Cobas amplicor hiv 1 monitor test v1

Absolute and log transformed VL. HIV-RNA quantification was performed using the COBAS AMPLICOR HIV-1 Monitor Test v1.5 or COBAS Taqman HIV-1 Test v2.0 (Roche Molecular Systems).

Clinical and laboratory parameters were assessed at baseline, week 24, and week 96. CD4+ T cell count was measured by single- and dual-platform flow cytometry (Becton-Dickinson). HIV-1 RNA in plasma was performed using the COBAS AMPLICOR HIV-1 Monitor Test v1.5 or COBAS TaqMan HIV-1 Test v2.0 (Roche Molecular Systems), with lower limits of quantification (LLQ) of 50 and 20 copies/mL, respectively. CSF samples were run in batch and diluted fourfold for volume requirements for detection of HIV-1 RNA, with an LLQ of 80 copies/mL using the TaqMan platform. HIV-1 RNA measurements below the LLQ that tested positive were designated detectable but not quantifiable. Neuropsychological testing was performed at standardized intervals at weeks 0, 12, 24, and 96 ^{[11 (link)]}.

Samples with viral loads below 1000 copies/mL underwent standard population-based sequencing using methodology identical to that performed on higher viral load samples. However these methods evolved over the years with successive generations of various laboratory technologies. For instance, viral load values were obtained using the Roche COBAS Amplicor HIV-1 Monitor Test v1.5 until 2009 and the Roche COBAS TaqMan HIV-1 v1.0 assay after 2009. HIV RNA was extracted from 500 uL of plasma using either manual or automated methodologies depending on the testing year. The protease and reverse transcriptase regions were amplified using nested RT-PCR, with a product spanning from the beginning of protease to codon 400 of RT. Bidirectional sequencing was performed using one of several ABI sequencers (3100, 3130, 3700, 3730), followed by sequence analysis using Sequencher (Genecodes) or RECall [27 (link)]. Samples which failed this process were re-extracted and reamplified with primers spanning a smaller region of pol (to codon 250 of RT), with the proportion of such cases increasing as viral loads decreased (Gonzalez-Serna 2013, Accepted, Clinical Infectious Diseases). In total, there were 4915 LLV samples tested for drug resistance from a total of 2492 patients.

We asked women for their verbal consent to collect a blood sample for biologic testing at the National HIV Reference Laboratory (NHRL) in Nairobi. We tested blood specimens for HIV antibody and if positive, HIV RNA concentration. We tested all specimens for HIV antibody [Vironostika HIV-1/2 UNIF II Plus O Enzyme Immunoassay (EIA) assay; bioMérieux SA, Marcy l’Etoile, France] and confirmed HIV antibody-positive results with the Murex HIV.1.2.O HIV EIA (DiaSorin, SpA, Saluggia, Italy). Repeat testing was done for discordant results and if results remained discordant, final results were obtained using polymerase chain reaction (Cobas Amplicor HIV-1 Monitor Test, v1.5; Roche Molecular Diagnostics, Pleasanton, CA). We tested all HIV-positive specimens for HIV RNA concentration (Abbott m2000 Real-Time HIV-1 assay; Abbott Park, IL). Virologic suppression was defined as HIV RNA concentration <1000 copies per milliliter.