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Updated: Aug 30, 2026
Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
Published on: December 28, 2010
Performance characteristics of human immunodeficiency virus type 1 (HIV-1) genotyping systems in sequence-based
Linda L Jagodzinski1, John D Cooley, Mark Weber
1Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland 20850, USA. ljagodzinski@hivresearch.org
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.
