Virologic Failures on Initial Boosted-PI Regimen Infrequently Possess Low-Level Variants with Major PI Resistance Mutations by Ultra-Deep Sequencing

It is unknown whether HIV-positive patients experiencing virologic failure (VF) on boosted-PI (PI/r) regimens without drug resistant mutations (DRM) by standard genotyping harbor low-level PI resistant variants. CASTLE compared the efficacy of atazanavir/ritonavir (ATV/r) with lopinavir/ritonavir (LPV/r), each in combination with TVD in ARV-naïve subjects.To determine if VF on an initial PI/r-based regimen possess low-level resistant variants that may affect a subsequent PI-containing regimen.Patients experiencing VF on a Tenofovir/Emtricitabine+PI/r regimen were evaluated by ultra deep sequencing (UDS) for mutations classified/weighted by Stanford HIVdb. Samples were evaluated for variants to 0.4% levels. 36 VF subjects were evaluated by UDS; 24 had UDS for PI and RT DRMs. Of these 24, 19 (79.2%) had any DRM by UDS. The most common UDS-detected DRM were NRTI in 18 subjects: M184V/I (11), TAMs(7) & K65R(4); PI DRMs were detected in 9 subjects: M46I/V(5), F53L(2), I50V(1), D30N(1), and N88S(1). The remaining 12 subjects, all with VLs<10,000, had protease gene UDS, and 4 had low-level PI DRMs: F53L(2), L76V(1), I54S(1), G73S(1). Overall, 3/36(8.3%) subjects had DRMs identified with Stanford-HIVdb weights >12 for ATV or LPV: N88S (at 0.43% level-mutational load 1,828) in 1 subject on ATV; I50V (0.44%-mutational load 110) and L76V (0.52%-mutational load 20) in 1 subject each, both on LPV. All VF samples remained phenotypically susceptible to the treatment PI/r.Among persons experiencing VF without PI DRMs with standard genotyping on an initial PI/r regimen, low-level variants possessing major PI DRMs were present in a minority of cases, occurred in isolation, and did not result in phenotypic resistance. NRTI DRMs were detected in a high proportion of subjects. These data suggest that PIs may remain effective in subjects experiencing VF on a PI/r-based regimen when PI DRMs are not detected by standard or UDS genotyping

Prevalence and Clinical Significance of HIV Drug Resistance Mutations by Ultra-Deep Sequencing in Antiretroviral-Naïve Subjects in the CASTLE Study

CASTLE compared the efficacy of atazanavir/ritonavir with lopinavir/ritonavir, each in combination with tenofovir-emtricitabine in ARV-naïve subjects from 5 continents.Determine the baseline rate and clinical significance of TDR mutations using ultra-deep sequencing (UDS) in ARV-naïve subjects in CASTLE.A case control study was performed on baseline samples for all 53 subjects with virologic failures (VF) at Week 48 and 95 subjects with virologic successes (VS) randomly selected and matched by CD4 count and viral load. UDS was performed using 454 Life Sciences/Roche technology.Of 148 samples, 141 had successful UDS (86 subtype B, 55 non-B subtypes). Overall, 30.5% of subjects had a TDR mutation at baseline; 15.6% only had TDR(s) at <20% of the viral population. There was no difference in the rate of TDRs by B (30.2%) or non-B subtypes (30.9%). VF (51) and VS (90) had similar rates of any TDRs (25.5% vs. 33.3%), NNRTI TDRs (11.1% vs.11.8%) and NRTI TDRs (24.4% vs. 25.5%). Of 9 (6.4%) subjects with M184V/I (7 at <20% levels), 6 experienced VF. 16 (11.3%) subjects had multiple TAMs, and 7 experienced VF. 3 (2.1%) subjects had both multiple TAMs+M184V, and all experienced VF. Of 14 (9.9%) subjects with PI TDRs (11 at <20% levels): only 1 experienced virologic failure. The majority of PI TDRs were found in isolation (e.g. 46I) at <20% levels, and had low resistance algorithm scores.Among a representative sample of ARV-naïve subjects in CASTLE, TDR mutations were common (30.5%); B and non-B subtypes had similar rates of TDRs. Subjects with multiple PI TDRs were infrequent. Overall, TDRs did not affect virologic response for subjects on a boosted PI by week 48; however, a small subset of subjects with extensive NRTI backbone TDR patterns experienced virologic failure

