title: Optimization of a genotypic assay applicable to all human immunodeficiency virus type 1 protease and reverse transcriptase subtypes.
abstract: Genotypic assays are used often to guide clinicians in decisions concerning the treatment of patients. An optimized sequence-based genotypic assay was used to determine the whole protease and reverse transcriptase (RT) gene, including the gag cleavage site region and RNase H region. Since non-B subtypes are increasing in countries where subtype B was the most prevalent subtype, and treatment becomes more available in developing countries where the epidemic is characterized by a high prevalence of non-B subtypes, it was important that the genotypic test was evaluated using a panel of different subtypes. Amplification was successful for different subtypes: A, B, C, D, F, G, H, J, CRF01_AE, CRF02_AG, CRF11_cpx, CRF13_cpx and an uncharacterized recombinant sample. The detection limit of the PCR was 1000 copies/ml, except for 1 subtype C sample (PL3) and 1 CRF02_AG sample (PL8). The detection limit for these samples was 5000 copies/ml. A sequence could be obtained in both directions for most of the samples.
authors.affiliation: Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
authors.forename: J
authors.initials: J
authors.lastname: Snoeck
authors.forename: C
authors.initials: C
authors.lastname: Riva
authors.forename: K
authors.initials: K
authors.lastname: Steegen
authors.forename: Y
authors.initials: Y
authors.lastname: Schrooten
authors.forename: B
authors.initials: B
authors.lastname: Maes
authors.forename: L
authors.initials: L
authors.lastname: Vergne
authors.forename: K
authors.initials: K
authors.lastname: Van Laethem
authors.forename: M
authors.initials: M
authors.lastname: Peeters
authors.forename: A-M
authors.initials: AM
authors.lastname: Vandamme
mesh_terms: D017931:DNA Primers; D018076:DNA, Complementary / Q000378:metabolism; D024882:Drug Resistance, Viral / Q000235:genetics; D015683:Gene Products, gag / Q000737:chemistry / Q000378:metabolism; D005838:Genotype; D015658:HIV Infections / Q000821:virology*; D016333:HIV Protease / Q000145:classification* / Q000235:genetics; D054303:HIV Reverse Transcriptase / Q000145:classification* / Q000235:genetics; D015497:HIV-1 / Q000145:classification* / Q000187:drug effects / Q000201:enzymology / Q000235:genetics*; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods*; D012367:RNA, Viral / Q000302:isolation & purification; D016914:Ribonuclease H / Q000235:genetics
chemical_list: D017931:DNA Primers; D018076:DNA, Complementary; D015683:Gene Products, gag; D012367:RNA, Viral; D054303:HIV Reverse Transcriptase; D016914:Ribonuclease H; D016333:HIV Protease