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Genotype Testing in HIV


HIV Genotype testing is the application of DNA sequencing technology to reveal the genetic sequence of an individual’s HIV strains. This insight can be extremely valuable because specific mutations are associated with HIV resistance to specific drugs; using this technology, physicians may soon be able to ensure maximum durable patient response to treatment.

Two genotype testing methods are currently available: one sequences the entire genome of HIV; the other looks only for "point mutations" at residues, or specific sites on the HIV genome that are known to confer resistance to various HIV drugs. Although genotypic testing has been used in clinical trials, it has not been widely used outside these trials because of the difficulty in interpreting results generated by each assay. Now F. Hoffmann - La Roche Ltd of Basel, Switzerland, has joined forces with Virology Networks of Utrecht, The Netherlands, and PE Biosystems of Foster City, California, to make genotyping a valuable tool for optimizing and individualizing HIV therapy.

A Hypothetical Case Study for the Future Management of an HIV-Infected Person…

Sarah, 32 years old, was diagnosed HIV-positive four years ago. She has been taking a three-drug, protease inhibitor-containing treatment regimen since her diagnosis; one of the drugs she is taking is AZT (an NRTI). Having heard that HIV can mutate easily, Sarah is very careful to take her medication every day at the appropriate times. While she has responded well to treatment, her HIV viral load, previously undetectable, has begun to creep upward.

Sarah’s doctor, curious as to why the regimen seems to be losing its effectiveness, orders a genotype test run on her blood. The results show a mutation at codons 41 and 215 on the RT gene.

Sarah’s doctor then consults the RetroGramTM decision support software to provide an interpretation of the significance of these mutations. The program indicates that these mutations confer resistance to AZT, indicating that this drug is unlikely to continue being a useful component of Sarah’s treatment regimen.

He decides, in the absence of any other known mutations to the other drugs she is taking, that he will switch Sarah from AZT to another drug in the same class; they agree that she will continue to take the other two drugs, and he’ll conduct another viral load test in six weeks.

Why It’s Important

As seen in the example above, HIV genotype testing has the potential to give doctors and patients unprecedented insight into any mutations present in an individual’s HIV genome. Armed with this knowledge, physicians could make treatment decisions to maximize the impact of anti-HIV drugs. In two examples of this approach, preliminary data from the VIRADAPT study in France and the GART study in the USA show that knowing the genetic sequence of the HIV quasi-species can provide information with real clinical significance. These data are important for rational drug selection when assembling a combination regimen in at least four important patient populations:

  • those choosing first-line therapy, specifically in the increasingly common context of mono- or multi-drug-resistant HIV being transmitted
  • those whose therapy is now beginning to fail, who need to consider changing their treatment regimens
  • those needing post-exposure prophylaxis, especially in a clinical setting where AZT resistance is becoming more prevalent, and
  • pregnant women, especially in the context of a failing regimen since studies have shown that viral load at delivery is the main correlate of vertical transmission.

The GREAT Trial

To put genotype data into the hands of practicing physicians in an understandable and clinically useful way, Roche is partnering with Virology Networks and PE Biosystems to sponsor a prospective clinical trial called GREAT -- Genotypic Resistance Evaluation to Aid Therapy-switching. GREAT will evaluate the benefit of resistance testing in the HIV treatment setting and will include a variety of different treatment approaches and a wide range of anti-HIV medications. The trial’s purpose is to explore the clinical impact of applying a sequencing-based genotyping method, the recently launched PE Biosystems’ HIV Genotyping System, and to test a rules-based software algorithm that ultimately will provide information to support treatment decisions.

GREAT is a randomized, international, parallel-group, open-label, 48-week trial enrolling up to 360 patients who are currently failing their first-line protease inhibitor-based anti-HIV combination regimens; failure is defined by at least 24 consecutive weeks' experience with a PI-containing combination regimen and a viral load of at least 5,000 copies/ml (or 3.7 log10) at screening. Participants will be randomized to a new regimen by one of two methods: either best clinical judgment or best clinical judgment in conjunction with real-time HIV resistance genotyping.

The GREAT trial also will test the prototype RetroGram Decision Support Software. This experimental software, designed jointly by Virology Networks and Roche and developed by UK-based decision support specialists InferMed, uses an electronic rule-based algorithm to interpret genotype data and guide physicians and patients in treatment decisions.

Roche and Virology Networks believe that by creating and validating such software to interpret the results of genotype testing, they will provide a clinically

useful tool to physicians and patients. This would represent an advance in rational combination drug regimen design, hopefully maximizing individuals' therapeutic options over the long term.

"From Roche’s perspective, we are trying to redefine the way pharmaceutical companies approach the development and marketing of drugs in this disease area. We want to drive the best use of our drugs by understanding when they should be used and, more importantly, when they should not. If we can do this, we can offer unprecedented value for physicians, we can increase the value of our therapies to patients, and we can heighten the intrinsic value of our franchise," said Martin Hangarter, Ph.D., Roche’s Business Director for Virology and Infectious Diseases.

Although Roche is providing significant support to the GREAT study, the trial has been designed to include the entire armamentarium of approved HIV treatments. This will ensure that the GREAT data are thorough, accurate, impartial, and applicable to the broadest array of patients in the real world. Virology Networks, together with an expert panel of investigators, will interpret new information to refine the rules governing the software on an ongoing basis. This will allow the software to incorporate each patient’s experience to generate rules that reflect real-world experiences.

"Roche has purposely left this component of the program in the hands of Virology Networks and an independent expert panel that will interpret the data separate from of any pharmaceutical company. We believe that this approach -- one that provides independent confirmation of the value of our medications and others’ -- will best serve the physician and the patient," said Dr. Hangarter.

An Evolving Field

While the tests have been shown to be accurate and reliable, the role of genotyping in the clinical setting is still evolving. There is some disagreement among scientists about what a particular result actually means in terms of treatment decisions.

Because genotype tests characterize only a representative sampling of the quasi-species of HIV present in a particular individual, the validity of the tests is questionable if an individual’s viral load is below 1,000 copies/ml. Clinicians should

use genotypic testing in conjunction with viral load assessments and prior treatment history in making treatment decisions.

Another concern is that these tests show only what resistance might occur, not which drugs will work -- they cannot guarantee the success of a particular regimen.

Like HIV RNA viral load tests before it, HIV genotype testing is a novel approach that requires refinement and testing to ensure that the information it provides is used to maximize results for the patient. The use of PE Biosystems’ HIV Genotyping System will provide greater standardization across participating laboratories, will simplify and accelerate the data assessment, and will minimize variables that might exist in the absence of standardized methodology. As with genotype testing, results will help physicians make more informed therapeutic decisions. Testing does not replace a physician's clinical judgment, but serves to enhance it.

By adding this new technology to the HIV armamentarium, physicians and patients can move one step closer to keeping HIV down for the long term.

1 Durant J, Clevenbergh P, Halfon P, Delgiudice P, Porsin S, Simoner P, Montagne N, Dohin E, Dellamonice P. Can HIV genotype determination be useful for individualized adaptation of antiretroviral therapy: The VIRADAPT French Study. 4th International Congress on Drug Therapy in HIV Infection. 8-12 November 1998, Glasgow, UK. Abstract OP7.1.

2 Hirsch MS et al. Consensus Statement: Antiretroviral Drug Resistance Testing in Adults with HIV Infection: Implications for Clinical Management. JAMA 279/24 (June 24, 1998):1984-1991.