitis B during pregnancy and neonatal vaccination are the main preventive measures., Aim: To evaluate the efficacy of HBV vaccination combined with one dose of immunoglobulin in children born to hepatitis B surface antigen (HBsAg)-positive mothers in Djibouti city., Methods: We conducted a study in a prospective cohort of HBsAg-positive pregnant women and their infants. The study ran from January 2021 to May 2022, and infants were followed up to 7 mo of age. HBV serological markers and viral load in pregnant women were measured using aVidas microparticle enzyme-linked immunosorbent assay (Biomérieux, Paris, France) and the automated Amplix platform (Biosynex, Strasbourg, France). All infants received hepatitis B immunoglobulin and were vaccinated against HBV at birth. These infants were closely monitored to assess their seroprotective response and for failure of immunoprophylaxis. Simple logistic regression was also used to identify risk factors associated with immunoprophylaxis failure and poor vaccine response. All statistical analyses were performed with version 4.0.1 of the R software., Results: Of the 50 pregnant women recruited, the median age was 31 years, ranging from 18 years to 41 years. The MTCT rate in this cohort was 4% (2/50) in HBsAg-positive women and 67% (2/3) in hepatitis B e antigen-positive women with a viral load > 200000 IU/mL. Of the 48 infants who did not fail immunoprophylaxis, 8 (16%) became poor responders (anti-HB < 100 mIU/mL) after HBV vaccination and hepatitis B immunoglobulin, while 40 (84%) infants achieved a good level of seroprotection (anti-HB > 100 mIU/mL). Factors associated with this failure of immunoprophylaxis were maternal HBV DNA levels (> 200000 IU/mL) and hepatitis B e antigen-positive status (odds ratio = 158, 95% confidence interval: 5.05-4958, P < 0.01). Birth weight < 2500 g was associated with a poor immune response to vaccination (odds ratio = 34, 95% confidence interval: 3.01-383.86, P < 0.01)., Conclusion: Despite a failure rate of immunoprophylaxis higher than the World Health Organization target, this study showed that the combination of immunoglobulin and HBV vaccine was effective in preventing MTCT of HBV. Therefore, further studies are needed to better understand the challenges associated with immunoprophylaxis failure in infants in Djibouti city., Competing Interests: Conflict-of-interest statement: All the authors report no relevant conflicts of interest for this article., (©The Author(s) 2024. Published by Baishideng Publishing Group Inc. All rights reserved.)

Introduction: In Senegal, molecular diagnosis was widely used for the detection and management of COVID-19 patients. However, genomic surveillance was very limited in the public sector. This study aimed to share the experience of a Senegalese public sector laboratory in response to the COVID-19 pandemic, and to describe the distribution of variants circulating in 2020 and 2021., Methodology: From July 2020 to December 2021, SARS-CoV-2 qRT-PCR was performed on nasopharyngeal samples from travelers and symptomatic patients at the Bacteriology and Virology Laboratory (LBV) of the Aristide le Dantec University Teaching Hospital. Samples with a cycle threshold (Ct) ≤ 30 were selected for whole-genome sequencing (WGS) using the Nanopore technology. In-house scripts were developed to study the spatial and temporal distribution of SARS-CoV-2 variants in Senegal, using our sequences and those retrieved from the GISAID database., Results: Of 8,207 patients or travelers screened for SARS-CoV-2, 970 (11.8%) were positive and 386 had a Ct ≤ 30. WGS was performed on 133 samples. Concomitantly with high-quality sequences deposited in the GISAID database covering nine cities in Senegal in 2020 and 2021 (n = 1,539), we observed a high circulation of the 20A (B.1, B.1.416 and B.1.620) and 20B (B.1.1.420) lineages in 2020, while most of the samples belonged to Delta variants (AY34 and AY.34.1, 22%) in 2021., Conclusions: Despite its late involvement, COVID-19 diagnosis was routinely performed in LBV, but genomic characterization remained challenging. The genomic diversity of SARS-CoV-2 strains in Senegal reflected that observed worldwide during the first waves of the pandemic., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2024 Adjiratou Aissatou Ba, Romain Coppée, Assane Dieng, Jarra Manneh, Mengue Fall, Khadim Gueye, Pauline Yacine Sene, Samba Ndiour, Dianké Samaté, Pascaline Manga, Oumy Diop Diongue, Abdoulaye Camara, Abdou Padane, Sada Diallo; Sokhna Bousso Gueye; Makhtar Camara, Abdul Karim Sesay, Coumba Toure-Kane, Souleymane Mboup, Charlotte Charpentier, Halimatou Diop-Ndiaye.)

The hepatitis E virus (HEV) is a zoonotic pathogen with various hosts, including pigs, which act as reservoirs. In industrialized countries, sporadic cases caused by genotype 3, contracted by ingesting contaminated uncooked or undercooked meat, have been reported. However, in developing countries, HEV infection is mainly dominated by genotype 2 and often associated with poor hygiene conditions and drinking water supplies. HEV infection and its circulation in domestic fauna in West Africa are poorly documented. This study aimed to assess the presence of HEV in pork sold in Saint-Louis, Senegal. Meat products (250 g samples, n = 74) were purchased in August 2022 from three locations. Then, 2 g/sample was minced to extract total nucleic acids using the Purelink™ Viral DNA/RNA kit. RT-PCR reactions were performed using the One-Taq™ One-Step RT-PCR kit targeting the HEV ORF2 genomic region. The products obtained were visualized on a 1% agarose gel. Of a total of 74 samples, divided into pork meat ( n = 65) and pork liver ( n = 9), 5.4% ( n = 4) tested positive for HEV. In both cases, two samples were positive, representing a rate of 3.1% and 22.2% for meat and pork liver, respectively. All new viral sequences were obtained from a monophyletic group within HEV genotype 3. This study is the first to report the presence of HEV in pork sold in Senegal and the results reveal a potential circulation of HEV in the pig population. The high proportion of contamination in the pork liver samples highlights a major risk associated with their consumption.

Point-of-Care for HIV viral RNA quantification seems to be a complementary strategy to the existing conventional systems. This study evaluated the performance of the m-PIMA™ HIV1/2 Viral Load for the quantification of both HIV-1 and HIV-2 RNA viral load. A total of 555 HIV-1 and 90 HIV-2 samples previously tested by Abbott RealTime HIV-1 (Abbott, Chicago, USA) and Generic HIV-2® Charge virale (Biocentric, France) were tested using the m-PIMA™ HIV1/2 Viral Load at the HIV National Reference lab in Senegal. For HIV-1, Pearson correlation and Bland-Altman plots showed a coefficient r = 0.97 and a bias of -0.11 log 10 copies/ml (95% confidence interval [CI]: -0.086 to -0.133 log 10 copies/ml) for the m-PIMA™ HIV1/2 Viral Load, respectively. Sensitivity and specificity at 3 log 10 copies/ml (threshold of virological failure) were 93.6% (95%[CI]: 91.5% to 95.6%) and 99.1% (95%[CI]: 98.3% to 99.9%), respectively. For HIV-2, a correlation of r = 0.95 was also noted with a bias of - 0.229 log 10 copies/ml (95%[CI]: -0.161 to -0.297 log 10 copies/ml). Sensitivity and specificity at 3 log 10 copies/ml were 97.6% (95%[CI]: 94.3% to 100%) and 93.9% (95%[CI]: 88.9% to 98.8%), respectively. These results confirmed that m-PIMA™ HIV1/2 VL could be a good alternative for HIV-1 and HIV-2 viral load testing in decentralized settings in Senegal., Competing Interests: Declaration of Competing Interest The authors do not declare any conflict of interest., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

