From Capillary Electrophoresis to Deep Sequencing: An Improved HIV-1 Drug Resistance Assessment Solution Using In Vitro Diagnostic (IVD) Assays and Software.

Background: Drug-resistance mutations were mostly detected using capillary electrophoresis sequencing, which does not detect minor variants with a frequency below 20%. Next-Generation Sequencing (NGS) can now detect additional mutations which can be useful for HIV-1 drug resistance interpretation. The objective of this study was to evaluate the performances of CE-IVD assays for HIV-1 drug-resistance assessment both for target-specific and whole-genome sequencing, using standardized end-to-end solution platforms.

Comparison of HIV-1 drug resistance profiles generated from novel software applications for routine patient care.

Introduction: Clinical laboratories performing routine HIV-1 genotyping antiviral drug resistance (DR) testing need reliable and up-to-date information systems to provide accurate and timely test results to optimize antiretroviral treatment in HIV-1-infected patients.

Materials And Methods: Three software applications were used to compare DR profiles generated from the analysis of HIV-1 protease (PR) and reverse transcriptase (RT) gene sequences obtained by Sanger sequencing assay in 100 selected clinical plasma samples from March 2013 through May 2014. Interpretative results obtained from the Trugene HIV-1 Genotyping assay (TG; Guidelines v17.

Comparison of ultra-deep versus Sanger sequencing detection of minority mutations on the HIV-1 drug resistance interpretations after virological failure.

Objective: Drug-resistance mutations are routinely detected using standard Sanger sequencing, which does not detect minor variants with a frequency below 20%. The impact of detecting minor variants generated by ultra-deep sequencing (UDS) on HIV drug-resistance interpretations has not yet been studied.

Design: Fifty HIV-1 patients who experienced virological failure were included in this retrospective study.

Effect of pulmonary tuberculosis on mortality in patients receiving HAART.

Objective: To estimate the effect of ongoing treatment for pulmonary tuberculosis (PTB) at time of initiation of HAART on subsequent risk of death.

Design: Evaluation of an open cohort of 7512 patients who initiated HAART between April 2004 and March 2007 in the Themba Lethu Clinic in Johannesburg, South Africa.

Methods: Mortality hazard ratios were estimated using marginal structural Cox proportional hazards models to control for bias due to both confounding and loss to follow-up.

A direct comparison of drug susceptibility to HIV type 1 from antiretroviral experienced subjects as assessed by the antivirogram and PhenoSense assays and by seven resistance algorithms.

HIV-1 drug resistance methodologies are being increasingly utilized to guide treatment decisions; however, information comparing the various assays is limited. Duplicate plasma samples from 70 ART-experienced subjects were analyzed by both the Antivirogram and PhenoSense phenotypic assays and the results compared. HIV genotypes were also obtained and analyzed using seven different resistance algorithms.

Comparison of HIV type 1 protease inhibitor susceptibility results in viral samples analyzed by phenotypic drug resistance assays and by six resistance algorithms: an analysis of a subpopulation of the CHORUS cohort.

Drug resistance testing is increasingly used to guide treatment decisions in patients infected with HIV-1. A number of rules-based algorithms have been designed to predict drug resistance profiles based on the HIV-1 genotypic data. Drug-resistance mutations in 206 viral samples from protease inhibitor (PI)-experienced subjects with HIV-1 infection were assessed, and the level of susceptibility of the samples predicted using seven unique algorithms.

Viral load and CD4 cell response to protease inhibitor-containing regimens in subtype B versus non-B treatment-naive HIV-1 patients.

We compared the response to protease inhibitor-containing highly active antiretroviral therapy in 175 HIV-1 treatment-naive patients harbouring subtype B versus non-B. No difference in the proportion of patients with viral loads below 400 copies/ml was observed at month 24. However, there was a significant difference in the median CD4 cell increase at month 24.

Uncommon mutations at residue positions critical for enfuvirtide (T-20) resistance in enfuvirtide-naive patients infected with subtype B and non-B HIV-1 strains.

Enfuvirtide (T-20) is the lead compound of the new class of antiretroviral drugs called fusion inhibitors. T-20 resistance-associated mutations located in the heptad repeat 1 (HR-1) domain of gp41 have been described in vitro and in clinical trials. In this study, the authors investigated the primary genotypic T-20 resistance in subtype B and non-B HIV-1 strains from patients at the beginning of their follow-up in the Luxembourg HIV Cohort as well as the emergence of primary resistance to T-20 in patients who had long-term infection with subtype B HIV-1 strains.

Epidemiology of sepsis and infection in ICU patients from an international multicentre cohort study.

Objectives: To examine the incidence of infections and to describe them and their outcome in intensive care unit (ICU) patients.

Design And Setting: International prospective cohort study in which all patients admitted to the 28 participating units in eight countries between May 1997 and May 1998 were followed until hospital discharge.

Patients: A total of 14,364 patients were admitted to the ICUs, 6011 of whom stayed less than 24 h and 8353 more than 24 h.