Clinical use of HIV integrase inhibitors : a systematic review and meta-analysis

Background: Optimal regimen choice of antiretroviral therapy is essential to achieve long-term clinical success. Integrase inhibitors have swiftly been adopted as part of current antiretroviral regimens. The purpose of this study was to review the evidence for integrase inhibitor use in clinical settings. Methods: MEDLINE and Web-of-Science were screened from April 2006 until November 2012, as were hand-searched scientific meeting proceedings. Multiple reviewers independently screened 1323 citations in duplicate to identify randomized controlled trials, nonrandomized controlled trials and cohort studies on integrase inhibitor use in clinical practice. Independent, duplicate data extraction and quality assessment were conducted. Results: 48 unique studies were included on the use of integrase inhibitors in antiretroviral therapy-naive patients and treatment-experienced patients with either virological failure or switching to integrase inhibitors while virologically suppressed. On the selected studies with comparable outcome measures and indication (n = 16), a meta-analysis was performed based on modified intention-to-treat (mITT), on-treatment (OT) and as-treated (AT) virological outcome data. In therapy-naive patients, favorable odds ratios (OR) for integrase inhibitor-based regimens were observed, (mITT OR 0.71, 95% CI 0.59-0.86). However, integrase inhibitors combined with protease inhibitors only did not result in a significant better virological outcome. Evidence further supported integrase inhibitor use following virological failure (mITT OR 0.27; 95% CI 0.11-0.66), but switching to integrase inhibitors from a high genetic barrier drug during successful treatment was not supported (mITT OR 1.43; 95% CI 0.89-2.31). Integrase inhibitor-based regimens result in similar immunological responses compared to other regimens. A low genetic barrier to drug-resistance development was observed for raltegravir and elvitegravir, but not for dolutegravir. Conclusion: In first-line therapy, integrase inhibitors are superior to other regimens. Integrase inhibitor use after virological failure is supported as well by the meta-analysis. Careful use is however warranted when replacing a high genetic barrier drug in treatment-experienced patients switching successful treatment

A pilot study to investigate respiratory ill health in people living with HIV

Background: Helping people living with HIV (PLWH) to maintain long‐term health as they age is central to HIV care and involves monitoring for chronic HIV‐associated co‐morbidities. Chronic lung disease (CLD) is recognised to be more common in PLWH as they age, but UK data on CLD prevalence and phenotype in PLWH are limited, particularly in female, non‐white, never smoking groups, and studies of progression over time are lacking. This pilot study aimed to obtain preliminary data on CLD in these subgroups and establish a simple scheme for monitoring lung health of PLWH for a future longitudinal study. Methods: Cross‐sectional pilot of CLD prevalence among PLWH on ART by age, gender, ethnicity and smoking status using convenience sampling of PLWH attending routine clinics. PLWH completed a web‐based questionnaire of self‐reported chronic cough, wheeze & phlegm production using the BOLD study questions; dyspnoea using the Medical Research Council (mMRC) scale; health related quality of life (EQ‐5D‐5L); respiratory, smoking and other lung exposure history. Forced Expiratory Volume (FEV)1 and Forced Vital Capacity (FVC) were measured by spirometry and z‐scores derived from Global Lung Initiative age, sex and ethnicity predicted values. We extracted HIV data from clinical records and evaluated the suitability and acceptability of the measurements. 50 HIV negative controls matched for smoking status were also assessed. Results: We recruited 150 PLWH, median age 46, 31% female, 47% white. 65% were never smokers, 45% reported childhood exposure to solid cooking fuel. 49% reported a history of PCP, TB or pneumonia and 26% a diagnosis of COPD, asthma or bronchiectasis. All groups had lung ill‐health (table) that correlated with EQ5D5L. Conclusion: CLD may affect all PLWH subgroups. These data and methods can inform a longitudinal study of CLD in UK PLWH