The eradication of neonatal Group B Streptococcus (GBS) infections, considered as a major public health priority, necessarily requires a mastery of the data on vaginal carriage in pregnant women. The aims of this study were to determine the prevalence of vaginal carriage of GBS in pregnant women, antibiotic susceptibility, and associated risk factors. This was a cross-sectional, descriptive study conducted over a period of 9 months (July 2020 to March 2021) in pregnant women between 34 and 38 weeks of gestation (WG) followed at the Nabil Choucair health center in Dakar. Identification and antibiotic susceptibility of GBS isolates were performed on the Vitek 2 from vaginal swabs cultured on Granada medium. Demographic and obstetric interview data were collected and analyzed on SPSS (version 25). The level of significance for all statistical tests was set at P  < .05. The search of GBS vaginal carriage had involved 279 women aged 16 to 46 years, with a median pregnancy age of 34 (34-37) weeks' gestation. GBS was found in 43 women, for a vaginal carriage rate of 15.4%. In 27.9% (12/43) of volunteers screened, this carriage was monomicrobial, while in 72.1% (31/43) of women, GBS was associated with other pathogens such as Candida spp. (60.5%), Trichomonas vaginalis (2.3%), Gardnerella vaginalis (34.9%) and/or Mobiluncus spp. (11.6%). The level of resistance was 27.9% (12/43) for penicillin G, 53.5% (23/43) for erythromycin, 25.6% (11/43) for clindamycin and 100% for tetracycline. However, the strains had retained fully susceptible to vancomycin and teicoplanin. The main risk factor associated with maternal GBS carriage were ectocervical inflammation associated with contact bleeding (OR = 3.55; P  = .005). The high rate of maternal vaginal GBS carriage and the levels of resistance to the various antibiotics tested confirm the importance of continuous GBS surveillance in our resource-limited countries., Competing Interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2023.)

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.

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.

Introduction: the introduction of the point-of-care in HIV-1 viral load quantification appears to be a complementary strategy to the existing conventional system of the acceleration plan for the achievement of the three 90s in Senegal. The objective of this study was to evaluate the performance of the Xpert® HIV-1 viral load in the context of circulation of non-B, non-C subtypes., Methods: two hundred samples, were tested on Xpert® HIV-1 Viral Load using 1 ml of plasma in comparison to 600 μl on Abbott Real-time HIV-1 assay. The difference between viral load values was considered significant for Dlog <0.5 log copies/ml., Results: a good correlation (r=0.985) was noted and confirmed using passing-bablok regression (slope 1.048; 95% CI: 1.036 to 1.069) for 188 samples with samples. A mean difference of 0.0075 log10 copies/ml for a 95% confidence interval (CI) of 0.002 log10 copies/ml to 0.013 log10 copies/ml was obtained. Sensitivity and specificity were respectively 93.6% and 93.5% at the threshold of 1.6 log10 copies/ml and 100% and 99% at the threshold of 3.0 log10 copies/ml., Conclusion: these results show that Xpert® HIV-1 Viral Load has excellent performance. In Senegal, and can be used for HIV viral load monitoring., Competing Interests: The authors declare no competing interest., (Copyright: Pauline Yacine Sène et al.)

Hepatitis B virus (HBV) is generally endemic in resource-limited countries, which are characterized by a deficit of technical facilities that could delay diagnosis and treatment. To facilitate the accessibility to diagnostic and connection to treatment, evaluation, and promotion of alternatives and/or simplified strategies and inexpensive tools such as dried blood specimens need to be investigated and implemented. This study aimed to evaluate dried blood spots (DBS) for the detection and quantification of HBsAg. This study included 100 DBS from subjects tested positive for HBsAg, and 50 DBSs from subjects tested negative for HBsAg by the automate Architect i1000sr (Abbott Diagnostics, Ireland). Hepatitis B surface antigen detection was performed with determine HBsAg Alere® tests (Alere International Limited, Ireland) and Architect® HBsAg Qualitative II Assays (Abbott, Diagnostics, Ireland) after 15 and 30 days (D15, D30). For HBsAg-positive subjects, the quantification of HBsAg was performed at day zero (D0) from plasma and at D15 and D30 from the DBSs. At D15, the sensitivity and specificity were 96% and 100% for the Determine® tests and 100% and 100% for the Architect® tests, respectively. At D30, the sensitivity and specificity were 96% and 100% for the Determine® tests and 100% and 100% for the Architect® tests, respectively. For HBsAg quantification, the agreement rates were 96%, 96% and 100% between D0-D15, D0-D30 and D15-D30, respectively. This work showed that DBSs can be very useful for HBsAg detection and quantification and therefore in the management of HBV infection in resource-limited settings., Competing Interests: The authors declare no competing interests., (Copyright: Anna Julienne Selbé Ndiaye et al.)

Purpose: Use of circulating tumor DNA (ctDNA) for diagnosis is limited regarding the low number of target molecules in early-stage tumors. Human papillomavirus (HPV)-associated carcinomas represent a privileged model using circulating viral DNA (ctHPV DNA) as a tumor marker. However, the plurality of HPV genotypes represents a challenge. The next-generation sequencing (NGS)-based CaptHPV approach is able to characterize any HPV DNA sequence. To assess the ability of this method to establish the diagnosis of HPV-associated cancer via a blood sample, we analyzed ctHPV DNA in HPV-positive or HPV-negative carcinomas., Experimental Design: Patients (135) from France and Senegal with carcinoma developed in the uterine cervix (74), oropharynx (25), oral cavity (19), anus (12), and vulva (5) were prospectively registered. Matched tumor tissue and blood samples (10 mL) were taken before treatment and independently analyzed using the CaptHPV method., Results: HPV prevalence in tumors was 60.0% (81/135; 15 different genotypes). Viral analysis of plasmas compared with tumors was available for 134 patients. In the group of 80 patients with HPV-positive tumors, 77 were also positive in plasma (sensitivity 95.0%); in the group of 54 patients with HPV-negative tumors, one was positive in plasma (specificity 98.1%). In most cases, the complete HPV pattern observed in tumors could be established from the analysis of ctHPV DNA., Conclusions: In patients with carcinoma associated with any HPV genotype, a complete viral genome characterization can be obtained via the analysis of a standard blood sample. This should favor the development of noninvasive diagnostic tests providing the identification of personalized tumor markers. See related commentary by Rostami et al., p. 5158., (©2021 The Authors; Published by the American Association for Cancer Research.)

Objectives: With the perspective of prophylactic vaccination against high-risk human papillomavirus (HPV), we analyzed the viral epidemiology of cervical neoplasia in Senegal., Methods: All patients were treated at the Institut Joliot Curie du Cancer in Dakar. HPV genotypes were characterized using a real-time polymerase chain reaction-based approach and sequencing., Results: Histologically, there were 224 invasive carcinomas, 17 high-grade intraepithelial neoplasia (CIN), and five undetermined histologies. Molecular analysis was conclusive in 241 cases. HPV DNA was found in 207/241 (85.9%) cases while 34/241 (14.1%) remained HPV negative. There was one single genotype in 127/207 (61.4%) cases and several in 80/207 (38.6%) corresponding to 308 genotypes identified. Viral genotyping found HPV16 in 175 (56.8%) cases, HPV18 in 45 (14.6%), HPV45 in 40 (13.0%), HPV58 in 35 (11.4%), HPV33 in 6 (2.0%), HPV35 in 3 (1.0%), HPV31 in 2 (0.6%), HPV39 and HPV56 in one (0.3% each)., Conclusion: Our analysis showed that 98.4% of the HPV-positive cases were associated with viral genotypes covered by the 9-valent HPV vaccine. However, 14.1% of cases remained HPV negative. Therefore, prophylactic vaccination using a 9-valent vaccine should dramatically reduce the incidence of HPV-associated neoplasia but the detection and treatment of CIN remain necessary for the optimal prevention of cervical cancer., (© 2021 Wiley Periodicals LLC.)

