title: Performance characteristics of human immunodeficiency virus type 1 (HIV-1) genotyping systems in sequence-based analysis of subtypes other than HIV-1 subtype B.
abstract: Given the diversity of human immunodeficiency virus type 1 (HIV-1) subtypes and the emergence of subtypes other than HIV-1 subtype B in the United States, genotypic assays must be capable of delivering sequence data on diverse HIV-1 subtypes. We evaluated the performance of Visible Genetics TRUGENE HIV-1 genotyping kit and Applied Biosystems ViroSeq HIV-1 genotyping system on a panel of 34 well-characterized HIV-1 viral stocks (subtypes A through H). Both assays perform well on diverse HIV-1 subtypes despite being designed for HIV-1 subtype B. The TRUGENE assay produced sequence data for 31 isolates but not for one C and two G isolates. The TRUGENE assay using prototype 1.5 RT-PCR primers and the ViroSeq assay were both successful for all variants tested, although five isolates lacked double-strand sequence coverage in the ViroSeq assay. The availability of standardized HIV-1 genotyping kits that perform reliably with all HIV subtypes will facilitate broad implementation of HIV-1 resistance testing.
authors.affiliation: Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland 20850, USA. ljagodzinski@hivresearch.org
authors.forename: Linda L
authors.initials: LL
authors.lastname: Jagodzinski
authors.forename: John D
authors.initials: JD
authors.lastname: Cooley
authors.forename: Mark
authors.initials: M
authors.lastname: Weber
authors.forename: Nelson L
authors.initials: NL
authors.lastname: Michael
mesh_terms: D005838:Genotype; D015497:HIV-1 / Q000145:classification* / Q000235:genetics; D006801:Humans; D012367:RNA, Viral / Q000032:analysis*; D011933:Reagent Kits, Diagnostic
chemical_list: D012367:RNA, Viral; D011933:Reagent Kits, Diagnostic