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Updated: Jul 18, 2026
Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach
Published on: December 1, 2011
Development and characterization of a novel single-cycle recombinant-virus assay to determine human immunodeficiency
Jeannette M Whitcomb1, Wei Huang, Signe Fransen
1Monogram Biosciences, Inc., 345 Oyster Point Boulevard, South San Francisco, CA 94080, USA.
Abstract:
Most human immunodeficiency virus type 1 (HIV-1) strains require either the CXCR4 or CCR5 chemokine receptor to efficiently enter cells. Blocking viral binding to these coreceptors is an attractive therapeutic target. Currently, several coreceptor antagonists are being evaluated in clinical trials that require characterization of coreceptor tropism for enrollment. In this report, we describe the development of an automated and accurate procedure for determining HIV-1 coreceptor tropism (Trofile) and its validation for routine laboratory testing. HIV-1 pseudoviruses are generated using full-length env genes derived from patient virus populations. Coreceptor tropism is determined by measuring the abilities of these pseudovirus populations to efficiently infect CD4+/U87 cells expressing either the CXCR4 or CCR5 coreceptor. Viruses exclusively and efficiently infecting CXCR4+/CD4+/U87 cells are designated X4-tropic. Conversely, viruses exclusively and efficiently infecting CCR5+/CD4+/U87 cells are designated R5-tropic. Viruses capable of infecting both CXCR4+/CD4+/U87 and CCR5+/CD4+/U87 cells are designated dual/mixed-tropic. Assay accuracy and reproducibility were established by evaluating the tropisms of well-characterized viruses and the variability among replicate results from samples tested repeatedly. The viral subtype, hepatitis B virus or hepatitis C virus coinfection, and the plasma viral load did not affect assay performance. Minority subpopulations with alternate tropisms were reliably detected when present at 5 to 10%. The plasma viral load above which samples can be amplified efficiently in the Trofile assay is 1,000 copies per ml of plasma. Trofile has been automated for high-throughput use; it can be used to identify patients most likely to benefit from treatment regimens that include a coreceptor inhibitor and to monitor patients on treatment for the emergence of resistant virus populations that switch coreceptor tropism.
Insights
A new automated assay, Trofile, accurately determines human immunodeficiency virus type 1 (HIV-1) coreceptor tropism. This method is crucial for selecting patients for coreceptor inhibitor therapies and monitoring treatment resistance.
Area of Science:
- Virology
- Immunology
- Medical Diagnostics
Background:
- Human immunodeficiency virus type 1 (HIV-1) entry into host cells depends on coreceptor binding, primarily to CXCR4 or CCR5.
- Coreceptor antagonists are a therapeutic strategy, necessitating accurate tropism determination for patient selection in clinical trials.
Purpose of the Study:
- To develop and validate an automated, accurate assay (Trofile) for determining HIV-1 coreceptor tropism for routine laboratory use.
- To establish the reliability and performance characteristics of the Trofile assay.
Main Methods:
- Generation of HIV-1 pseudoviruses from patient env genes.
- Infection of CD4+/U87 cells expressing CXCR4 or CCR5 to measure infectivity.
- Classification of tropism as X4, R5, or dual/mixed based on infection patterns.
Main Results:
- The Trofile assay demonstrated accuracy and reproducibility across various viral subtypes and coinfections.
- Minority tropism subpopulations (5-10%) were reliably detected.
- Assay performance was consistent for plasma viral loads above 1,000 copies/ml.
Conclusions:
- The automated Trofile assay is a validated tool for routine HIV-1 coreceptor tropism testing.
- Trofile facilitates patient identification for coreceptor inhibitor therapy and monitoring of treatment-emergent tropism shifts.