Background: The feasibility of antiretroviral therapy (ART) monitoring remains problematic in decentralized HIV clinic settings of sub-Saharan Africa. We assessed the rates and correlates of HIV-1 virological failure (VF) and drug resistance (DR) in 2 pre-test-and-treat urban clinic settings of Senegal., Methods: Consenting HIV-1-infected adults (⩾18 years) receiving first-line ART for ⩾12 months were cross-sectionally enrolled between January and March 2015, at the referral outpatient treatment center of Dakar (n = 151) and decentralized regional hospital of Saint-Louis (n = 127). In the 12 months preceding plasma specimens' collection patients at Saint-Louis had no viral load (VL) testing. Significant predictors of VF (VL ⩾ 1000 copies/ml) and DR (clinically relevant mutations) were determined using binomial logistic regression in R software., Results: Of the 278 adults on EFV-/NVP-based regimens, 32 (11.5% [95%CI: 8.0-15.9]) experienced VF. Failing and non-failing patients had comparable median time [interquartile] on ART (69.5 [23.0-89.5] vs 64.0 [34.0-99.0] months; P  = .46, Mann-Whitney U -test). Of the 27 viraemic isolates successfully genotyped, 20 (74.1%) carried DR mutations; most frequent were M184VI (55.6%), K103N (37.1%), thymidine analog mutations (29.6%), Y181CY (22.2%). The pattern of mutations did not always correspond to the ongoing treatment. The adjusted odds of VF was significantly associated with the decentralized clinic site ( P  < .001) and CD4 < 350 cells/mm 3 ( P  < .006). Strong correlates of DR also included Saint-Louis ( P  < .009), CD4 < 350 cells/mm 3 ( P  <. 001), and nevirapine-based therapies (comparator: efavirenz-based therapies; P  < .027). In stratification analyses by site, higher rate of VF at Saint-Louis (20.5% [95%CI: 13.8-28.5] vs 4.0% [95%CI: 1.5-8.5] in Dakar) was associated with nevirapine-based therapies (OR = 3.34 [1.07-11.75], P  = .038), self-reported missing doses (OR = 3.30 [1.13-10.24], P  = .029), and medical appointments (OR = 2.91 [1.05-8.47], P  = .039) in the last 1 and 12 months(s), respectively. The higher rate of DR at Saint-Louis (12.9% [95%CI: 7.6-20.1] vs 2.7% [95%CI: 0.7-6.7] in Dakar) was associated with nevirapine-based therapies (OR = 5.13 [1.12-37.35], P  = .035)., Conclusion: At decentralized urban settings, there is need for enhanced virological monitoring and adherence support. HIV programs in Senegal should intensify early HIV diagnosis for effective test-and-treat. These interventions, in addition to the superiority of efavirenz-based therapies provide a favorable framework for transitioning to the recommended potent drug dolutegravir, thereby ensuring its long-term use., Competing Interests: Declaration of conflicting interests:The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2021.)

Background: First ambitious target by 2020 of UNAIDS is that 90% of people living with HIV know their HIV status. In people older than 18 months of age, serological confirmation test is recommended to confirm HIV infection., Case Presentation: Here we report the case of a patient tested positive with HIV-1, ELISA, Murex ® Ag⁄Ab Combination assay (OD450 = 0.802 and cutoff-OD = 0.279) and negative by using FIRST RESPONSE HIV1-2.O CARD TEST (version 2.0) RAPID HIV CARD TEST. Viral load performed with Cobas ® TaqMan ® 96/Cobas ® Ampliprep ® was 6.49log 10. The virus could be sequenced in partial gag and pol genes and belonged to CRF02&#95;AG clade., Conclusion: Conventional PCR is a complementary method for the diagnosis of inconclusive HIV-1 serologies by antibodies.

Background and Aims: Sub-Saharan Africa (SSA) is the region with the most patients co-infected with the human immunodeficiency virus (HIV) and the hepatitis B virus (HBV) worldwide. However, few studies have focused on SSA children who are at a higher risk of developing a chronic infection than adults. Furthermore, children on first-line antiretroviral therapy (ART) including low genetic barrier drugs may develop both HBV and HIV resistance mutations. The aim of this work was to document HIV-HBV co-infection and to characterize the HBV isolates in children in Senegal., Methods: This is a retrospective study of 613 children infected with HIV on ART or not. Dried blood spot (DBS) specimens were used to detect hepatitis B surface antigen (HBsAg) with a rapid diagnostic test (RDT). Confirmation of HBsAg status and hepatitis B e antigen (HBeAg) detection was performed on an automated platform using the chemiluminescence assay technology. HBV viral DNA was quantified by real-time polymerase chain reaction (PCR) and the preS1/preS2/HBsAg region was genotyped by nested PCR followed by sequencing using the Sanger technique., Results: The prevalence of HIV-HBV co-infection was 4.1% (25/613). The median age of co-infected children was 13 years (2 years-16 years) and 40% (10/25) were girls. Almost all 19/20 (95%) were infected with HIV-1 and 79% (19/24) were treated with 3TC-based triple combination ART. The median duration of time on ART was 15 months (3 months-80 months). More than half of the children 53% (9/17) were experiencing HIV virologic failure and 75% (6/8) had at least one HIV-related resistance-associated mutation (RAM). Of the six children with resistance, none of the three administered treatments were effective on HIV. Of the 25 co-infected children, 82% (18/22) were HBeAg-positive, while the median HBV viral load (VL) was 6.20 log 10 IU/mL (24/25 patients), and 62,5% (10/16) of the children had a persistent HBV viremia. Combination of ART was the only factor associated with HBV viremia persistence. Amplification was successful in 15 out of 16 patients (rate of 94%), and the ensuing phylogenetic analysis revealed that eight strains (53%) belonged to genotype A and seven (47%) to genotype E. HBV-related 3TC RAMs were uncovered in 20% of these patients (3/15). HBsAg escape mutations were found in 20% of the children (3/15)., Conclusions: Our results showed a high level of drug resistance mutations to both HIV and HBV, a significant level of HBsAg escape mutations, HBV DNA persistence and HIV virologic failure in co-infected children in Senegal. The HBV genotypes found were A and E., (Copyright © 2020 Elsevier Masson SAS. All rights reserved.)

