Performance of Applied Biosystems ViroSeq HIV-1 Genotyping System for sequence-based analysis of non-subtype B human immunodeficiency virus type 1 from Uganda

The Applied Biosystems ViroSeq HIV-1 Genotyping System is a commercially av ailable, integrated system for sequence-based analysis of drug resistance m utations in human immunodeficiency virus type 1 (HIV-1) protease and revers e transcriptase (RT). We evaluated the performance of this system for analy sis of non-subtype B HIV-1 by analyzing plasma samples from Ugandan women a nd infants. Plasma samples were obtained from 105 women and 25 infants enro lled in a Ugandan clinical trial. HIV-1 analysis was performed with the Vir oSeq system according to the manufacturer's instructions, except that the v olume of plasma used for analysis was less than the recommended 0.5 mi for some samples. Viral loads ranged from 2,313 to 2,336,400 copies/ml. PCR pro ducts suitable for sequencing were amplified from all samples tested. Compl ete sequences for protease (amino acids 1 to 99) and RT (amino acids 1 to 3 20) were obtained for 102 of 105 (97%) of the maternal samples tested and a ll 25 of the infant samples tested. Complete double-stranded sequences were obtained for 90 of 105 (86%) of the maternal samples tested and 22 of 25 ( 88%) of the infant samples tested. The sequences obtained with this system were used for HIV-1 subtyping. The subtypes identified were A, C, D, and A/ D recombinant HIV-1. The performances of the seven sequencing primers were similar for the subtypes examined. The ViroSeq system performs well for ana lysis of Ugandan plasma samples with subtypes A, C, D, and A/D recombinant HIV-1. The availability of this genotyping system should facilitate studies of HIV-1 drug resistance in countries where these subtypes are prevalent.