First next-generation sequencing test for HIV drug resistance could help combat AIDS worldwide

The use of antiretroviral therapy to treat HIV has skyrocketed over the past decade as part of worldwide efforts to end AIDS as a public health threat. According to the World Health Organization, however, a concurrent increase in HIV drug resistance could undermine these efforts by compromising the ability of antiretroviral drugs to suppress HIV and stop its progression to AIDS. Testing for HIV drug resistance is key to ensuring that patients receive effective treatment and that public health initiatives have the information needed to manage antiretroviral drug resistance. However, almost all genetic sequencing tests for HIV drug resistance mutations are currently off the market. The only remaining commercial sequencing test dates from the early 2000s and is based on Sanger sequencing, an older technology that is expensive, can take 1-2 weeks to produce results, and has low sensitivity for drug resistance mutations that occur at a frequency below 15-20%.

A team of researchers led by Gerd Michel, PhD, Charlie Lee, PhD, and Elian Rakhmanaliev, PhD, from Vela Diagnostics in Singapore set out to fill this void by developing the first next-generation sequencing based test that can detect HIV drug resistance mutations. Known as the Sentosa SQ HIV-1 genotyping assay, it integrates automated sample processing and analysis with software for result reporting into one complete workflow. To evaluate the efficacy of the Sentosa, the researchers compared its performance with that of a Sanger sequencing-based test, the TruGene HIV-1 genotyping kit, which is no longer on the market. With both tests, the researchers tested 111 blood samples from HIV-1 patients for mutations in the virus's protease and reverse transcriptase genes, which are the two main genes that are typically analyzed in drug resistance testing.

The Sentosa demonstrated unprecedented sensitivity, detecting 100% of all drug resistance mutations in the protease gene compared to 90.45% detected by the TruGene, and identifying 98.16% of all drug resistance mutations in the reverse transcriptase gene compared to 74.48% identified by the TruGene. In total, the Sentosa detected 130 drug resistance mutations not found by the TruGene, while the TruGene only found 8 drug resistance mutations that the Sentosa missed. Another advantage of the Sentosa is that it produces results in 2.5 days, enabling patients to receive treatment much quicker than with Sanger sequencing testing. It also detects drug resistance mutations in the HIV integrase gene -- a gene that is becoming increasingly important as a drug target in the U.S.

"To our knowledge, nobody else has developed an assay like this," said Michel. "Now we have the opportunity to do HIV drug resistance testing much faster, at a lower cost, and also to test for mutations that are not visible with Sanger sequencing. The impact of these mutations that have not been seen by Sanger is not known yet. But now we have the tools to detect them so that researchers can determine how relevant they are clinically and physicians can determine if there should be a change in treatment."

Vela Diagnostics plans to start making this test available to select collaborators this summer, and is aiming to get the CE mark for it in September.