Objective: We aimed to assess the frequency of tenofovir (TDF) resistance in people failing tenofovir/lamivudine or emtricitabine (XTC)/nonnucleotide reverse-transcriptase inhibitor-based first-line antiretroviral treatment (ART) using data from 15 nationally representative surveys of HIV drug resistance conducted between 2014 and 2018 in Cameroon, Guatemala, Honduras, Nicaragua, Senegal, Uganda, Vietnam and Zambia., Methods: Prevalence of nucleoside reverse-transcriptase inhibitor resistance among participants with virological nonsuppression (viral load ≥1000 copies/ml) who had received TDF-based ART for 12-24 months (early ART group) and at least 40 months (long-term ART group) was assessed using Sanger sequencing and resistance was interpreted using the Stanford HIVdb algorithm. For each group, we estimated a pooled prevalence using random effect meta-analysis., Results: Of 4677 participants enrolled in the surveys, 640 (13.7%) had virological nonsuppression, 431 (67.3%) were successfully genotyped and were included in the analysis; of those, 60.3% (260) were participants in the early ART group. Overall, 39.1, 57.9, 38.5 and 3.6% patients in the early ART group and 42.9, 69.3, 42.9 and 10.0% patients on long-term ART had resistance to TDF, XTC, TDF + XTC and TDF + XTC + zidovudine, respectively. Overall, tenofovir resistance was mainly due to K65R or K70E/G/N/A/S/T/Y115F mutations (79%) but also due to thymidine analogue mutations (21%) which arise from exposure to thymidine analogues but causing cross-resistance to TDF., Conclusion: Dual resistance to TDF + XTC occurred in more than 40% of the people with viral nonsuppression receiving tenofovir-based first-line ART, supporting WHO recommendation to optimize the nucleoside backbone in second-line treatment and cautioning against single drug substitutions in people with unsuppressed viral load.

Condom use remains a mainstay of HIV prevention programs around the world. However, data characterizing economic determinants of condom use among female sex workers (FSW) are limited, including in Senegal. We recruited 718 FSWs via respondent-driven sampling. Bivariate and multivariable regressions were conducted to assess the associations between economic variables and condom use at last sex. Paying rent (aRR: 1.07, 95%CI 1.01-1.13) was positively associated with condom use at last sex with new clients. No statistically significant associations were found between condom use and financial responsibility for dependent children, having additional source of income, sharing sex work earnings, or the ability to borrow from other FSWs, regardless of sexual partner types. The relationship between economic marginalization and consistent condom use among sex workers is complex reinforcing the need for behavioral economic research and prevention to be integrated into HIV prevention and treatment research and programs.

Objective: Seventeen years after the start of the IBAARV (Beninese initiative for access to antiretrovirals), transmitted drug resistance mutations in ARV-naïve patients and HIV-1 genetic diversity were investigated in Benin., Results: Drug resistance mutations were detected in (27/248; 10.9%) according to the WHO SDRM 2009 list, with a predominance of mutations directed against NNRTIs drugs (24/248; 10%). Phylogenetic and recombination analyses showed a predominance of CRF02&#95;AG strains (165/248; 66.5%) and a high genetic diversity with five other variants and 39 URFs (15.7%) which contained portions of strains that co-circulate in Benin. Eight recent transmission chains revealed active ongoing transmission of HIV-1 strains among ARV-naïve patients. Our study showed a moderate primary drug resistance mutations rate and also provided recent data on the HIV-1 variants that circulate in Benin. Regular monitoring of primary drug resistance is required to adapt HIV-1 treatment strategies and adoption of new WHO recommendations in Benin.

Objectives: Several studies have documented the HPV genotypes in the Senegalese general population. The objective was to explore the HPV genotype distribution in Senegalese FSWs in order to assess the potential relevance of currently-available vaccines., Methods: Vaginal swabs samples collected as part of the National Integrated Biological and Behavioral Survey in 14 regions throughout the country were randomly selected for HPV testing using bead-based multiplex genotyping (TS-MPG)., Results: Among the 436 FSW samples analyzed, the overall HPV prevalence was 79.8% (N = 348), with 70.1% (N = 244) cases presenting as multiple infections. High Risk HPV genotypes affecting at least 10% of FSWs included in order of decreasing frequency: 52, 16, 35, 51, 33, 31, 18, and 45. Sixty-seven (15.4%) FSWs were HIV positive and they were significantly more affected by HPV (94% vs 77%; p < 0.01) than seronegative FSWs as well as infections with multiple genotype., Conclusion: The present study indicates that FSW in Senegal experience a high burden of HPV infection with a high frequency of coinfection with HIV and multiple HPV genotypes. Public health interventions for this key population should include an earlier cervical dysplasia/cancer detection and preventative measures such as vaccination programs that must consider the HPV genotype distribution., (Copyright © 2019 The Authors. Published by Elsevier B.V. All rights reserved.)

Background: To improve the care and treatment of HIV-exposed children, early infant diagnosis (EID) using dried blood spot (DBS) sampling has been performed in Senegal since 2007, making molecular diagnosis accessible for patients living in decentralized settings. This study aimed to determine the evolution of the HIV transmission rate in children from 2008 to 2015 and to analyze associated factors, particularly the mother's treatment status and/or child's prophylaxis status and the feeding mode., Methods: The data were analyzed using EID reports from the reference laboratory. Information related to sociodemographic characteristics, HIV profiles, the mother's treatment status, the child's prophylaxis status, and the feeding mode was included. Descriptive statistics were calculated, and bivariate and multivariate logistic regression analyses were performed., Results: During the study period, a total of 5418 samples (5020 DBS and 398 buffy coat) from 168 primary prevention of HIV mother-to-child transmission (PMTCT) intervention sites in Senegal were tested. The samples were collected from 4443 children with a median age of 8 weeks (1-140 weeks) and a sex ratio (M/F) of 1.1 (2309/2095). One-third (35.2%; N = 1564) of the children were tested before 6 weeks of age. Twenty percent (N = 885) underwent molecular diagnostic testing more than once. An increased number of mothers receiving treatment (57.4%; N = 2550) and children receiving prophylaxis (52.1%; N = 2315) for protection against HIV infection during breastfeeding was found over the study period. The transmission rate decreased from 14.8% (95% confidence interval (CI): 11.4-18.3) in 2008 to 4.1% (95% CI: 2.5-7.5) in 2015 (p < 0.001). However, multivariate logistic regression analysis revealed that independent predictors of HIV mother-to-child transmission included lack of mother's treatment (adjusted odd ratio (aOR) = 3.8, 95% CI: 1.9-7.7; p˂0.001), lack of child's prophylaxis (aOR = 7.8, 95% CI: 1.7-35.7; p = 0.009), infant age at diagnosis (aOR = 2.2, 95% CI: 1.1-4.3 for ≤6 weeks versus 12-24 weeks; p = 0.025) and protective effect of breastfeeding on ART against formula feeding (aOR = 0.4, 95% CI: 0.2, 0.7; p = 0.005)., Conclusion: This study demonstrates the effectiveness of PMTCT interventions in Senegal but indicates also that increased efforts should be continued to reduce the MTCT rate to less than 2%., Competing Interests: The authors have declared that no competing interests exist.

Background: Female sex workers (FSWs) are disproportionately affected by HIV even in the most generalized HIV epidemics. Although structural HIV risks have been understood to affect condom negotiation among FSWs globally, there remain limited data on the relationship between structural determinants of HIV risk, including violence and socioeconomic status, and condom use among FSWs across sub-Saharan Africa. Here, we describe the prevalence of structural determinants and their associations with condom use among FSWs in Senegal., Methods: In 2015, 758 FSWs >18 years of age were recruited using respondent driven sampling in Senegal. Data on individual, community, network, and structural-level risks were collected through an interviewer-administered questionnaire. Poisson regression with robust variance estimation was used to model the associations of consistent condom use (CCU) and selected structural determinants., Results: The respondent driven sampling-adjusted prevalence of CCU in the last 10 sexual acts was 76.8% [95% confidence interval (CI): 70.8 to 82.8]. Structural determinants that were significantly associated with lower CCU were as follows: physical violence [adjusted prevalence ratio (aPR): 0.71; 95% CI: 0.52 to 0.98]; working primarily in a hotel or guest house (aPR: 0.85; 95% CI: 0.73 to 0.99); and difficultly accessing condoms (aPR: 0.72; 95% CI: 0.52 to 0.96). High income from sex work (aPR: 1.23; 95% CI: 1.04 to 1.46) was significantly associated with higher CCU., Conclusions: Taken together, these data highlight the role of structural risk determinants on condom use among FSWs in Senegal. Moreover, these results highlight the need for structural interventions, including safe working spaces and violence mitigation programs, to support condom negotiation and access. Combined with condom distribution programs, structural interventions could ultimately increase condom use among FSWs in Senegal.

