bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relationship between discordant response to HAART, Tregs, immune activation and low‐level viraemia
Authors: Saison Julien , Ferry Tristan , Demaret Julie , Maucort‐Boulch Delphine , Venet Fabienne , Perpoint Thomas , Ader Florence , Icard Vinca , Chidiac Christian , Monneret Guillaume 
Published: November 2014

IntroductionThe incomplete immune recovery upon effective long‐term highly active antiretroviral therapy (HAART) has been associated with increased morbidity and mortality in HIV infected patients [1]. Immune cellular activation, Tregs or very low‐level viraemia has been alternatively suspected, but never investigated simultaneously [2].Materials and MethodsWe performed a cross‐sectional study in 87 aviraemic patients (men=62, mean CD4+T cells=570/mm3, mean duration of HAART=12 years). Patients with at least 500 CD4+ T cells /mm3 were classified as complete immunological responders (cIR), whereas remaining patients were classified as inadequate immunological responder (iIR). Tregs were characterized based on CD4+CD25highFoxP3+phenotype using a one‐step intracellular staining. Effector Tregs and terminal effectors Tregs were respectively defined as CD4+CD25+FoxP3+CD45RA‐, and CD4+CD25+FoxP3+CD45RA‐HLADR+phenotypes as recently described [3]. Activated T cells were identified using (i) elevated HLA‐DR expression for CD4+T cells, and (ii) increased expressions of HLA‐DR, or CD38, or both (HLADR+CD38+cells) for CD8+T cells. Very low‐level viraemia was defined as detectable viraemia between 1 and 39 cp/mL. Univariate and multivariate analyses were performed to identify determinants of iIR.ResultsThirty‐nine patients were classified as iIR, and 48 as cIR. Patients from the iIR group were significantly older (55 vs 50 years, p=0.027), and had percentages of activated CD4+ T cells, Tregs, effector Tregs and terminal effector Tregs significantly higher (5.3 vs 4%, p=0.014; 9 vs 7.5%, p=0,022; 8 vs 6.3%, p=0.01 and 1.8 vs 1.3%, p=0,033 among CD4+T cells, respectively). Neither the percentage of activated CD8+T cell nor very low‐level viraemia were found to be associated with iIR. In the multivariate analysis, nadir of CD4+T cell count and percentage of Tregs were the only two parameters independently associated with iIR (OR=2.339, p=0.001, and OR=0.803, p=0.041, respectively).ConclusionsWe present here the largest study investigating simultaneously immune response to long‐term HAART, immune activation of CD4+ and CD8+ T cells, Tregs percentages and very low‐level viraemia. Our results highlight the importance of Tregs in CD4 homeostasis. This aspect should now be prospectively explored in a large cohort of patients.
Validation of an ultrasensitive digital droplet PCR assay for HIV‐2 plasma RNA quantification
Authors: Ruelle Jean , Yfantis Vasilieios , Duquenne Armelle , Goubau Patrick 
Published: November 2014

IntroductionLow or undetectable plasma viral load (VL) using current qPCR assays is common for HIV‐2 patients. Digital PCR is an emerging technology enabling more precision and reproducibility than qPCR at low DNA/RNA copy numbers. Available data related to digital droplet PCR (ddPCR, Bio‐Rad) underscore issues linked to the threshold definition of positivity, coupled to the specificity of low copy results [1].Materials and MethodsA RT‐PCR protocol was set up using the One‐Step RT‐ddPCR Kit for Probes on the QX200 platform (Bio‐Rad, Hercules, CA) in an accredited environment (ISO15189:2012 norm). Parameters tested were in line with the digital MIQE guidelines [2]. Inter‐run coefficient of variation (CV) was established using synthetic RNA controls diluted in HIV‐negative plasma. The ddPCR assay was compared to a qRT‐PCR previously used in routine (LOQ 50 cop/mL [3]) using 46 clinical samples and the NIBSC international HIV‐2 RNA standard.ResultsThe optimal PCR efficiency and the best separation between positive and negative droplets were obtained with a mixture containing 0.5 mM manganese acetate, 700 nM primers and 250 nM of the 5′FAM‐probe. Using a manual threshold to define positivity, 7.74% of negative controls (n=168) were scored as positive due to one positive droplet. The presence of two positive droplets or more was