Risky sexual practices and related factors among ART attendees in Addis Ababa Public Hospitals, Ethiopia: A cross-sectional study

Background Many HIV-positive persons avoid risky sexual practices after testing HIV sero-positive. However, a substantial number continue to engage in risky sexual practices that may further transmit the virus, put them at risk of contracting secondary sexually transmitted infections and lead to problems with drug resistance. Thus, this study was intended to assess risky sexual practices and related factors among HIV- positive ART attendees in public hospitals of Addis Ababa. Methods A cross-sectional study was conducted among ART attendees from February to March, 2009. Questionnaire-based face-to-face interviews were used to gather data. SPSS software was used to perform descriptive and logistic regression analyses. Results Six hundred and one ART attendees who fulfilled the inclusion criteria was included in the study and interviewed. More than one-third (36.9%) had a history of risky sexual practices in the three months prior to the study. The major reasons given for not using condoms were: partner's dislike of them, both partners being positive for HIV and the desire to have a child. Factors associated with risky sexual practices included: lack of discussion about condom use (Adjusted Odds Ratio (AOR = 7.23, 95% CI: 4.14, 12.63); lack of self-efficacy in using condoms (AOR = 3.29, 95% CI: 2.07, 5.23); lack of sexual pleasure when using a condom (AOR = 2.39, 95% CI: 1.52, 3.76); and multiple sexual partners (AOR = 2.67, 95% CI: 1.09, 6.57). Being with a negative sero-status partner (AOR = 0.33, 95% CI: 0.14, 0.80), or partners of unknown sero-status (AOR = 0.19, 95% CI: 0.09, 0.39) were associated with less risky practice. Conclusions A considerable proportion (36.9%) of respondents engaged in unprotected sexual intercourse, potentially resulting in re-infection by a new virus strain, other sexually transmitted infections and onward transmission of the HIV virus. Health education and counseling which focuses on the identified factors has to be provided. The health education and counseling can be provided to these people at ART appointments on follow- up care. It can be provided in a one-on-one basis or through patient group educational discussions at the clinics

Application of Broad-Spectrum, Sequence-Based Pathogen Identification in an Urban Population

A broad spectrum detection platform that provides sequence level resolution of target regions would have a significant impact in public health, case management, and means of expanding our understanding of the etiology of diseases. A previously developed respiratory pathogen microarray (RPM v.1) demonstrated the capability of this platform for this purpose. This newly developed RPM v.1 was used to analyze 424 well-characterized nasal wash specimens from patients presenting with febrile respiratory illness in the Washington, D. C. metropolitan region. For each specimen, the RPM v.1 results were compared against composite reference assay (viral and bacterial culture and, where appropriate, RT-PCR/PCR) results. Across this panel, the RPM assay showed ≥98% overall agreement for all the organisms detected compared with reference methods. Additionally, the RPM v.1 results provide sequence information which allowed phylogenetic classification of circulating influenza A viruses in ∼250 clinical specimens, and allowed monitoring the genetic variation as well as antigenic variability prediction. Multiple pathogens (2–4) were detected in 58 specimens (13.7%) with notably increased abundances of respiratory colonizers (esp. S. pneumoniae) during viral infection. This first-ever comparison of a broad-spectrum viral and bacterial identification technology of this type against a large battery of conventional “gold standard” assays confirms the utility of the approach for both medical surveillance and investigations of complex etiologies of illness caused by respiratory co-infections

A comparative stratigraphy of cilicia : Results of the first three cilician chronology workshops

