Testing for HIV drug resistance

By Dr Matt Wilkinson

- Last updated on GMT

Related tags Dna

The development of a highly sensitive assay for the detection of
drug-resistant HIV strains could aid our understanding of how the
virus mutates, helping new drug discovery programs.

The scientists from Duke University have developed an assay to identify drug-resistant strains of HIV and provide a new way to study the effectiveness of antiviral therapies and predict patient drug response. The implementation of the assay could provide the 40 million worldwide sufferers of HIV new hope of more effective therapies and treatment regimes.

The HIV virus not only reproduces very rapidly, it also mutates very easily. This leads to infected people having many different forms of the virus in their body and a few of these mutations can lead to drug resistance.

Talking to DrugResearcher.com, Feng Gao, MD and associate professor of medicine at Duke University, said: "The test identifies drug-resistant strains of HIV in patients blood systems and could allow clinicians to choose the right drugs to help delay resistance."

"It may also help scientists understand how the constantly evolving virus develops drug resistance."

Strains that have developed drug resistance quickly become the most prominent in the body during antiretroviral therapies that do not fully suppress the virus. This causes problems for pharmaceutical companies trying to develop antiretroviral therapies as the virus can quickly mutate into resistant types

"The problem with HIV is that it is so variable that sooner or later most patients will develop resistance,"​ said Dr Gao.

Of the 20 drugs commonly available for treating the HIV virus, all but one target two of the virus' genes, reverse transcriptase and protease. The test examines these genes for mutations that can confer resistance to antiviral drugs.

The researchers developed a highly sensitive assay known as a parallel allele-specific sequencing (PASS) assay that simultaneously analyses a large number of viral genomes and detects minor drug resistant populations, between 0.1 and 0.01 per cent of the total population.

The PASS assay applies the polymerase colony (polony) technique, which involves pouring a small amount of sample onto a slide so that the individual DNA samples are separated. The new technique uses a slide that has one polymerase chain reaction (PCR) primer covalently linked to the gel matrix. This means that the PCR products accumulate around individual DNA templates and form distinct spots (polonies) at the amplification sites.

After the amplification the solid phase negative DNA strands are then hybridised to sequencing primers. Single-base extension of these primers with fluorescence labelled nucleotides allows imaging with a microarray scanner to distinguish between wild type and mutated populations.

The test was so successful that it could identify a single mutated drug resistant virus out of a sample of 10,000 non-mutated viruses.

"The sensitivity of the assay is about 1000 times more sensitive that the most widely used genotypic and phenotypic assays on the market for detecting drug-resistant HIV viruses,"​ said Dr Gao.

He continued: "we have filed a patent to protect the intellectual property issues and are looking for partners to move this forward."

"We are also looking into automation to speed up the process to cut down the turn around time, currently a couple of weeks for most primary resistance mutations, to turn this into a more practical assay."

Dr Gao envisages that is may be possible to turn this into a device for both clinical and research use. The researchers are currently exploring the technique with other pathogens that can develop drug resistance such as in hepatitis B and tuberculosis.

Related topics Preclinical Research

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