Introduction: Hepatitis B virus (HBV) infection is highly endemic in Senegal. HBV vaccine of all children has been introduced in 1999 and included in the Expanded Programme on Immunization in 2004. The aim of this study was to assess the HBV prevalence and immunity status against HBV amongst children in Senegal., Methods: Between March and August 2016, consecutive children aged from 6 months to 16 years old were recruited in outpatient department of three main children hospitals in Senegal. Serum samples were analyzed for HBV serology (HBsAg, HBcAb, HBsAb) using ARCHITECT analyzer. Children with HBsAb levels ≥ 10 IU/l) were considered as seroprotected against HBV., Results: During the study period, 295 children fulfilled the criteria for the study and were further analyzed. Three children were HBsAg positive giving a seroprevalence at 1.1% (95% CI: 0.2-3.3), 12/267 (4.5%, 95% CI=2.3-7.7) had positive HBcAb and 226/295 (76.6%, 71.4-81.3) had positive HBsAb including 191 (77.3%, 71.6-82.4) with isolated HBsAb related to previous active immunization. However only 165 children (56%, CI 50-62) had seroprotective HBsAb levels (HBsAb ≥ 10 UI/L) and 63 (21.4, 16.8-26) had a strong seroprotectiondefined by HBsAb ≥ 100 IU/L., Conclusion: Our results suggest that although HBV prevalence has significantly decreased in children in Senegal following a better HBV vaccine coverage, the number of children correctly seroprotected is insufficient (56%). Assessing the levels of HBsAb and providing HBV vaccine boosters should be considered in children in Senegal., Competing Interests: The authors declare no competing interests.

Objectives: Disruption in HIV care provision may enhance the development and spread of drug resistance due to inadequate antiretroviral therapy. This study thus determined the prevalence of HIV-1 transmitted drug resistance (TDR) in settings of decentralized therapy and care in Senegal and, the Ebola outbreak in Guinea. Antiretroviral-naïve patients were enrolled following a modified WHO TDR Threshold Survey method, implemented in Senegal (January-March 2015) and Guinea (August-September 2015). Plasma and dried blood spots specimens, respectively from Senegalese (n = 69) and Guinean (n = 50) patients, were collected for direct sequencing of HIV-1 pol genes. The Stanford Calibrated Population Resistance program v6.0 was used for Surveillance Drug Resistance Mutations (SDRMs)., Results: Genotyping was successful from 54/69 (78.2%) and 31/50 (62.0%) isolates. In Senegal, TDR prevalence was 0% (mean duration since HIV diagnosis 4.08 ± 3.53 years). In Guinea, two patients exhibited SDRMs M184V (NRTI), T215F (TAM) and, G190A (NNRTI), respectively. TDR prevalence at this second site, however, could not be ascertained because of low sample size. Phylogenetic inference confirmed CRF02&#95;AG predominance in Senegal (62.96%) and Guinea (77.42%). TDR prevalence in Senegal remains extremely low suggesting improved control measures. Continuous surveillance in both settings is mandatory and, should be done closest to diagnosis/transmission time and with larger sample size.

Background: In this work, we investigated the genetic diversity of HIV-1 and the presence of mutations conferring antiretroviral drug resistance in 50 drug-naïve infected persons in the Republic of Congo (RoC). Samples were obtained before large-scale access to HAART in 2002 and 2004., Methods: To assess the HIV-1 genetic recombination, the sequencing of the pol gene encoding a protease and partial reverse transcriptase was performed and analyzed with updated references, including newly characterized CRFs. The assessment of drug resistance was conducted according to the WHO protocol., Results: Among the 50 samples analyzed for the pol gene, 50% were classified as intersubtype recombinants, charring complex structures inside the pol fragment. Five samples could not be classified (noted U). The most prevalent subtypes were G with 10 isolates and D with 11 isolates. One isolate of A, J, H, CRF05, CRF18 and CRF37 were also found. Two samples (4%) harboring the mutations M230L and Y181C associated with the TAMs M41L and T215Y, respectively, were found., Conclusion: This first study in the RoC, based on WHO classification, shows that the threshold of transmitted drug resistance before large-scale access to antiretroviral therapy is 4%.

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., (© 2015 Wiley Periodicals, Inc.)

The goal of this study was to evaluate using the molecular diagnosis, infection transmission rate of HIV in children born to HIV-1 positive mothers as part of the prevention of mother-to-child transmission (PMTCT) in Benin. The sample consisted of 524 dried blood spots (DBS) of children born to HIV-1 positive mothers, from 30 sites (PMTCT) taken between October 2009 and June 2010. The diagnosis of HIV-1 was performed by the qualitative detection of viral nucleic acids (RNA and DNA) in DBS on filter paper using the Abbott RealTime(®) HIV-1 Qualitative assay. We found that 51 DBS were positive (9.7%) and 473 were negative (90.3%). The failure rate of PMTCT among 420 mothers who received antiretroviral prophylaxis was 6.7% (28/420). This failure rate was significantly higher among children born to infected mothers on antiretroviral monotherapy than on triple therapy (HAART). The results of our study enrich the data in the literature on highly active antiretroviral chemoprophylaxis to reduce the transmission of HIV-1 from mother to child.

Hepatitis B is a major public health problem in Senegal, a country with high prevalence and a transmission occurring mainly during infancy. Only, one 6-8 weeks vaccination campaign was initiated in 2005 and it was part of the expanded program of immunization. The aim of this study was to determine the prevalence of HBsAg in children born from HIV-seropositive mothers by using dried blood specimens. Specimens were collected between July 2007 and November 2012 from children aged 2-48 weeks in Dakar and decentralized sites working on HIV mother-to-child transmission prevention. HBsAg detection was performed using Architect HBsAg Qualitative II kit (Abbott Diagnostics, Ireland) and for all reactive samples confirmation was done using Architect HBsAg Qualitative II Confirmatory kit (Abbott Diagnostics, Ireland). Nine hundred thirty samples were collected throughout the country with 66% out of Dakar, the capital city. The median age was 20 weeks and 88% of children were less than 1 year of age with a sex ratio of 1.27 in favor of boys. HBsAg was detected in 28 cases giving a global prevalence of 3%. According to age, HBsAg prevalences were 5.1% for children less than 6 weeks, 4.1% and 4.6%, respectively, for those aged 12-18 weeks and 18-24 weeks of age. The HIV prevalence was 2.6% with no HIV/HBV co-infection. This study showed a high rate of HBV infection in children under 24 months, highlighting the need to promote birth-dose HBV vaccination as recommended by WHO., (© 2015 Wiley Periodicals, Inc.)