not observed for negative controls. Serial dilutions of a positive control showed excellent linearity (R2=0.999) and enabled us to define a limit of quantification of two positives droplets, which corresponds to 0.14 copies/μL in the reaction mixture and to seven copies per mL of plasma. The inter‐run coefficient of variation was 3.37% at a mean value of 4,468 cop/mL, 19.59% at 416 cop/mL and 32.28% at 8 cop/mL. The NIBSC standard of 1,000 IU was quantified 1,400 copies by ddPCR and close to 5,000 copies by qPCR (delta log superior to 0.5). Among 46 clinical samples, 22 were undetectable with both qPCR and ddPCR, 12 were detected with both methods (respective means of 10,612 and 2,224 cop/mL, delta log=0.68) and 12 others were quantified by ddPCR only below 50 cop/mL (mean=16 cop/mL).ConclusionsWe validated a ddPCR HIV‐2 VL assay that is more sensitive and more reproducible than the qPCR assay used as comparator, with a limit of quantification of 7 cop/mL of plasma. A careful definition of the limit of blank allows the management of false positive droplets, but the variable user‐defined positive threshold may be an issue for compliance to the quality norms.
Acute HIV infection (AHI) in a specialized clinical setting: case‐finding, description of virological, epidemiological and clinical characteristics
Authors: Ammassari Adriana , Abbate Isabella , Orchi Nicoletta , Pinnetti Carmela , Rozera Gabriella , Libertone Raffaella , Pierro Paola , Martini Federico , Puro Vincenzo , Girardi Enrico , Antinori Andrea , Rosaria Capobianchi Maria 
Published: November 2014

IntroductionDiagnosis of HIV infection during early stages is mandatory to catch up with the challenge of limiting HIV viral replication and reservoirs formation, as well as decreasing HIV transmissions by immediate cART initiation.ObjectivesAims were to describe (a) virological characteristics of AHI identified, (b) epidemiological and clinical factors associated with being diagnosed with AHI.MethodsCross‐sectional, retrospective study. All individuals diagnosed with AHI according to Fiebig's staging between Jan 2013 and Mar 2014 at the INMI “L. Spallanzani” were included. Serum samples reactive to a fourth generation HIV‐1/2 assay (Architect HIV Ag/Ab Combo, Abbott) were retested with another fourth generation assay (VIDAS DUO HIV Ultra, Biomérieux) and underwent confirmation with HIV‐1 WB (New Lav I Bio‐Rad) and/or with Geenius confirmatory assay (Bio‐Rad). WHO criteria (two env products reactivity) were used to establish positivity of confirmatory assays. In case of clinically suspected AHI, HIV‐1 RNA (Real time, Abbott) and p24 assay (VIDAS HIV P24 Bio‐Rad) were also performed. Avidity test was carried out, on confirmed positive samples lacking p31 reactivity, to discriminate between recent (true Fiebig V phase) and late infections; to avoid possible misclassifications, clinical data were also used. Demographic, epidemiological, clinical and laboratory data are routinely, and anonymously recorded in the SENDIH and SIREA studies.ResultsDuring the study period, we observed 483 newly HIV diagnosed individuals, of whom 40 were identified as AHI (8.3%). Fiebig classification showed: 7 stage II/III, 13 stage IV, 20 stage V. Demographic, epidemiological, and clinical characteristics of patients are shown in the Table. Overall, the study population had a median S/Co ratio at fourth generation EIA (Architect) of 49.50 (IQR, 23.54–98.05): values were significantly lower in Fiebig II‐IV than in Fiebig V (38.68 [IQR, 20.08–54.84] vs 75.72 [IQR, 42.66–249.80], p=0.01). Overall, median HIV‐1 RNA was 5.44 log copies/mL (IQR, 4.29–6.18) and the value observed in Fiebig phase II‐IV was higher than that found in Fiebig stage V (6.10 [IQR, 5.49–7.00] vs 4.69 [3.71–5.44], p<0.001). Median CD4+ cell count was 596/mmc (IQR, 410–737). cART was started in 26 patients: TDF/FTC/DRV/r/RAL=18; TDF/FTC/DRV/r=2; TDF/FTC/ATV/r=2; TDF+FTC+EFV=2; TDF/FTC/RAL=1; DRV/r+RAL=1.ConclusionsIntegration of careful epidemiological investigation, partner notification, and technical advances in virological testing are key elements in AHI case‐finding. Significant differences were found between Fiebig stages II–IV and Fiebig V with regard to virological exams.
