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Comparative Study
. 2001 Jun;39(6):2157-65.
doi: 10.1128/JCM.39.6.2157-2165.2001.

Human immunodeficiency virus type 1 drug resistance testing: a comparison of three sequence-based methods

M Erali  1 , S Page, L G Reimer, D R Hillyard
Affiliations
Comparative Study

Human immunodeficiency virus type 1 drug resistance testing: a comparison of three sequence-based methods

M Erali et al. J Clin Microbiol. 2001 Jun.

Abstract

The use of genotypic assays for determining drug resistance in human immunodeficiency virus (HIV) type 1 (HIV-1)-infected patients is increasing. These tests lack standardization and validation. The aim of this study was to evaluate several tests used for the determination of HIV-1 drug resistance. Two genotypic tests, the Visible Genetics TruGene HIV-1 Genotyping Kit and the Applied Biosystems HIV Genotyping System, were compared using 22 clinical samples. Genotyping results were also obtained from an independent reference laboratory. The Visible Genetics and Applied Biosystems genotyping tests identified similar mutations when differences in the drug databases and reference strains were taken into account, and 19 of 21 samples were equivalent. The concordance between the two assays was 99% (249 of 252 mutation sites). Mutations identified by the reference laboratory varied the most among those identified by the three genotypic tests, possibly because of differences in the databases. The concordance of the reference laboratory results with the results of the other two assays was 80% (201 of 252). Samples with 500 to 750 HIV RNA copies/ml could be sequenced by the Visible Genetics and Applied Biosystems assays using 1 ml of input. The Visible Genetics and Applied Biosystems assays both generated an accurate sequence. However, the throughput of the Visible Genetics assay is more limited and may require additional instruments. The two assays differ technically but are similar in overall complexity. Data analysis in the two assays is straightforward, but only the reports provided by Visible Genetics contain information relating mutations to drug resistance. HIV drug resistance genotyping by sequencing is a complex technology which presents a challenge for analysis, interpretation, and reporting.

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Figures

FIG. 1
FIG. 1
Electropherogram for sample 13 at protease codon 54. (A) VG electropherogram set at 20% threshold; (B) AB electropherogram set at 30% threshold. Arrows indicate a mixture of wild-type codon ATC and mutant codon GTC.
See this image and copyright information in PMC

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