TORONTO - Research has shown that HIV, like many other infectious organisms, is a highly polymorphic virus that constantly mutates within infected individuals. The virus is so variable that it is unlikely that HIV viruses isolated from any two patients infected with HIV will have the same DNA sequence. Because of this rapid mutation rate, drugs used to treat HIV, while often effective for a period of time, eventually lose efficacy to newly resistant HIV mutants. Development of such resistant HIV strains frequently leads to the return of high virus levels in the patient.

It was originally thought that DNA probes, DNA chips and other indirect genotyping methods would be effective detectors of important HIV quasi-species. As it has turned out, the high rate of mutation of the virus has rendered these methods ineffective.

John Stevens, CEO of genomics company Visible Genetics Inc. (VGI), of Toronto, said the only reliable method for determining the state of the virus's genome is to sequence it. Experts and ongoing research have demonstrated that by genotyping HIV, it may be possible to treat individual patients by selecting drugs to which the virus has not yet developed resistance, and thus keep the virus at low levels.

When drug selection is based on genotypic analysis there is statistically significant evidence to suggest that this has a greater impact on lowering the viral load. Stevens was commenting on data from a trial comparing current standard of care (SOC) triple-therapy drug selection practices in HIV patients and drug selection based on genotypic analysis. His company's TruGene HIV-1 assay and OpenGene system are being utilized in a clinical trial at the Centre Hospitalier Universitaire de Nice, under the direction of Pierre Dellamonica, an infectious disease specialist. Three sites and five physicians are involved in the trial.

The data show that after six months, 39.1 percent of the patients tracked with genotyping have undetectable levels of HIV, while only 9.5 percent of the SOC control group have undetectable viral levels. The data further shows a six-fold decrease in viral load in favor of therapy adapted to genotypic analysis.

The study sponsored by Visible Genetics is ongoing, and an additional 61 patients still have to reach the six-month analysis point before the study is completed. All 108 patients participating in the study have reached the three-month point, and 47 patients have reached the six-month point. All the patients entered the study with high HIV viral loads (average 4.7 log units), all had failed triple drug therapy at least once, and all were taking at least one protease inhibitor.

This study is pivotal since it strongly suggests that drug selection in HIV patients based on the virus's genotype may play a critical role in the treatment of AIDS. However, Stevens pointed out that any definite conclusions will have to wait until all the patients have completed the trial.

Genotyping by Visible Genetics' OpenGene automated DNA sequencing system and TruGene HIV kit provides rapid, high-resolution read-out of the virus's DNA codes, irrespective of polymorphic variability. The process is cost-competitive compared to other genotyping methods and is highly accurate.

The kit contains all the reagents and standards required to sequence the DNA from the protease and reverse transcriptase (RT) regions of the AIDS virus, making it possible to genotype these therapeutically critical regions of the virus. These regions are known to develop mutations that make the virus resistant to drugs. Over 140 different resistant mutations have been discovered within the protease and RT regions. Combinations of these mutations develop over time within an individual patient and eventually confer resistance to the more than 100 combinations of drugs now commonly used to fight AIDS.

Visible Genetics specializes in pharmacogenomics, using genetic information in the identification, analysis and treatment of medical conditions. The company has just introduced its new automated DNA sequencer, the Long-Read Tower, a two-dye instrument that allows a user to read 300 to 400 bases in approximately 30 minutes, or 1,000 bases with a longer run time of two to four hours. According to the company, the sequencing times on the new instrument are at least three times faster than comparable machines on the market today. Stevens predicts that the new technology will have some value in diagnostic applications, particularly in human genetic diseases. However, the largest market will be in gene discovery research. *

Clarification
An article on “transporter“ peptides in the Sept. 16, 1998, issue of BioWorld International should have noted that the peptides, known as transportan and pAntennapedia (penetratin-1), were licensed by the inventors to Cyclacel Ltd., of Dundee, Scotland, for a broad range of applications.

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