The effect of tenofovir in renal function in HIV‐positive adult patients in the Roma health service area, Lesotho, southern Africa
Authors: Mugomeri Eltony , Olivier Dedré , van den Heever‐Kriek Elmien 
Published: November 2014

IntroductionThe government of Lesotho introduced tenofovir disoproxil fumarate (TDF) for first‐line antiretroviral treatment (ART), as recommended by the World Health Organization (1), in 2008. The use of TDF has been associated with renal toxicity (2); furthermore, renal function outcomes following the use of TDF has not been studied at Roma Health Service Area (RHSA) in Lesotho. Lesotho is a small landlocked country surrounded by South Africa. The study used an analytical design to compare retrospective creatinine clearance (CrCl) data of 312 (64%) antiretroviral treatment naïve adults exposed to TDF and 173 (36%) unexposed patients.MethodsImpaired renal function was defined as CrCl less than 50 mL/min calculated using the Cockcroft‐Gault equation. The Ministry of Health and Social Welfare of Lesotho approved the study on 13 January 2012. The study included adult (excluding pregnant females) HIV patients enrolled on ART between December 2006 and December 2012 at St Joseph's Mission Hospital and at Nazareth Health Centre (RHSA). Patients at Nazareth Health Centre and at St Joseph's Mission Hospital made up 80% of the circa 4 116 HIV patients on ART. Only 485 patients met the set inclusion criteria.ResultsIn 56 patients (17.9%), TDF was found to be contraindicated. The use of TDF was marginally significant factor for renal toxicity (p=0.054) in univariate analysis, but was insignificant (p=0.122) in multivariate logistic analysis. Univariate (p<0.1) and multivariate logistic regression (p<0.05) were performed using STATA® 11. Female gender (p=0.016), hypertension (p=0.009), and age>60 (p=0.004) were significantly associated with CrCl<50 mL/min outcome.ConclusionsIn this study, TDF proofed to be a weak contributing factor of renal impairment. Routine baseline renal function screening should however be adopted to prevent patients with impaired renal function receiving TDF.
Molecular epidemiology of HIV‐1 strains in Antalya, Turkey
Authors: Inan Dilara , Sayan Murat 
Published: November 2014

IntroductionThe aim of this study was to determine the subtype distribution of HIV‐1 strains isolated from antiretroviral therapy (ART)‐naive and on treatment patients in Antalya, the city of southern Turkey.Materials and MethodsThe study included 77 of 92 newly diagnosed HIV‐1 positive patients of last two years (between February 2012 and June 2014). HIV‐1 subtypes and circulating recombinant forms (CRFs) were identified by phylogenetic analysis of reverse‐transcriptase (codon 41–238) and protease (codon 1–99) domains (~667 bp) of pol gene region in HIV‐1 strains.ResultsSubtype B (48%, 37/77) was identified as the most common HIV‐1 subtype in Antalya that similar the other Turkish patients. Non‐B subtypes were followed as CRFs (39%, 30/77). Interestingly, CRF14_BG (12.9%, 10/77) was found for the first time in Antalya in contrast to previous observations in the other reports in Turkey. Also, subtype G (6.5%, 5/77) was detected more often than HIV‐1 subtypes in circulation of Turkey.ConclusionsThese findings may be associated with specific geographic localization of Antalya that touristic movements of city. Recognized HIV‐1 subtype diversity is major challenges in the development of a globally effective HIV vaccine.
