Evaluation of the Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 Test and Identification of Rare Polymorphisms Potentially Affecting Assay Performance

• Published in: Journal of Clinical Microbiology Vol. 48; no. 8; pp. 2852 - 2858
• Main Authors: Pyne, Michael T, Brown, Katherine L, Hillyard, David R
• Format: Journal Article
• Language: English
• Published: Washington, DC American Society for Microbiology 01.08.2010; American Society for Microbiology (ASM)
• Subjects: Base Pair Mismatch; Biological and medical sciences; Diagnostic Errors; DNA Primers - genetics; Fundamental and applied biological sciences. Psychology; Genotype; HIV Infections - virology; HIV-1 - classification; HIV-1 - genetics; HIV-1 - isolation & purification; Human immunodeficiency virus 1; Humans; Microbiology; Miscellaneous; Molecular Diagnostic Techniques - methods; Oligonucleotide Probes - genetics; Reagent Kits, Diagnostic; Reproducibility of Results; RNA, Viral - genetics; Sensitivity and Specificity; Viral Load - methods; Virology; Virus; HIV-1 virus; Retroviridae; Identification; Human immunodeficiency virus; Lentivirus; Polymorphism
• ISSN: 0095-1137; 1098-660X
• DOI: 10.1128/JCM.00776-10

We evaluated the FDA-approved Roche Cobas AmpliPrep/Cobas TaqMan (CAP/CTM) HIV-1 viral load assay for sensitivity, reproducibility, linearity, HIV-1 subtype detection, and correlation to the Roche Amplicor HIV-1 monitor test, version 1.5 (Amplicor). The limit of detection calculated by probit analysis was 23.8 copies/ml using the 2nd International WHO Standard and 30.8 copies/ml using Viral Quality Assurance (VQA) standard material. Serial dilutions of six patient samples were used to determine inter- and intra-assay reproducibility and linearity, which were very good (<8% coefficient of variation [CV]; between ~1.7 and 7.0 log₁₀ copies/ml). Subtype detection was evaluated in the CAP/CTM, Amplicor, and Bayer Versant HIV-1 bDNA 3.0 (Versant) assays using a commercially available panel. Versant averaged 0.829 log₁₀ copies/ml lower than CAP/CTM and Amplicor averaged 0.427 log₁₀ copies/ml lower than CAP/CTM for the subtype panel. Correlation with samples previously tested by Amplicor was excellent (R² = 0.884; average difference [Amplicor value minus CAP/CTM value], 0.008 log₁₀ copies/ml). Of the 305 HIV samples tested, 7 samples generated CAP/CTM titers between 1.0 and 2.75 log₁₀ copies/ml lower than those for Amplicor. Three of these samples revealed primer and probe mismatches that could account for the discrepancies. Otherwise, the CAP/CTM assay exhibits excellent sensitivity, dynamic range, reproducibility, and correlation with Amplicor in an automated format.