Ceq 8000 analyzer

Routine laboratory results, including CD4 cell count and hemoglobin, were obtained from local laboratory records and/or clinical notes. Before initiation of ART, an additional phlebotomy was performed, and EDTA-anticoagulated plasma specimens were stored at −80°C and batch shipped to the JCRC reference laboratory in Kampala for determination of reference HIV RNA, as well as genotypic resistance testing on all specimens with HIV RNA above 1,000 copies/ml. For HIV RNA determination, the COBAS AmpliPrep/COBAS TaqMan HIV-1 test (Roche, Branchburg, NJ) was used. For HIV-1 genotyping, an in-house sequencing method encompassing the whole of protease and codons 1–300 of reverse transcriptase with a Beckman Coulter CEQ 8000 Analyzer (Beckman Coulter, Inc., Fullerton, CA) was used.^{19 (link)} Sequences were assembled and manually edited using BioEdit version 7.0. All final sequences were submitted to the ViroScore database (Advanced Biological Laboratories SA, France) for data storage. Drug resistance mutations (DRMs) were scored according to the 2010 International AIDS Society–USA list.^{20 (link)} Subtypes were determined using the SCUEAL HIV-1 subtyping tool^{21 (link)} and additional analysis with the REGA algorithm version 2.0^{22 (link)} once required.