Using dried blood spots collected under field condition to determine HIV‐1 diversity and drug resistance mutations in resource limited Tanzania
Authors: Kimaro James , Shao Elichilia , Nyombi Balthazar , Kifaro Emanuel , Maruapula Dorcas , Gaseitsiwe Simani , Musonda Rosemary 
Published: November 2014

IntroductionA dried blood spot (DBS) on filter paper has been used for different tests globally and has gained popularities in resource limited settings especially during HIV/AIDS epidemic. We assessed the efficiency of molecular characterization of HIV‐1 subtypes using DBS collected under field conditions in northern Tanzania.Materials and MethodsIn 2011 and 2012, 60 DBS samples were collected under field conditions from exposed and newly diagnosed HIV‐1 infected children from Kilimanjaro (n=20), Arusha (n=20), Tanga (n=10) and Manyara (n=10).Results and discussionOf 60 DBS analyzed at both Protease (PR) and Reverse Transcriptase (RT) regions, 45 (75%) were analyzed, including 17 (85%) from Kilimanjaro, 15 (75%) from Arusha, 8 (80%) from Tanga, and 5 (50%) from Manyara region. All 45 DBS characterized had viral load above 1000 copies/mL with mean log10 viral loads of 3.87 copies/mL (SD 0.995). The phylogenetic results indicated presence of subtype and circulating recombinant form (CRF). In which, 24 were subtype A1 (53.33%), 16 were subtype C (35.55%), 3 were subtype D (6.67%) and 2 were CRF10_CD (4.35%). All major mutations were detected in the RT region, none from protease (PR) region. The mutations detected were Y181C (n=8), K103 (n=4) and G190A (n=1), conferring resistance to non‐nucleoside reverse transcriptase inhibitors (NNRTIs), and M184V (n=1), conferring resistance to lamivudine and emtricitabine.ConclusionsOur results indicate that DBS collected from field conditions in resource scarcity areas can be used to determine the phylogeny of the virus and drug resistance mutations in areas with diverse HIV‐1 group M subtypes.
Temporal increase in HIV‐1 non‐R5 tropism frequency among antiretroviral‐naive patients from northern Poland
Authors: Parczewski Milosz , Leszczyszyn‐Pynka Magdalena , Witak‐Jêdra Magdalena , Maciejewska Katarzyna , Urbañska Anna 
Published: November 2014

IntroductionSequencing of the third hypervariable loop allows to identify genotype‐based HIV tropism. R5‐tropic viruses associated with early stages of infection are preferentially transmitted, while non‐R5 HIV‐1 tropism has been associated with severe immunodeficiency and lower lymphocyte CD4 nadir and may reflect delayed HIV diagnosis. In this study, we investigate the changes in tropism frequency from 2007 to 2013.Materials and MethodsStudy included 194 patients with confirmed HIV infection linked to care in 2007–2013. Baseline plasma samples from treatment naive patients were used for HIV‐1 genotypic tropism assessment based on triplicate V3 loop sequencing. Non‐R5 tropism prediction thresholds were assigned using a false positive rate (FPR) of 10% and 5.75% FPR and associated with clinical and laboratory data (age, gender, date of HIV diagnosis, route of transmission, CDC clinical category at diagnosis, pretreatment HIV viral load, baseline and nadir lymphocyte CD4 counts). For statistics, chi‐square and Mann–Whitney U tests were used, time trends were examined using logistic regression (R statistical platform, v. 3.1.0) for binary variables and linear regression for continuous ones.ResultsOverall non‐R5 tropism frequency for the 5.75% FPR was 15.5% and 27.8% for 10% FPR. Frequency of the non‐R5 tropism predicted using 5.75% FPR increased significantly from 2007 (0%) to 2013 (25%) [OR: 1.44 (95% CI 1.14–1.86), p=0.003, rough slope +3.89%/year] (Figure 1a). With 10% FPR, the frequency changed from 7% (2007) to 33% (2013) [OR: 1.17 (95% CI 0.99–1.39), p=0.054, rough slope +3.0%/year] (Figure 1b). Baseline lymphocyte CD4 count and nadir, as well as pretreatment HIV‐1 viral loads were stable over time of observation (r=0.014, p=0.84; r=0.13, p=0.085; r=0.016, p=0.83 for CD4 baseline, nadir and HIV load, respectively). Frequency of AIDS at HIV diagnosis increased from 21.4% in 2007 to 38.0% in 2013, however trend over time was insignificant [OR: 1.1 (95% CI 0.95–1.31), p=0.19]. Temporal trends for HIV transmission route, gender, non‐B variant frequencies also were not significant.ConclusionsR5 tropism predominates among the treatment naive individuals but increase in the frequency of non‐R5 tropic variants may limit clinical efficacy of the coreceptor inhibitors. Increased prevalence of non‐R5 HIV‐1 may be related to late care entry and higher number of AIDS diagnoses in the recent years.
