Human Immunodeficiency Virus Type 1 Drug Resistance Testing: a Comparison of Three Sequence-Based Methods

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%

Quality Assessment Program for Genotypic Antiretroviral Testing Improves Detection of Drug Resistance Mutations

“…Two commercially available GART kits are available: TRUGENE HIV-1 from Visible Genetics Inc. (Toronto, Ontario, Canada) and the ViroSeq HIV-1 genotyping system from Applied Biosystems (Foster City, Calif.). These assays have been shown to provide highly concordant sequences when the assays are tested in parallel (6).…”

“…Several studies have indicated a high level of sequence concordance between participating laboratories when various aspects of GART are examined (4,6,14). However, there have been few reports of studies that have considered the entire GART procedure (16).…”

Sources and Magnitude of Intralaboratory Variability in a Sequence-Based Genotypic Assay for Human Immunodeficiency Virus Type 1 Drug Resistance

“…Studies comparing different commercial and in-house sequencing methods for resistance testing in clinical samples have found that concordance across methods at key mutation sites can range from 80 to 99% (6,7,9). Since genotypic tests are relatively complex to perform, careful attention to performance consistency and quality control are necessary to ensure reliable results (6,7,9,16,17). Routine use of quality measures to assess PCR contamination, instrument performance, and raw sequence data can minimize methodological variability (10).…”

“…Other studies have shown that interlaboratory concordance can be quite high (19,20), particularly when laboratories with high levels of sequencing experience are using similar methods. Studies comparing different commercial and in-house sequencing methods for resistance testing in clinical samples have found that concordance across methods at key mutation sites can range from 80 to 99% (6,7,9). Since genotypic tests are relatively complex to perform, careful attention to performance consistency and quality control are necessary to ensure reliable results (6,7,9,16,17).…”

Presente y futuro del laboratorio de microbiología en el control de la infección por el virus de la inmunodeficiencia humana

“…Los sistemas comercializados en la actualidad para la determinación de la resistencia del VIH-1 por secuenciación automática son HIV Genotyping System (Applied Biosystems, California; http://www.appliedbiosystems.com) y TruGene HIV-1 Genotyping System (Visible Genetics, Canadá; http://www.visgen.com) 10 . Las principales diferencias entre ambos son las reacciones necesarias en el procesamiento de cada muestra, así como los diferentes pasos de purificación y precipitación 11 .…”