In the context of early infant diagnosis (EID) decentralization in sub-Saharan Africa, dried blood spot (DBS) is now widely used for HIV proviral DNA detection in resource-limited settings. A new version of CAP/CTM (version 2) has been introduced, recently by Roche Diagnosis as a new real-time PCR assay to replace previous technologies on qualitative detection of HIV-1 DNA using whole blood and DBS samples. The objective of this study was to evaluate CAP/CTM version 2 compared to CAP/CTM version 1 and Amplicor on DBS. A total of 261 DBS were collected from children aged 4 weeks to 17 months born from HIV-seropositive mothers and tested by the three techniques. CAP/CTM version 2 showed 100% of agreement with Amplicor including 74 positive results and 187 negative results. CAP/CTM version 2 versus CAP/CTM version 1 as well as CAP/CTM version 1 versus Amplicor showed two discordant results giving a sensitivity of 98.6%, specificity of 99.5%, positive predictive value of 98.6% and negative predictive value of 99.5%. The concordance was 99.12% (95% of confidence interval) giving a Kappa coefficient of 0.97 (p<0.001). These findings confirmed the expected good performance of CAP/CTM version 2 for HIV-1 EID., (Copyright © 2015 Elsevier B.V. All rights reserved.)

The study aimed to estimate the prevalence of Hepatitis B virus (HBV) infection and to describe the HBV virological profiles among Senegalese HIV-1-infected patients. We conducted a retrospective study between 2006 and 2010 among Senegalese HIV-1-infected patients from the antiretroviral therapy cohort. Samples were screened using Determine(®) HBsAg or MONOLISA(®) POC test. The HBsAg positivity status was confirmed by Architect(®) HBsAg. Detection of HBeAg, anti-HBe Ab, and HBV DNA load were done for the HBsAg-positive samples. Then, Anti-HBcAb was tested for the HBsAg-negative samples. Microsoft Excel was used for data collection and statistical analyses were performed using Epi info 3.5.1. Overall, 466 HIV-infected patients were enrolled including 271 women (58.4%), and 193 men (41.6%) with a median age of 39 years (19-74 years). The global prevalence of HIV/HBV coinfection (HBsAg positive) was 8.8% (41/466). For HBsAg positives samples, the prevalence of HBeAg and the anti-HBeAb were, respectively, 24.4 and 69.2% and the median of HBV DNA viral load, for 27 HBsAg-positive samples, was 3.75 log10 copies/ml. The virological profiles were the following: 7, 15, and 5 patients infected, respectively, by a replicative virus, an inactive virus and a probably mutant virus. For HBsAg-negative samples, 83 out of 109 were positive for anti-HBcAb. This study showed a significant decrease of the prevalence of HBV/HIV coinfection between 2004 and 2014 (P = 0.003), which highlighted the performance of the Senegalese HBV vaccine program. However, implementing a systematic quantification of HBV DNA viral load could improve the monitoring of HBV-infected patient., (© 2015 Wiley Periodicals, Inc.)

Introduction: Herpes simplex virus (HSV) is the main co-factor for heterosexual transmission of the human immunodeficiency virus (HIV) in sub-Saharan Africa, and could be involved in the dynamics of the HIV epidemic in Senegal., Methodology: Genital shedding of HSV was evaluated in adult females who had visited the provincial healthcare centres in Diass, Louga, and Kebemer in Senegal. Study subjects were interviewed by a healthcare worker for sociodemographic characteristics and sexual behavior, and HIV serology was offered. In addition, cervical secretion lavage samples were evaluated for HSV DNA by real-time polymerase chain reaction (PCR), the melting curve analysis of which permitted distinction between HSV type 1 (HSV-1) and HSV type 2 (HSV-2)., Results: Among 302 women (mean age, 40 years) enrolled, none were infected by HIV. The mean age at first sexual intercourse was 20 years, and the mean number of sexual partners in the previous year was 1.3 (range, 1-7). Only 6 of 302 (1.9%) women had cervico-vaginal secretions positive for HSV DNA. No association between HSV DNA shedding and any sociodemographic or biological variables was found. Surprisingly, genital shedding of HSV-1 was found in two (0.7%) women, representing 33% of herpes-shedding women, and HSV-2 in four (1.5%) women., Conclusions: Taken together, our observations indicate a low prevalence of HSV DNA genital shedding in adult Senegalese women.

The aim of this study was to compare four HIV-1 viral quantitation platforms, Nuclisens EasyQ v2.0(®) (EQ), COBAS AmpliPreP/Cobas Taqman(®) HIV-1 test v 2.0 (CTM), GENERIC HIV CHARGE VIRALE(®) (GEN), with Abbott Real Time HIV-1(®) (m2000sp/rt) as reference technique. The study had first evaluated m2000sp/rt performances and then compared quantitation between techniques. Discordant samples were genotyped on gag and pol gene and sequences were analyzed using Sequence locator and SeqPublish to detect eventual mismatches. Performance analysis of m2000sp/rt showed good results with coefficients of variation values (CV) of 1.35%, 0.65%, and 0.54% for repeatability testing of low, intermediate and high concentrations, respectively. Reproducibility tests showed low CV values with 2.36% and 1.42% for low and high concentration levels, respectively and contamination test was very low value with 0.94%. Correlation and concordance between techniques ranged from r(2)=0.98 and bias=-0.00185 (for m2000sp/rt vs CTM) to r(2)=0.90 and bias=-0.135 (for EQ vs GEN). Discrepancies were observed on 37 samples mostly CRF02&#95;AG but despite some mismatches, sequence analysis (26/37) did not show any remarkable differences between CRF02&#95;AG queries and references. This study showed good correlation and good concordance between techniques. However, EQ yielded under-quantitation of CRF02&#95;AG., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Introduction: Chlamydia trachomatis and Neisseria gonorrhoeae are the most common causes of sexually transmitted disease in Senegal and worldwide. Molecular techniques have become the standard for their detection, and due to the frequency of co-infections, these tests can detect both agents and can be used on urine samples, vaginal swabs, or endocervical samples. In developing countries, the use of these molecular techniques is very limited and there is a need for evaluations of these techniques to be done., Methodology: A total of 181 samples were tested with the Abbott RealTime CT/NG assay and compared with the Roche Cobas Amplicor CT/NG assay. Specimens were collected from the key population of men having sex with men (urine, n = 60), female sex workers (genital swabs, n = 60) and from women visiting the laboratory for a gynecological checkup (urine, n = 60 and endocervical samples, n = 61)., Results: The agreement between the two techniques was 98.90% with a Kappa coefficient of 0.98. A sensitivity of 93.3%, a specificity of 100%, a positive predictive value of 100%, and a negative predictive value of 93.3% were found for both Chlamydia trachomatis and Neisseria gonorrhoeae., Conclusion: These results showed that both methods are similar and suitable for the detection of CT/NG in all types of samples examined in this study.

Introduction: This report documents a rare case of Chryseobacterium indologenes urinary tract infection in Senegal. Chryseobacterium indologenes is an uncommon human pathogen reported in hospital outbreaks in Taiwan and there have been some sporadic cases reported in Europe and in the USA mainly from immune-suppressed patients., Case Presentation: This case report describes a 42-year-old woman of Wolofa ethnicity who was hospitalized in our Department of Internal Medicine in a Senegalese university teaching hospital, with acute leukemia who died of severe sepsis 10 days following her hospitalization. A strain of Chryseobacterium indologenes isolated from her urine sample was resistant to several beta-lactams including ampicillin (minimum inhibitory concentrations ≥ 256 μg/mL), cefotaxime (minimum inhibitory concentrations 32 μg/mL) and imipenem (minimum inhibitory concentrations ≥ 32 μg/mL), whereas it was susceptible to piperacillin (minimum inhibitory concentrations 16 μg/mL), cefepime (minimum inhibitory concentrations 4 μg/mL), ceftazidime (minimum inhibitory concentrations 4 μg/mL), trimethoprim-sulfamethoxazole (minimum inhibitory concentrations ≤ 0.25 μg/mL) and all tested quinolones including nalidixic acid (minimum inhibitory concentrations ≤ 2 μg/mL)., Conclusions: Chryseobacterium indologenes although uncommon, is an important pathogen causing infection in hospitalized patients. The management of this infection needs better identification, drug susceptibility testing and monitoring of immunosuppressed patients with long hospitalizations.