Characteristics of late presenters in Bucharest
Authors: Elena Jipa Raluca , Manea Eliza , Benea Serban , Niculescu Iulia , Benea Otilia , Mardarescu Mariana , Andrei Cosmina , Moroti Ruxandra , Hristea Adriana 
Published: November 2014

IntroductionLate presentation is associated with increased healthcare costs, rates of HIV transmission and poor outcome. In Romania, in 2012, one third of individuals with new HIV diagnosis were late presenters (LP).ObjectiveThe aim of the study was to evaluate the epidemiological and clinical characteristics associated with late presentation.MethodsWe retrospectively studied patients over 18 years old, notified in our institution between January 2012 and December 2013, including 499 out of 727 newly diagnosed patients in Bucharest. LP were defined as patients presenting with CD4 T‐cell count below 350 cells/mm3 or with an AIDS defining event. Patients with advanced HIV disease (AHD) were defined as persons with a CD4 T‐cell count below 200 cells/mm3. Differences between groups were analyzed using the Mann‐Whitney U test for continuous variables and the chi‐square test for dichotomous variables. Multivariable analysis was performed using binary logistic regression.ResultsOut of 499 patients included, 362 (72%) were male. The median age was 30 (IQR 26–36). A total of 302 (61%) were LP and 184 (37%) were patients with AHD. A total of 170 (34%) were asymptomatic and 114 (23%) presented with an AIDS‐defining event. The median CD4 count was 293 cells/mm3 (IQR 125–471) and the median HIV viral load was 100,191 copies/mL (IQR 34,560–272,936). Characteristics of LP compared with non‐LP are shown in Table 1. Stage C disease has been shown by multivariable analysis to be associated with LP (p<0.001, OR=11.56, 95% CI 4.94–27.03).ConclusionsMore than half of newly HIV diagnosed patients in Bucharest were LP. The proportion of LP was highest among heterosexually acquired cases. Although most our patients were young, late presentation was associated with age over 35 years. The lower proportion of LP among IVDU compared with those heterosexually infected could be explained by a higher proportion of HIV screening tests among IVDU.
