Computational protocol: Implication of First-Line Antiretroviral Therapy Choice on Second-Line Options

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Protocol publication

[…] From the start of the Harvard/APIN PEPFAR program in 2004, blood samples were drawn at baseline (ie, ART initiation), 3 months, and every 6 months thereafter unless clinical indications suggested an earlier draw. Starting in 2010, the program dropped the practice of VL testing at 3 months, and by 2014, programmatic and national guidelines shifted the recommendations to VL testing at months 6, 12, and then every 12 months thereafter. For each sample, standardized tests were performed to monitor CD4+ T-cell counts, VL, hematology, and chemistry values, as previously described [].Drug resistance mutation genotypes were generated on the first available specimen after VF (S1: first of 2 samples with VL ≥1000 copies/mL) and on samples taken closest to the time of 2L switch (S2 sample). Drug resistance mutation assays for the S1 samples were conducted at the 3 laboratories in Nigeria using the ViroSeq HIV-1 Genotyping System 2.0 Assay (Abbot, Chicago, IL) or the American Type Culture Collection HIV-1 Drug Resistance Genotyping Kit (CDC, Atlanta, GA). Protease and reverse-transcriptase sequencing for the S2 samples were conducted at Harvard Chan using adapted in-house standardized primers []. All sequence data were edited and aligned with reference sequences from the Los Alamos HIV Sequence Database [] using CLUSTAL X []. Bootstrapped neighbor-joining trees were generated for subtype determination using NJ Plot []. Mutation profiles and drug susceptibility were evaluated using Stanford University’s HIVdb program, which follows International Antiviral Society-USA recommendations []. […]

Pipeline specifications

Software tools ViroSeq, Clustal W
Application Drug design
Organisms Homo sapiens
Diseases Virus Diseases, HIV Infections, Tuberculosis, Multidrug-Resistant, Renal Insufficiency
Chemicals Nucleosides, Zidovudine