Patients were followed for at least 1 year after initiation of therapy (Table 1). CD4 cells were isolated from 10 mL of whole blood [collected from patients in ethylenediaminetetraacetic acid (EDTA)] by an immunomagnetic method using anti-CD4 coated magnetic beads (Dynabeads M450 CD4; Dynal AS, Oslo, Norway) according to the manufacturer’s protocol and were stored at −80 °C until
use. The purity of the CD4 cell preparation was approximately 99% as estimated using Becton Dickinson FACScan Flow Cytometer technology (Franklin Lakes, New Jersey, USA) (data not shown). The 8E5 cell line was cultured in RPMI-1640 medium and the GDC-0973 chemical structure cells were counted using a Coulter automated haematology analyser, diluted to 106 cells per aliquot and stored at −80 °C. The 8E5 cell-free virus present in the culture supernatant was diluted and stored in aliquots of 30 000 HIV-1 RNA copies/mL. The HIV-1 RNA plasma viral load was assessed using the Versant HIV-1 RNA 3.0 assay (Siemens Medical
Diagnostics Solutions, Tarrytown, NY, USA) according to the manufacturer’s instructions. This assay is based on branched DNA (bDNA) technology. It requires 1 mL of sample and has a dynamic range of 50–500 000 copies/mL. Plasma samples and the 8E5 cell culture supernatant were frozen at −80 °C until tested for HIV-1 RNA viral load. A viral load result of <50 copies/mL was regarded as 50 copies/mL when calculating the mean viral load of a given patient group. DNA was extracted from purified patient CD4 cells diluted in 200 μL of phosphate-buffered Selleckchem CYC202 saline (PBS), using the High Pure® PCR Template Preparation
Kit (Roche Diagnostics GmbH, Mannheim, Germany) according to the manufacturer’s recommendations. Erastin To concentrate the HIV-1 target gene in patient samples, DNA was eluted in a volume of 50 μL. DNA from 106 T-lymphoblastoid 8E5 cells, used as positive control, was eluted in 200 μL. A negative control (in which the template was replaced with nuclease-free water) was included in each polymerase chain reaction (PCR) run. Particular attention was paid to using DNAse- and RNAse-free materials. Depending on the number of samples, the whole DNA purification process required approximately 1 h. HIV RNA was extracted from plasma and from the 8E5 cell culture supernatant using the QIAmp Viral Mini Kit™ (Qiagen, Leiden, the Netherlands) according to the manufacturer’s directions. Viral RNA and proviral DNA genotypic antiretroviral drug resistance mutations were identified using an in-house reverse transcriptase–polymerase chain reaction (RT-PCR) method applied to the RT and PR genes (adapted from Schmit et al. ). Direct cycle sequencing with BigDye terminator chemistry was carried out on the ABI Prism 310 sequencer (Applied Biosystems). In cases of PCR failure, samples were analysed using a TRUGENE HIV-1 Genotyping Kit (Siemens Medical Diagnostics Solutions).