The use of TDM in pregnant HIV‐positive women: a retrospective cross‐sectional review of five years practice in two large hospitals in Manchester
Authors: Whitfield Thomas , Dessain Amabel , Taylor Kelly , McQuillan Orla , Looi Evelyn , Kingston Margaret , Ajdukiewicz Katherine 
Published: November 2014

IntroductionDespite plasma levels of certain HIV drugs decreasing in the third trimester of pregnancy there is no definitive evidence that therapeutic drug monitoring (TDM) improves HIV control and prevents mother‐to‐child transmission (MTCT). Indeed “one‐off” TDM measurements are thought to poorly correlate with overall drug exposure [1]. We aim to describe baseline demographic and clinical characteristics of pregnant women with HIV, and to compare their HIV control, management during pregnancy and neonatal outcomes with respect to whether TDM was performed.Materials and MethodsRetrospective cross‐sectional case note analysis was performed on pregnant women with HIV who attended North Manchester General Hospital and Manchester Royal Infirmary from 1st January 2008 to 28th May 2013.ResultsA total of 171 pregnancies were included; 39% (n=66) had TDM. The majority of patients were of African origin (85%) and age range was 16–42 years (median 32 years). TDM was found to be associated with a history of poor adherence to therapy (TDM 23%, vs no TDM 10%, p=0.017), although baseline viral load (VL) and CD4 counts were comparable between TDM and non‐TDM groups (p=0.4756 and 0.9492, respectively). TDM was also associated with protease inhibitors (PI) (TDM 94% vs no TDM 77%, p= 0.004). Within the PI group, TDM was more strongly associated with atazanavir use than other PI's (55%, p=0.023). TDM was not associated with any other demographic variable or with either of the two hospital sites (p=0.427). TDM was associated with medication alterations during pregnancy (TDM 67% vs no TDM 13%, p=0.052), but was not associated with any difference in outcomes with similar proportions of newly detectable VL during pregnancy (TDM 12% vs no TDM 7%, p=0.220) and VL detectable at birth (TDM 14% vs no TDM 9%, p= 0.293). There were no instances of MTCT.ConclusionsTDM was associated with PI use and a history of poor adherence at baseline. TDM was not associated with improved HIV control during pregnancy and there was no MTCT. TDM was not shown to have any additional benefit in pregnancy and its routine use is not recommended to improve HIV control or reduce MTCT.
Transmitted drug resistance in women with intrapartum HIV‐1 diagnosis: a pilot epidemiological survey in Buenos Aires, Argentina
Authors: Cecchini Diego , Zapiola Ines , Fernandez Giuliano Silvina , Martinez Marina , Rodriguez Claudia , Belen Bouzas Maria 
Published: November 2014

IntroductionSurveillance of primary resistance to antiretroviral drugs is particularly important in pregnant population, in which infection by drug‐resistant HIV has not only implications for maternal treatment, but could also jeopardize the efficacy of neonatal prophylaxis. We aim to describe the prevalence of resistance associated mutations (RAMs) in pregnant women with intrapartum HIV diagnosis in a public hospital of Buenos Aires, Argentina.Materials and MethodsProspective pilot study (period from 2008 to October 2013). Plasma samples were tested for viral load by Versant HIV‐1 RNA 3.0 (bDNA) and sequenced using HIV‐1 TRUGENE™Genotyping Kit (Siemens). The prevalence of RAMs was analyzed according to World Health Organization (WHO) criteria.ResultsOf 231 HIV‐infected pregnant women assisted, 6% (n=14) had intrapartum diagnosis of HIV infection. 12 patients (85.7%) had previous pregnancies, 10 (71.4%) had inadequate prenatal care and 3 (23.1%) seroconverted during pregnancy. Maternal characteristics (expressed medians and ranges) were: age 25.5 (16–35) years; gestational age at birth: 39 (30–42) weeks; CD4 count: 500 (132–925) cells/µL; viral load: 9418 (1800–55299) copies/mL. No one had hepatitis B virus (HBV) or hepatitis C virus (HCV) coinfection; four (33.3%) had syphilis. Eight patients (57.1%) had vaginal delivery and six emergency C‐section (42.9%). In six cases (46.2%), membrane rupture was spontaneous; four patients (28.6%) failed to receive intrapartum zidovudine (ZDV) infusion. In 12 patients a genotypic resistance test was performed: two (16.7%) had WHO RAMs corresponding to K103N mutation in both cases, conferring high‐level resistance to nevirapine (NVP) and efavirenz. Two newborns (14.3%) were preterm. All received neonatal prophylaxis: ZDV in 1 case and combined prophylaxis (ZDV/3TC/NVP) in the remaining 13 (92.9%). All newborns were formula‐fed. Two (14.3%) had congenital syphilis, one of whom died. One newborn was HIV‐infected (positive proviral DNA at 24 hours of life, wild‐type HIV).ConclusionsThis pilot study suggests that levels of transmitted resistance in this high‐risk population of pregnant women could be moderate to high. We preliminarily observed high‐level resistance to NVP: if this finding is confirmed with a larger sample, it could potentially jeopardize the utility of this drug in the combined neonatal prophylaxis recommended in the absence of maternal antiretroviral therapy.