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

The use of genotypic assays for determining drug resistance in human immuno deficiency virus (HIV) type 1 (HIV-l)-infected patients is increasing. Thes e tests lack standardization and validation. The aim of this study was to e valuate 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 clinic al samples. Genotyping results were also obtained from an independent refer ence laboratory. The Visible Genetics and Applied Biosystems genotyping tes ts identified similar mutations when differences in the drug databases and reference strains were taken into account, and 19 of 21 samples were equiva lent. The concordance between the two assays was 99% (249 of 252 mutation s ites). Mutations identified by the reference laboratory varied the most amo ng those identified by the three genotypic tests, possibly because of diffe rences in the databases. The concordance of the reference laboratory result s,vith the results of the other two assays was 80% (201 of 252). Samples wi th 500 to 750 HIV RNA copies/ml could be sequenced by the Visible Genetics and Applied Biosystems assays using 1 mi of input. The Visible Genetics and Applied Biosystems assays both generated an accurate sequence. However, th e throughput of the Visible Genetics assay is more limited and may require additional instruments. The two assays differ technically but are similar i n overall complexity. Data analysis in the two assays is straightforward, b ut only the reports provided by Visible Genetics contain information relati ng mutations to drug resistance. HIV drug resistance genotyping by sequenci ng is a complex technology which presents a challenge for analysis, interpr etation, and reporting.