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HIV-1 Coreceptor Tropism with Reflex to Ultradeep SequencingTest code(s) 90666, 90954, 90955
This is an outdated version of this FAQ. It was effective 12/11/2012 to 04/16/2013.
The current version is available here.
Question 1. What is HIV tropism?
Tropism refers to the type of cytokine coreceptor used by HIV-1 when infecting the host cell. The viruses in most (>80%) treatment-naïve patients use the CCR5 (R5) coreceptor.1 Conversely, the viruses in up to 50% of treatment-experienced patients use either the CXCR4 (X4) coreceptor or both coreceptors (ie, R5 and X4).2 Viruses that use both coreceptors are called dual-mixed (D/M) viruses.
Question 2. What is a coreceptor tropism test, and when should I order one?
A coreceptor tropism test determines whether a patient exclusively harbors R5-tropic virus or has X4-tropic or D/M virus. Patients who exclusively harbor R5-tropic virus can be treated with CCR5 antagonists such as maraviroc (Selzentry®). CCR5 antagonists block R5 viruses from binding to the CCR5 coreceptor and infecting cells. They are ineffective in patients with X4 or D/M virus. Thus, coreceptor tropism testing can help determine patient eligibility for CCR5 antagonist therapy.
A coreceptor tropism test should be performed when the use of a CCR5 antagonist is being considered.3,4 Coreceptor tropism testing might also be considered for patients who exhibit virologic failure while taking a CCR5 inhibitor.3,4
Question 3. What methods are available for tropism testing?
Two methods are available: 1) phenotypic analysis of recombinant viruses and 2) genotypic analysis of the V3 loop of the HIV-1 gene.
Question 4. How do phenotypic tropism tests work?
Phenotypic tropism tests such as Trofile®(Monogram Biosciences) use a cloned envelope gene from a patient’s virus to infect R5 and X4 indicator cells that emit light when infected. The relative amount of light emitted by each cell type can then be measured to determine whether the patient’s virus is R5-tropic, X4-tropic, or D/M-tropic.
Question 5. How do genotypic tropism tests work?
Genotypic tropism tests determine the DNA sequence of the third variable loop (V3) region of the HIV-gene, the primary determinant of viral tropism. The patient’s viral RNA is reverse-transcribed to DNA and amplified using PCR. After DNA sequencing, a number of different bioinformatic algorithms can be used to infer viral coreceptor usage from the V3 loop sequence.
At Quest Diagnostics, we use triplicate population sequencing (TPS) to increase the chances of detecting minority X4 virus populations. Relative to single sequencing, the use of TPS can increase sensitivity by 20 percentage points.5 In a retrospective clinical study, TPS-predicted virologic responses to maraviroc were consistently similar to Trofile-predicted responses.6
When TPS detects only R5-tropic virus, we reflex to the more sensitive ultradeep sequencing (UDS) method. UDS can detect X4 virus in ≥95% of the cases when it makes up as little as 5% of the viral population (5% at 100,000 copies HIV-1/mL and 12% at 25,000 copies/mL).7 Conversely, TPS can detect X4 virus in ≥95% of the cases when it makes up at least 20% of the viral population.7 If X4-tropic virus is detected at a level of 2% or higher, the tropism test result is reported as X4, because CCR5 antagonists are unlikely to be effective in these cases.8
Question 6. What are the benefits of reflexing to ultradeep sequencing?
TPS can be performed very rapidly. When X4-tropic virus is detected, the report will usually be available in less than one week. When X4-tropic virus is not detected by TPS, a reflex (at an additional charge) to the more sensitive UDS method is needed. When UDS is used, final results will be available within 10 days of sample receipt.
Question 7. Has genotypic tropism testing been clinically validated?
Yes, testing has been clinically validated in both treatment-experienced and treatment-naïve patient populations. Predictions of maraviroc response determined by genotypic tropism methods are similar to predictions generated by phenotypic methods.6-9
Harrigan and Geretti summarized the results of several retrospective clinical studies and concluded genotypic tropism testing is suitable for clinical use.10 This review article is available at http://journals.lww.com/aidsonline/Fulltext/2011/01140/Genotypic_tropism_testing__evidence_based_or_leap.17.aspx#.
Treatment-experienced Patient Population
- In a retrospective clinical study, virologic responses to maraviroc predicted by TPS were consistently similar to the responses predicted by the original (less sensitive) Trofile assay.6
- When UDS was used to reanalyze more than 1,800 samples from treatment-experienced patients in the MOTIVATE and A4001029 clinical trials, 49% of maraviroc recipients with an R5 genotype maintained a viral load of <50 copies/mL after 48 weeks, compared to 46% with an R5 phenotype determined by the original Trofile method.8 A viral load of <50 copies/mL was maintained by 26% and 23% (genotype and phenotype, respectively) of patients predicted to harbor D/M or X4 virus.8
Using a subset of 327 patients from the MOTIVATE and A4001029 studies, maraviroc response predictions made by Quest Diagnostics genotypic tropism assay (TPS with reflex to UDS) were compared to that of the enhanced sensitivity Trofile assay (ESTA). Both assays predicted the same short-term virologic response to maraviroc treatment. At week 8, the proportion of patients with R5 virus who responded to treatment (positive predictive value) was 66% for the ESTA and 65% for the Quest Diagnostics assay. The proportion of patients with D/M or X4 virus who did not respond to treatment (negative predictive value) was 59% and 58% for ESTA and the Quest Diagnostics assay, respectively.7
Both assays also predicted the same immunologic response at week 24. In patients with R5 virus, the CD4+ T-cell count increased by 88.0 cells/mL and 88.5 cells/mL for the ESTA and Quest Diagnostics assays, respectively. In patients with X4 virus, the increase in T-cell count was much smaller: 48.3 cells/mL and 35.5 cells/mL for the ESTA and Quest Diagnostics assays, respectively.7
Treatment-naïve Patient Population
- The clinical performance of UDS was also evaluated in a reanalysis of the MERIT study which used maraviroc in a treatment-naïve patient population.9 Among patients identified as having R5 virus by UDS or by ESTA, 67% and 68%, respectively, achieved a viral load of <50 copies/mL at week 48. A lower proportion of patients found to harbor D/M or X4 virus achieved a virologic response at week 48: 46% for UDS and 45% for ESTA.