The aim of this cross-sectional study was to evaluate the drug resistance mutationprofile observed in patients receiving antiretroviral therapy with virological failure and to document the HIV-1 genetic diversity in Mauritania. Eighty-six subjects were included and 65 samples were amplified successfully and sequenced. HIV-1 genotyping was performed using the Agence Nationale de Recherche sur le SIDA AC11 resistance procedure. The median treatment duration was 32 months (range: 6-88) and the median viral load, 5 log10 copies/ml (range: 3.13-7). Fifty-nine patients (90.8%) were on first line regimens including 32.0% (19/59) on triomune fixed-dose and six on second-line therapy with NonNucleoside Reverse Transcriptase plus a protease inhibitor. Forty-seven patients (72.3%) had at least one drug resistance mutation including 73.0% (43/59) on first-line therapy. For the second-line, one out of six patients presented resistance mutations and only one presented PI DRM. Overall, the most common DRMs detected were M184V/I (n = 32; 49.2%), K103N (n = 28; 43%), and Y181C (n = 13; 20%). Thymidine Analog Mutations (TAMs) were found in 26.0% (n = 17) of strains and the most common was T215Y (n = 11, 16.9%). Phylogenetic analysis revealed 17 HIV-1 variants with the predominance of CRF02&#95;AG (n = 42; 64.6%). A high rate of DRM was found in this study and shows the potential need for a structured virological surveillance including viral load quantification and genotyping. Further studies may also be needed in regards to the great variability of HIV-1 strains in Mauritania., (© 2013 Wiley Periodicals, Inc.)

The prevalence of human immunodeficiency virus (HIV) drug resistance mutations (DRMs) was estimated in 25 untreated infants who were living with HIV-1, younger than 13 months and living in Senegal. Antiretroviral DRMs were detected in 8 of 25 (32%) children. Non-nucleoside reverse transcriptase inhibitor (NNRTI) DRMs were present in all (100%) children whose viruses harboured DRMs: K103N in 43%; Y181C, K101E and V106M each in 29%; and Y188L in 14%. The D67N thymidine-analogue mutation was observed in only two children whose mothers had received chemoprophylaxis of mother-to-child transmission (MTCT). The proportion of children whose viruses harboured DRMs was then 6.5-fold higher in children whose mother-child couples had received nevirapine (NVP)-based chemoprophylaxis than in other couples without prophylaxis [7 of 13 (53.8%) vs. 1 of 12 (8.3%)]. These findings point to the absolute need to address primary resistance mutations in case of virological failure in young children treated by antiretroviral drugs, and to make more effective treatment regimens available to NVP-exposed infants living with HIV-1 in Senegal.

The aim of this study was to evaluate the use for HIV-1 drug resistance testing dried blood spots collected in remote areas and sent under field conditions to a reference laboratory and also to document virological failure in patients with suspected treatment failure. Samples were collected from patients receiving first line ART at 11 hospital sites around country, kept at room temperature (<37°C) and sent within 15 days maximum to the reference laboratory. Viral nucleic acids were obtained by magnetic extraction with NucliSENS (bioMérieux, Marcy l'Etoile, France). Genotyping of HIV-1 pol gene was performed using the ANRS protocol. Drug resistance mutations were analyzed according to the Stanford University HIV database version 6.0.8. Two hundred thirty one HIV-infected adults' on HAART first line regimen composed study population. The median time on ART was 18 months (range 6-68). Regardless of the treatment duration, the overall rate of virological failure (VL ≥ 3 log10  cp/ml) was 23.8% (n = 55/231). HIV genotypes were obtained successfully in 94.5% (n = 52/55). Drug resistance mutation was found in 41/52 patients in virological failure, for 17.7% (n = 41/231) an overall rate of drug resistance mutations. M184V/I was the most frequent mutation occurring, followed by K103N. Phylogenetic analysis of the 52 genotyped viral isolates showed the predominance of CRF02&#95;AG with 62% (n = 32/52). Use of a DBS specimen is suitable to assist national programs for monitoring in remote areas HIV drug resistance in resources limited-settings., (© 2013 Wiley Periodicals, Inc.)

Circulating and unique recombinant HIV-1 strains continue to be identified and their number increases over time, suggesting that co-infection with multiple HIV-1 is frequent. In this study we analyzed to what extent dual infections with different HIV-1 variants occur in a population group with high risk behaviour, high HIV-1 prevalence and in an area where multiple HIV-1 subtypes and Circulating Recombinant Forms (CRFs) co-circulate. We studied 69 MSM with our recently developed multi-region hybridization assay (MHA), based on fluorescent probe detection for eight common variants circulating in West and West Central Africa. At least 11 (15.9%) of the 69 patients were simultaneously infected with two different HIV-1 subtypes and/or CRFs. Among the 29 samples identified as subtype C by MHA in gag, 15 (57.7%) reacted with both C1 and C2 probes. Sequence analysis suggests that the majority of the samples reactive with C1 and C2 probes are most likely infected with two different subtype C clades. Single genome amplification and DNA dilutions confirmed dual infection with subtype D and C for MSM1193, triple infection with two different C subtype strains and one CRF02&#95;AG strain in MSM1157 and showed that MSM3017 is at least co-infected with CRF06&#95;cpx and CRF02&#95;AG and another strain that could not be classified. Comparison of all subtype C sequences from the MSM population and from the general population from this and previous studies confirmed the intermixing of HIV-1 variants between low-risk women and high-risk men as shown by the intermixing of subtype C variants from MSM1157 and a female patient (02SN-HALD478). Comparison of dual infection rates between the general population and MSM in Senegal, show also clearly the importance of high HIV prevalence and high risk behavior in dual infections and subsequent intermixing of HIV-1 variants which can lead to emergence and spread of new recombinants (CRFs)., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Tuberculosis (TB) is a global public health problem exacerbated by the HIV epidemic. Here we evaluate a candidate TB vaccine, MVA85A, in a Phase I study in HIV-infected adults in Senegal. 24 patients were enrolled: Group 1∶12, antiretroviral therapy (ART) naïve, adults, with CD4 counts >300 and HIV RNA load <100,000 copies/ml. Group 2∶12 adults, stable on ART, with CD4 counts >300, and an undetectable HIV RNA load. Safety was evaluated by occurrence of local and systemic adverse events (AEs) and by monitoring of CD4 count, HIV RNA load, haematology and biochemistry. Immunogenicity was evaluated by ex-vivo interferon-gamma ELISpot assay. 87.7% of AEs were mild; 11.6% were moderate; and 0.7% were severe. 29.2% of AEs were systemic; 70.8% were expected local AEs. There were no vaccine-related Serious Adverse Events (SAEs) or clinically significant effects on HIV RNA load or CD4 count. In ART naive subjects, the first MVA85A immunisation induced a significant immune response at 1 and 4 weeks post-immunisation, which contracted to baseline by 12 weeks. Durability of immunogenicity in subjects on ART persisted out to 24 weeks post-vaccination. A second dose of MVA85A at 12 months enhanced immunogenicity in ART naïve subjects. Subjects on ART had higher responses after the first vaccination compared with ART naïve subjects; responses were comparable after 2 immunisations. In conclusion, MVA85A is well-tolerated and immunogenic in HIV-infected subjects in Senegal. A two dose regimen in ART naïve subjects is comparable in immunogenicity to a single dose in subjects on ART. Clinicaltrials.gov trial identifier NCT00731471.

