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Upland forest soils are known to be the main biological sink for methane, but studies have shown that net methane uptake of a forest ecosystem can be reduced when methane emissions by vegetation are considered. We estimated the methane budget of a young oak plantation by considering tree stems but also the understorey vegetation. Automated chambers connected to a laser‐based gas analyser, on tree stems, bare soil and soil covered with understorey vegetation, recorded CH4 fluxes for 7 months at 3 h intervals. Tree stem emissions were low and equated to only 0.1% of the soil sink. Conversely, the presence of understorey vegetation increased soil methane uptake. This plant‐driven enhancement of CH4 uptake occurred when the soil was consuming methane. At the stand level, the methane budget shifted from −1.4 ± 0.4 kg C ha−1 when we upscaled data obtained only on bare soil, to −2.9 ± 0.6 kg C ha−1 when we considered soil area that was covered with understorey vegetation. These results indicate that aerenchymatous plant species, which are known to reduce the methane sink in wetlands, actually increase soil methane uptake two‐fold in an upland forest by enhancing methane and oxygen transport and/or by promoting growth of methanotrophic populations.

To examine how patient characteristics combined with ART eligibility expansions affect the initiation of antiretroviral therapy (ART) among eligible patients attending a referral center in Senegal from 1998 to 2015. This is a retrospective observational study carried out at the outpatient treatment Centre (Centre de Traitement Ambulatoire) in Dakar, Senegal, based on computerized medical records, gathered from 1998 to 2015, of ART-naïve patients over 15 years of age. ART eligibility was defined as (CD4 count below 200) or as (WHO stage 4) or as (WHO stage 3 with (CD4 count below 350 or with unavailable CD4 count)) in 1998-2010; as (CD4 count below 350) or as (WHO stage 3 or 4) in 2011-2013; as (CD4 count below 500) or as (WHO stage 3 or 4) in 2014-2015. Four periods were defined according to ART eligibility expansions and Senegal's HIV care history: 1998-2003 (P 1), 2004-2010 (P 2), 2011-2013 (P3), and 2014-2015 (P4). Patients were expected to participate financially in their treatment during the first period (P1). A total of 3651 patient records were included. The median patient age was 40 years (IQR: 32-48). Women represented 56% of the population. The median CD4 count was 183 cells/mm3. Overall, 53% of patients had CD4 < 200 cells/mm3 at entry. This proportion reached 45% in 2014-2015. 2535 patients (69%) were eligible for therapy, including 1503 (41%) who started ART. The proportion of treated patients among those who were eligible at entry or later increased steadily from 25%, 47%, 75% to 82% in the four periods, respectively. The median time to treatment decreased from 5.6 months (IQR: 3-11) in P1 to 0.8 months (IQR: 0-2) in P4. Eligible patients with more advanced disease (CD4<200 cells/mm3 and/or clinical stage 3 or 4) were more likely to be ART initiated than those with CD4≥200 cells/mm3 and/or clinical stage 1 or 2 at each stage of ART eligibility expansion. ART eligibility expansions were marked by a sharp increase in the proportion of eligible patients initiating treatment. These results show that in terms of management, the target of \"Test and Treat\" can be easily reached but that HIV testing will remain a key element to improve treatment success, as illustrated by the high proportion of people with advanced stage of infection at the time of ART initiation.

IntroductionLe tabagisme doublerait la mortalité chez les PvVIH un risque accru de survenue de maladies non classant Sida. La prévalence de la consommation de tabac est plus élevée chez les PvVIH que dans la population générale. Nous nous sommes fixés comme objectifs d'évaluer la prévalence du tabagisme chez les PvVIH, de décrire les caractéristiques cliniques et spirométriques des fumeurs et ex-fumeurs et d'évaluer leurs connaissances et attitudes face au tabagisme.MéthodesNous avons donc mené une étude transversale, descriptive et analytique du 15 Juillet au 15 Décembre 2015, chez les PvVIH suivis au Centre de Traitement Ambulatoire du Centre Hospitalier Universitaire National de Fann.RésultatsLa population d'étude concernait trois cents (300) PvVIH. Le sex-ratio était de 0,8. Nous avons retrouvé 15% de fumeurs et 23,7% d'ex-fumeurs. L'âge moyen des fumeurs était de 44,38 ± 9,55 ans. La quasi-totalité des fumeurs 91,1% avait déjà commencé à fumer avant la connaissance de leur statut sérologique et 35,6% d'entre eux avaient majoré leur consommation de tabac après. Les signes respiratoires étaient dominés par la gêne respiratoire dans 64,4% des cas chez nos fumeurs. Parmi les fumeurs qui ont bénéficié de la spirométrie, 67% d'entre eux avait un trouble ventilatoire obstructif non amélioré par les béta2-mimétiques et 28,1% un syndrome restrictif. Parmi les ex-fumeurs, 40,8% affirmait que le statut sérologique était le motif de sevrage.ConclusionLe tabagisme peut être initié ou majoré après connaissance du statut sérologique. Il peut être à l'origine de nombreuses complications chez le PvVIH.

