New Test Accurately Detects Drug-Resistance Mutations in HIV-1

By Will Boggs MD

April 09, 2020

NEW YORK (Reuters Health) - A new, near-point-of-care test detects drug-resistance mutations in HIV-1 with greater than 90% accuracy across mutant frequency thresholds, according to a validation study in Mexico.

"We found that our simple test was able to detect HIV mutations nearly as well as the next-generation sequencing systems used at the CEINI/INER WHO-certified laboratory," Dr. Lisa M. Frenkel of Seattle Children's Research Institute and Dr. Barry R. Lutz of the University of Washington, also in Seattle, told Reuters Health in a joint email.

With increasing rates of resistance to antiretroviral therapy, the World Health Organization (WHO) now recommends countries with >10% pretreatment drug-resistance rates to begin treatment with a preferred first-line regimen containing dolutegravir/nucleoside reverse-transcriptase inhibitors (NRTIs).

Due to the high cost of these regimens, non-nucleoside reverse-transcriptase inhibitors (NNRTIs) are still preferred in many communities. In these places, the WHO recommends testing for pretreatment drug resistance to guide the selection of effective regimens, but testing is limited to centralized laboratories.

Dr. Frenkel, Dr. Lutz and their colleagues developed OLA-Simple, a near-point-of-care test that detects mutations associated with virological failure of first-line NRTI/NNRTI regimens with nearly 100% specificity. The test contains lyophilized reagents for easy assay set-up, and its software guidance can be run on an inexpensive tablet.

The group adapted the OLA-Simple kit to detect NRTI/NNRTI mutations prevalent in a Mexican population and validated the kits by genotyping pretreatment drug-resistance in 60 plasma specimens from a cohort in Mexico.

Among the 59 samples successfully amplified by RT-PCR (98.3%), genotyping was indeterminate for only 2.7% of all codons tested, the researchers report in AIDS.

Compared with the MiSeq deep sequencing standard using 10% mutant frequency as the diagnostic threshold, OLA-Simple had five false-positive, four false-negative and eight indeterminate results, which yielded 93.1% sensitivity and 97.8% specificity across all codons.

With MiSeq as the standard, the accuracy of OLA-Simple for classification of HIV-drug resistance results was 93.2% at a 2% mutant frequency threshold, 96.3% at 5%, 97.2% at 10%, 97.4% at 15% or 20%, and 98.8% at 25% mutant frequency threshold.

"Physicians know that using the wrong antiretroviral drug combinations is detrimental for the patient, and in low-resource settings patients have fewer treatment options, so using the best drug combination maximizes the patient's chance for good health," Dr. Frenkel and Dr. Lutz said. "Also, effective treatment helps prevent the chance of transmitting HIV, or worse, transmitting drug resistant HIV."

"'Test and treat' strategies have been working well in high-resource communities, and we hope that by providing simpler and faster drug resistance test results, we can improve treatment strategies in resource-limited settings," they conclude.

They add, "Commuting to the clinic can be a significant burden for patients, so it is ideal to have the test results ready within the single patient visit. The quicker turnaround time results of this OLA-Simple test can promptly guide providers to make an informed decision regarding whether a person should switch their medication. A patient can go home with new medications that will likely work more effectively instead of using ineffective medications for months, during which their health could decline and they could transmit drug resistant HIV."

Dr. Marc Noguera Julian of the Hospital Universitari Germans Trias i Pujol, in Badalona, Spain, who has researched the identification of HIV-drug resistance by ultra-deep sequencing, told Reuters Health by email, "I think OLA-Simple is a point-of-care device that is really close to the clinic right now, but not there yet."

In his view, he added, the need now is not so much to show the accuracy of the test but to focus on how to operationalize it. "That is, what is needed to take this to a real-life setting where it triggers clinical action? How can this impact the outcomes at the population level? How can it be distributed/used in low- and middle-income countries? etc.," Dr. Noguera said.

The University of Washington and Seattle Children's Research Institute have filed a patent application related to methods for OLA-Simple.

SOURCE: AIDS, online March 19, 2020.