The objective of this study was to investigate the performance of the ViroSeq HIV-1 Genotyping System v2.0 on HIV-1 non-B strains identified in Senegalese patients. The study involved 150 patients, and genotyping was performed using the ViroSeq HIV-1 Genotyping System v2.0 or an in-house method developed by the French National Agency on AIDS Research AC11 when the ViroSeq HIV-1 Genotyping System v2.0 failed. The sequences were edited to assess the performance of sequencing primers at their presumed binding regions. The Polymorphism was studied in the regions between the sequences of Senegalese patients and the subtype B strains used as references. The phylogenetic analysis showed a predominance of CRF02&#95;AG (88/150; 58.7%) and the circulation of 11 subtypes/CRFs, 16 unique recombinant forms (URFs) and one unclassified sample. The amplification and sequencing rates were 98% (147/150) and 96.6% (142/147), respectively. This study showed that only primer B exhibited 100% success, while the failure rate ranged from 1.4% to 71.4% for the other primers (D: 71.4%, A and H: 12.2%, F: 7.5%, G: 5.5% and C: 1.4%). These findings suggest the need for an alternative method or alternative primers for non-B strains that were not sequenced successfully using the ViroSeq HIV-1 Genotyping System v2.0., (Copyright © 2012 Elsevier B.V. All rights reserved.)

In this study, we investigated the prevalence of human immunodeficiency virus type 1 (HIV-1) drug resistance mutations and genetic variability among Senegalese patients undergoing highly active antiretroviral therapy (ART) in the public health system. We conducted a cross-sectional study of 72 patients with suspected therapeutic failure. HIV-1 genotyping was performed with Viroseq HIV-1 Genotyping System v2.0 or the procedure developed by the ANRS AC11 resistance study group, and a phylogenetic analysis was performed. The median follow-up visit was at 40 (range, 12 to 123) months, and the median viral load was 4.67 (range, 3.13 to 6.94) log(10) copies/ml. The first-line therapeutic regimen was nucleoside reverse transcriptase inhibitors (NRTIs) plus efavirenz (EFV) or NRTIs plus nevirapine (NVP) (54/72 patients; 75%), and the second-line therapy was NRTIs plus a protease inhibitor (PI/r) (18/72; 25%). Fifty-five patients (55/72; 76.39%) had at least one drug resistance mutation. The drug resistance rates were 72.22 and 88.89% for the first-line and second-line ARTs, respectively. In NRTI mutations, thymidine analog mutations (TAMs) were found in 50.79% and the M184V mutation was found in 34.92% of the samples. For non-NRTI resistance, we noted a predominance of the K103N mutation (46.27%). For PI/r, several cases of mutations were found with a predominance of M46I and L76V/F at 24% each. The phylogenetic analysis revealed CRF02&#95;AG as the predominant circulating recombinant form (43/72; 59.72%). We found a high prevalence of resistance mutations and a high rate of TAMs among Senegalese patients in the public health system. These findings emphasize the need to improve virological monitoring in resource-limited settings.

Laboratory follow-up of HIV patients in resource-limited settings requires appropriate instruments for CD4 T cell enumeration. In this study, we evaluated the application of a simplified, mobile and robust flow cytometry system, the Apogee Auto 40 analyzer (Auto40) using thermoresistant reagents, for CD4 T cell enumeration. We measured the absolute CD4 counts in fresh whole blood samples from 170 Senegalese subjects, including 129 HIV-positive (HIV+) patients and 41 HIV-negative (HIV-) controls. Based on volumetric primary CD4 gating, cells were stained with commercially available reagents (Easy MoAb CD4;Bio-D, Valenzano, Italy) and analyzed on the Auto40. The results were compared with those from the FACSCount system (Becton Dickinson, San Jose, USA). Repeatability analysis was performed on duplicate testing of 49 samples on both FACSCount and Auto40. The intra-run precision was measured by 10 replicates using 3 clinical blood samples with low, intermediate and high CD4 concentrations. The results from the two instruments were in good agreement. The percent similarity between the results of both instruments was 99%±relative standard deviation of 12.7%. The concordance correlation coefficient was 0.99. The absolute bias and limits of agreement (LOA) between the two instruments, calculated by Bland-Altman analysis, were clinically acceptable (bias: +4 cells/μl; LOA: -111 to +120 cells/μl). The clinical agreement between the two instruments at a cutoff of 200 CD4 cells/μl was 94%. The repeatability of measurements on the Auto40 was also similar to that observed with FACSCount system (bias +0.1 cells/μl, coefficient of variation 2.5% vs bias -1.1cells/μl, coefficient of variation 2.9% respectively). In conclusion, our results indicate that the Auto 40 system, using thermoresistant reagents, is suitable for CD4 T cell enumeration and will be a helpful tool to improve HIV laboratory monitoring in resource-limited settings., (Copyright © 2011 Elsevier B.V. All rights reserved.)

To evaluate the presence of drug resistance mutations in antiretroviral-naive patients in Dakar (Senegal), cross-sectional studies were conducted since the circulation of ARVs in the country. Protease and RT genes were sequenced in 96 baseline samples from patients included in the Senegalese Initiative for Antitretroviral Access treatment between 1998 and 2001 and for 104 samples from naive, recently diagnosed patients in 2003, 2005, and 2007. Phylogenetic analysis showed a predominance of CRF02&#95;AG [128/200 (64%)] and a high genetic diversity with 10 other variants and 25 URFs. Analysis for the presence of drug resistance mutations according to the WHO SDRM 2009 list showed a prevalence of 4.16% for nucleoside inhibitors and 1.04% for protease inhibitors at the start of the structured Senegalese ART initiative and 1.9% for protease inhibitors at the time of scaling up. The prevalence in untreated patients remains low and stable, below 5% after 10 years of ARV circulation.

The aim of this study was to determine hepatitis co-infection in a cohort of HIV infected patients at their inclusion in the Senegalese Initiative of ART Access. B, C, and D Hepatitis viruses serological markers were checked retrospectively on 363 stored plasma. For HBV, the Abbott laboratories equipment IMx was used to detect HBs Ag and anti Core Ab on negative HBs Ag samples. For HDV, anti Delta Ab was performed using the Abbott Murex Kit on all HBs Ag positive samples. For HCV, anti HCV Ab was detected by IMx as double screening test and confirmed by INNO-LIA(TM) HCV Core of Innogenetics laboratories. The statistical analysis was done with STATA V8. The study population was composed of 164 men and 199 women aged between 16 and 66 years. The immune and virological markers averages at their enrollment were 154 cell/mm(3) for TLCD4+ (n = 355 patients) and 4.9 log for viral load (n = 277 patients). HBs Ag was found in 61 patients or 16.8% and the prevalence of anti-HBc Ab was 83.2% (252/295). 2 patients or 3% on HBs Ag positive sample presents HBV/HDV co-infection Ab anti HCV was detects in 6 patients or 1.6% after confirmation and 2 patients had triple infection with HBV. These results showed that the prevalence of HBV and HCV in the population of persons living with HIV/AIDS in Senegal is similar to that found in the general population. Our data indicated that hepatitis pathology in the PLwHIV was essentially due to HBV. Further studies are needed to diagnose occult hepatitis in order to set up therapeutic strategies taking into account co-infections by hepatitis viruses in the ART programmes.

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.