Hepatitis B virus (HBV) infection is the first cause of liver cirrhosis and cancer in West Africa. Although the exposure to additional environmental and infectious risk factors may lead to the faster progression of liver disease, few large-scale studies have evaluated the determinants of HBV-related liver fibrosis in the region. We used transient elastography to evaluate the prevalence of liver fibrosis and assessed the association between HBV markers and significant liver fibrosis in a cohort of people living with HBV in Dakar, Senegal. The prevalence of significant liver fibrosis was 12.5% (95% confidence interval [CI] 9.6%–15.9%) among 471 people with HBV mono-infection (pwHBV) and 6.4% (95% CI 2.6%–12.7%) in 110 people with HIV/HBV co-infection (pwHIV/HBV) on tenofovir-containing antiretroviral therapy (p = 0.07). An HBV viral load > 2000 IU/mL was found in 133 (28.3%) pwHBV and 5 (4.7%) pwHIV/HBV, and was associated with significant liver fibrosis (adjusted odds ratio (aOR) 1.95, 95% CI 1.04–3.66). Male participants (aOR 4.32, 95% CI 2.01–8.96) and those with elevated ALT (aOR 4.32, 95% CI 2.01–8.96) were especially at risk of having significant liver fibrosis. Our study shows that people with an HBV viral load above 2000 IU/mL have a two-fold increase in the risk of liver fibrosis and may have to be considered for antiviral therapy, independent of other disease parameters.

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

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_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.

PLHA who smoke have twice the never-smoker mortality rate and have an increased risk of developing non-AIDS diseases. The prevalence of tobacco smoking is higher among PLHA than in the general population. The purpose of this study was to assess the prevalence of smoking among PLHA, to describe the clinical and spirometric features of smokers and ex-smokers and to assess their knowledge and attitudes toward smoking. We conducted a cross-sectional, descriptive and analytical study among PLHA followed up in the Outpatient Department of the National University Hospital Center of Fann from 15 July to 15 December 2015. Three hundred (300) PLHA were included in the study. Sex ratio was 0.8. Out of the study population, 15% were smokers and 23.7% were ex-smokers. The average age of patients was 44.38±9.55 years. The quasi-totality of the smokers (91.1%) had already started smoking before the detection of the serological status and 35.6% of them had increased tobacco use after. Respiratory symptoms among smokers were dominated by respiratory distress (64.4%). Smokers who underwent spirometry had obstructive ventilatory impairment not improved by beta-2-mimetic agents (67%) and restrictive disease (28.1%). Out of ex-smokers, 40.8% reported that their serological status was the reason for smoking cessation. eople may begin or increase smoking after knowledge of serological status. In PLHA, smoking causes cardiovascular and respiratory diseases as well as complications.

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/mm3 (P < .006). Strong correlates of DR also included Saint-Louis (P < .009), CD4 < 350 cells/mm3 (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.

Babanki virus is a subtype of the Sindbis virus, a widespread arthropod-borne alphavirus circulating in Eurasia, Africa, and Oceania. Characterized by rashes and arthritis, clinical infections due to Sindbis were mainly reported in Africa, Australia, Asia, and Europe. However, its sub-type, Babanki virus, was reported in Northern Europe and Africa, where its epidemiology potential remains poorly understood. The diagnosis of alphaviruses is mainly based on serological testing and conventional PCR methods, which have considerable limits. In this study, we developed a real-time qRT-PCR assay for the detection of Babanki virus. The analytical sensitivity and specificity of the newly established assay were evaluated using in vitro standard RNA and related viruses relevant to the African context, respectively. In addition, its diagnostic sensitivity was assessed using a subset of Babanki virus-positive and -negative mosquito pools collected from the field. The new real-time qRT-PCR assay exhibited a 100% specificity, a 95% detection limit of 1 RNA molecule/reaction, and a diagnostic sensitivity of up to 120 pfu/reaction. This newly established assay could be useful not only for the detection of Babanki virus during epidemics but also in future experimental and surveillance studies focusing on their epidemiology and pathogenicity.