Question 8. Is genotypic tropism testing as sensitive as phenotypic testing?
The original Trofile phenotypic assay was able to reliably detect 10% minority X4 variants, based on mixtures of R5 and X4 DNA clones.11When the same clonal experiments were conducted with the enhanced sensitivity assay (ESTA), 0.3% minority X4 clones could be reliably detected.12 Similarly, the UDS instrument used for Quest Diagnostics genotypic tropism testing can detect 0.5% X4 in mixed clones.7
Biological sensitivity is defined as the ability to reliably detect X4 virus in mixed R5/X4 plasma samples similar to those taken from HIV-1 patients. Unlike clonal analysis, biological sensitivity measures the sensitivity of the entire assay, which may be influenced by the efficiency of nucleic acid extraction and PCR amplification of minor variants as well as the viral load in the sample.
The biological sensitivity of the Quest Diagnostics TPS assay to detect X4 virus in ≥95% of dual-mixed samples is 20% X4 at a viral load of 25,000 copies/mL. The biological sensitivity of our UDS assay is 12% X4 at a viral load of 25,000 copies/mL and 5% X4 at a viral load of 100,000 copies/mL.7 The biological sensitivity of the Trofile assay, however, is unpublished. Because the Trofile assay also uses extraction and amplification, its biological sensitivity is likely higher than the published technical sensitivity.
Regardless of these potential differences in sensitivity, our genotype assay and the current Trofile assay appear equal when predicting maraviroc response.7
Question 9. How are results from the genotypic tropism test reported?
When X4 virus is detected in the TPS step:
CXCR4 (X4) Population Seq DETECTED UDS X4 Reflex testing not required Net Tropism Assessment DM/X4 MVC Activity Anticipated NO
When X4 virus is detected in the UDS step:
CXCR4 (X4) Population Seq NOT DETECTED UDS X4 DETECTED Net Tropism Assessment DM/X4 MVC Activity Anticipated NO
When X4 virus is not detected in either step
CXCR4 (X4) Population Seq NOT DETECTED UDS X4: NOT DETECTED Net Tropism Assessment R5 MVC Activity Anticipated YES
Note: when the UDS method is used, the Net Tropism Assessment is based on interpretation of the UDS result.
Question 10. Can I order a tropism test if my patient has a low or undetectable viral load?
If the plasma viral load is <1,000 copies/mL, we might not be able to amplify sufficient viral RNA to perform a standard tropism test. A proviral DNA tropism test (HIV-1 Coreceptor Tropism, Proviral DNA, test code 91299) is available for tropism testing in these patients. For more information about the proviral DNA test, go to http://education.QuestDiagnostics.com/faq/FAQ87.
- Clotet B. CCR5 inhibitors: promising yet challenging. J Infect Dis. 2007;196:178-180.
- Poveda E, Briz V, de Mendoza C, et al. Prevalence of X4 tropic HIV-1 variants in patients with differences in disease stage and exposure to antiretroviral therapy. J Med Virol. 2007;79:1040-1046.
Panel on Antiretroviral Guidelines for Adults and Adolescents. Guidelines for the use of antiretroviral agents in HIV-1–infected adults and adolescents. Department of Health and Human Services. March 27, 2012. Available at:
http://www.aidsinfo.nih.gov/contentfiles/lvguidelines/adultandadolescentgl.pdf. Accessed November 2, 2012.
- Thompson MA, Aberg JA, Hoy JF, et al. Antiretroviral treatment of adult HIV infection: 2012 recommendations of the International Antiviral Society-USA panel. JAMA. 2012;308:387-402.
- Swenson LC, Moores A, Low AJ, et al. Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA. J Acquir Immune Defic Syndr. 2010;54:506-510.
- McGovern RA, Thielen A, Mo T, et al. Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies. AIDS. 2010;24:2517-2525.
- Kagan RM, Johnson EP, Siaw M, et al. A genotypic test for HIV-1 tropism combining Sanger sequencing with ultradeep sequencing predicts virologic response in treatment-experienced patients. PloS One. 2012;7:e46334.
- Swenson LC, Mo T, Dong WW, et al. Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients. J Infect Dis. 2011;203:237-245.
- Swenson LC, Mo T, Dong WW, et al. Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc. Clin Infect Dis. 2011;53:732-742.
- Harrigan PR, Geretti AM. Genotypic tropism testing: evidence-based or leap of faith? AIDS. 2011;25:257-264.
- Whitcomb JM, Huang W, Fransen S, et al. Development and characterization of a novel single-cycle recombinant-virus assay to determine human immunodeficiency virus type 1 coreceptor tropism. Antimicrob Agents Chemother. 2007;51:566-575.
- Reeves JD, Coakley E, Petropoulos CJ, et al. An enhanced-sensitivity Trofile™ HIV coreceptor tropism assay for selecting patients for therapy with entry inhibitors targeting CCR5: a review of analytical and clinical studies. J Viral Entry. 2009;3:94-102.
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