This article presents a preliminary comparative stratigraphy of excavated sites in Plain Cilicia and one in Rough Cilicia. It is the outcome of three workshops held in 2014, 2015 and 2017. Plain Cilicia at the junction of Anatolia, Syro-Mesopotamia and Cyprus is one of the most fertile regions of the Ancient Near East. In recent years, archaeological research in the region has intensified, re-opening questions of chronology. The comparative stratigraphy discussed in the workshops is presented here in form of a gazetteer of the participating sites and a chart. This is to be understood as a first step towards a more comprehensive chronology

Survival of the Fittest: Positive Selection of CD4+ T Cells Expressing a Membrane-Bound Fusion Inhibitor Following HIV-1 Infection

Although a variety of genetic strategies have been developed to inhibit HIV replication, few direct comparisons of the efficacy of these inhibitors have been carried out. Moreover, most studies have not examined whether genetic inhibitors are able to induce a survival advantage that results in an expansion of genetically-modified cells following HIV infection. We evaluated the efficacy of three leading genetic strategies to inhibit HIV replication: 1) an HIV-1 tat/rev-specific small hairpin (sh) RNA; 2) an RNA antisense gene specific for the HIV-1 envelope; and 3) a viral entry inhibitor, maC46. In stably transduced cell lines selected such that >95% of cells expressed the genetic inhibitor, the RNA antisense envelope and viral entry inhibitor maC46 provided the strongest inhibition of HIV-1 replication. However, when mixed populations of transduced and untransduced cells were challenged with HIV-1, the maC46 fusion inhibitor resulted in highly efficient positive selection of transduced cells, an effect that was evident even in mixed populations containing as few as 1% maC46-expressing cells. The selective advantage of the maC46 fusion inhibitor was also observed in HIV-1-infected cultures of primary T lymphocytes as well as in HIV-1-infected humanized mice. These results demonstrate robust inhibition of HIV replication with the fusion inhibitor maC46 and the antisense Env inhibitor, and importantly, a survival advantage of cells expressing the maC46 fusion inhibitor both in vitro and in vivo. Evaluation of the ability of genetic inhibitors of HIV-1 replication to confer a survival advantage on genetically-modified cells provides unique information not provided by standard techniques that may be important in the in vivo efficacy of these genes

La Cappadoce méridionale de la Préhistoire à l'époque byzantine

Il y a environ 25 ans, Olivier Pelon organisait à l’Institut Français d’Études Anatoliennes d’Istanbul un colloque destiné à faire l’état des recherches sur la Cappadoce méridionale jusqu’à la fin de l’époque romaine. Un quart de siècle après ce premier colloque, il était intéressant de faire un nouveau point sur l’avancée des recherches dans cette Cappadoce méridionale, de la préhistoire à la période byzantine. Ce nouveau colloque, placé cette fois encore sous l’égide de l’Institut Français d’Études Anatoliennes et intégré à la série des Rencontres d’archéologie de l’IFEA réunit vingt-trois communications. Si les périodes néolithique et chalcolithique ont été particulièrement bien représentées, ce qui témoigne bien de l’importance de cette phase de la préhistoire cappadocienne, liée aux gisements d’obsidienne des Melendiz Dağları, on soulignera en revanche l’absence presque totale du Bronze Ancien. Cette phase est en effet peu représentée dans l’archéologie locale. La même remarque peut s’appliquer au Bronze Moyen. La fin du Bronze Moyen, fort heureusement, est représentée à Porsuk, de même que le Bronze Récent qui bénéficie, depuis peu, tout comme l’Âge du Fer, du démarrage fructueux des fouilles de Kınık Höyük. Enfin, l’Antiquité tardive et Byzance ont pu être représentées, principalement autour de Tyane, ce qui n’avait pas pu être le cas lors du premier colloque. En octobre 2012, quelques semaines avant la tenue de la Rencontre, on apprenait malheureusement le décès brutal et inattendu d’Olivier Pelon, ancien directeur de la mission de Porsuk (jusqu’en 2002) et organisateur de ce premier colloque cappadocien. C’est bien en hommage à sa mémoire que notre Rencontre cappadocienne de 2012 et sa publication ont été naturellement dédiées